Plant speciation across environmental gradients and the occurrence of hybrid zones

Abstract

The success of individual plant species to spread across environmental gradients is dependent on their ability to adapt to changed local conditions via adaptive phenotypic plasticity and/or adaptive genetic divergence. There are many examples of heritable adaptive changes in phenotype across environmental gradients and the underlying molecular genetic bases for some of these changes are beginning to be resolved. Such heritable change can occur in the presence or absence of gene flow and may be manifested as continuous change in phenotype (clinal variation) or the establishment of discrete ecotypes. In both cases, reproductive barriers may evolve, often gradually, between locally adapted forms and ultimately result in the formation of new species.

At an intermediate stage in this process, hybrid zones may originate as a result of primary intergradation (with continuous gene flow) or through secondary contact between locally adapted forms previously isolated by means of an eco-geographical barrier. The study of both types of hybrid zone can be highly informative of reproductive barriers that evolve between incipient species across an environmental gradient. Whereas in animal groups hybrid zones are recognised as useful systems for studying the nature and sequence of reproductive barriers that evolve across the speciation continuum, rather surprisingly, they have been little used for this purpose in plants, where they remain a relatively underutilised resource in studies of plant speciation. Nonetheless, a few recent studies of plant hybrid zones involving detailed genomic analysis have been conducted and begun to shed light on the nature of breeding barriers that may evolve during divergence across environmental gradients. These studies provide direction for the future use of hybrid zones in plant speciation research.

One possible reason for why studies of plant hybrid zones are relatively rare in the current literature is that though hybridization occurs frequently among plant species, the establishment of hybrid zones may be uncommon, particularly under relatively stable conditions, i.e. low levels of disturbance. Rarity of hybrid zones, if true, would be an interesting phenomenon in itself and raise questions as to why it is the case. However, more information is required on the occurrence of hybrid zones between plant species before reaching conclusions on their frequency.

Saving Plants

Abstract

The international botanical community, meeting here in Shenzhen, is far more aware than most people in wider society of the fundamental role played by plants in shaping and maintaining the biosphere.  However, a significant proportion of plant species are now threatened with extinction and plant biodiversity is being lost in other ways, so that even species that were once common are becoming rare.  As botanists we also recognise that our current knowledge of plant diversity is far from complete: many plant species remain to be discovered and we are still in the early stages of exploring the genetic diversity.  Maintaining plant diversity, at ecosystem, species and genetic levels, Is especially important in an era of global change and has direct relevance to future resilience and adaptation.  The continuing erosion of plant diversity has major consequences for our planet and all of its inhabitants: threatening biodiversity in general and making the internationally agreed Sustainable Development Goals even more difficult to achieve.

I will explore some of the key actions humanity needs to undertake in order to conserve global plant diversity, considering conservation in the broadest sense to include any and all interventions that help to secure pant diversity and the ecosystem services delivered by plants.  I will emphasise that many different sectors and stakeholders will need to work closely together if we are to succeed in passing on the Earth’s rich, green inheritance to future generations.  Direct action to conserve plants is carried out by agencies and disciplines as diverse as forestry, agriculture, conservation biology, urban and rural development planning, protected area management and other fields.  An even wider set of institutions and organisations are involved in education and outreach, enabling people in wider society to understand the issues and to engage in addressing them.

My focus will be on the potential contribution of botanic gardens, arboreta, seed banks and other collections of living and preserved plants and on the strategic challenges they and other players need to overcome for global efforts in plant conservation to accelerate and expand to an appropriate degree.

Key words: biodiversity, conservation, Sustainable Development Goals,

Genes gone wild: Experimental evolution meets synthetic biology

Abstract

In my talk, I will describe experimental approaches to study genome evolution in real time. I will discuss three fundamental processes in eukaryotic genome evolution and show how they can be reconstructed in laboratory experiments: (i) the transfer of organellar (plastid and mitochondrial) genes to the nuclear genome, (ii) the horizontal movement of organellar DNA between plants, and (iii) the movement of nuclear genetic material between plants by horizontal genome transfer. Finally, I will show how horizontal gene transfer can be employed as a versatile tool in plant biotechnology and synthetic biology.

Molecular mechanisms of histone demethylases in genome-wide targeting in Arabidopsis

Abstract

Transcription activity of chromatin is regulated by covalent modifications on nucleosomes and DNA. Recent efforts have identified a lot of chromatin modifiers, which play important roles in various aspects of biological processes. These chromatin modifiers normally bind a subset of specific genomic loci. Discovering the mechanisms of recruiting these modifiers is essential for understanding the biological function of them. We previously identified Arabidopsis JMJ14 and JMJ12/REF6 as H3K4 and H3K27-specific histone demethylases, which use two distinct mechanisms to their genome-wide targets. The C-terminal FYR domain of JMJ14 interacts with a pair of NAC domain containing transcription factors, which bring JMJ14 to their common target genes; whereas REF6 recognizes its target loci by direct recognizing specific DNA sequence through its tandem C2H2-Zinc finger domains. In this talk, I will illustrate how other factors affect REF6 genome-wide targeting in Arabidopsis.

Plant sesquiterpenes: biosynthesis and bio-interactions

Abstract

Terpenoids constitute the largest group of plant secondary (or specialized) metabolites, and they play important roles in plant adaptation to environments. Sesquiterpenes are derived from the 15-carbon farnesyl diphosphate. We are interested in sesquiterpene biosynthesis in plant and the role of sesquiterpene phytoalexins in plant defense against insect pests.

The plant defense hormone jasmonate (JA) plays an important role in regulation of secondary metabolism pathways. The Arabidopsis MYC2, a bHLH transcription factor, acts as a key regulator of JA response. We found that in Arabidopsis inflorescence MYC2 integrates both gibberellin (GA) and JA signals in regulating the expression of terpene synthase genes. In addition, transcription factors of other families, such as WRKY and AP2/ERF, are also involved in induced formation of sesquiterpenes.

The level and accumulation of secondary metabolites change during plant development and growth. The miR156-targeted SPLs function as an age cue in plant phase transition and maturation, our recent study demonstrated that the SPL factors directly regulate sesquiterpene synthase genes in Arabidopsis and of Pogostemon cablin, linking the plant age cue to elevated accumulation. The SPLs also attenuate JA signaling through direct interaction with JAZ proteins, leading to age-dependent JA response decay. Conversely, phytoalexins may accumulate constitutively to a higher level in later stages, providing a strong insect resistance to old plants.

*I thank Ying-Bo Mao, Zong-Xia Yu, Gao-Jie Hong and others who contributed to this research.

Mechanisms of microRNA degradation

Abstract

The abundance of miRNAs is determined by both biogenesis and degradation. While the mechanisms of miRNA biogenesis are fairly well understood, how miRNAs are degraded in vivo, especially when miRNAs are associated with their effector protein ARGONAUTE 1 (AGO1), is poorly understood. In 2005, my group showed that miRNA degradation entails 3’ truncation and 3’ uridylation, but the enzymes responsible for these processes were unknown. In recent years, we identified the exonucleases and nucleotidyl transferases that are responsible for miRNA 3’ truncation and 3’ uridylation, respectively. We showed that these enzymes not only act on free miRNAs but also AGO1-bound miRNAs. While these enzymes are largely non-sequence-specific, the degradation of specific miRNAs in vivo can be achieved. One example of specificity determination is the promotion of miR165/6 degradation by AGO10. My talk will be focused on the molecular framework of miRNA degradation.

O-GlcNAc signaling mediates vernalization sensing in wheat

Abstract

Wheat and rice show different preference to low temperature since their various origin and evolution. Cold can damage for living of rice, but be required for flowering of winter wheat. Sensitivity of rice for cold limits its planting only in certain climate-zones. Our previous study suggests COLD1 with a localization on plasmamembrane and ER, interacts with rice G-protein α subunit 1 (RGA1) to activate the Ca²⁺ channel for sensing chilling and to accelerate G-protein GTPase activity. Based on the characters of temperature sensor in mammalians and its Calcium signaling and electriphysiological response to temperature changes, COLD1 is a cold sensor in plants. Vernalization is the acquisition of a plant’s ability to flower which requires a prolonged cold temperature. It is controlled by a genetic network such as VRNs. However, it’s less known that sensing mechanism for prolonged cold, vernalization. Here reports that the O-GlcNAcylation and phosphorylation signaling were involved in sensing vernalization in wheat, and O-GlcNAc signaling mediated flowering through effecting epigenetic process in Arabidopsis.

The post-translational O-linked N-acetylglucosamine (GlcNAc) modification of proteins, catalyzed by O-GlcNAC transferase (OGT), is involved in multiple important biological processes in animals. However, whether protein O-GlcNAcylation affects plant development is largely unknown. Here, we show that loss of function of SECRET AGENT (SEC), an OGT in Arabidopsis, leads to weak early flowering time phenotype, which results from decreased transcription of FLC. And ChIP analysis indicates that H3K4me3 level is significantly reduced in sec-5 mutant comparing with that of wild type. We also found that SEC can interact with a protein and catalyzed O-GlcNAcylation in vivo to regulate H3K4 methylation impacting the transcription of FLC. So the O-GlcNAc signaling plays an important role in flowering by affecting the activity of specific protein and the epigenetic process in Arabidopsis. Meanwhile we studied the possible functions of O-GlcNAc signaling in wheat vernalization. The approaches of LWAC and iTRAQ-TiO2 were used to enrich O-GlcNAcylated peptides and phosphopeptides of the plumules from vernalization and non-vernalization wheat, respectively. As a result, about 200 O-GlcNAcylated proteins and 164 alternatively changed phosphoproteins were identified. Functional analysis showed that these proteins are mainly involved in metabolic processing, cellular processing and response to stimulus. The inhibitors, such as alloxan for OGT and PUGNAc for OGA were used to treat wheat plants with nonvernalization and vernalization. And the data showed that O-GlcNAc signaling in vernalization accelerated flowering transition in winter wheat. During vernalization, gradually increased O-GlcNAc modification was detected for TaGRP2, the RNA-binding protein directly binding to TaVRN1 pre-mRNA to repress its activation. Phosphorylated VER2, a jacalin lectin, recognizes the O-GlcNAcylated TaGRP2 to repress its accumulation in the nucleus and attenuate its binding to TaVRN1, thereby releasing the repression of TaVRN1, ultimately promoting flowering. We speculated that O-GlcNAcylation and phosphorylation modification may act as signals to sense vernalization and regulate the network of VRNs for flowering in wheat.

Fitter with litter: plant traits and their legacy for ecosystem services

Abstract

Litter, i.e. the finer fraction of dead plant material, provides a wide variety of important ecosystem services. However, the role of litter in regulating ecosystem processes and services has mostly been studied in terms of litter presence or amount. Besides in biogeochemistry, we still do not know how litters from distinct plant species differ in their effects on other ecosystem processes and services including biodiversity support. I will propose a new conceptual model that will help us to investigate these differences based on species traits, by explicit reference to two highly distinct and possibly interacting plant ‘trait  spectra’: the widely known (Plant or) Resource Economics Spectrum (RES), and the newly defined Size and Shape Spectrum (SSS). Different ecosystem services provided by plant litter are driven by either one of the trait spectra or by both. I will introduce this concept by drawing from examples from a range of contrasting ecosystem services, including regulatory, recreational, provisioning and biodiversity support services. I will encourage the audience to start empirical work to quantify the linkages between the multi-species RES-SSS trait space and these various services, thereby enhancing our understanding about how exactly dead plant matter matters not only to ecosystems but also to people in different parts of the world.

Seed Germination and Seedling Emerging Out of Soil: Life and Death Decisions

Abstract

In natural and agriculture systems, seeds often germinate and emerge from the soil to start new life cycles. How plants regulate seed germination and seedling development to emerge from soil is crucial for plants’ survival and growth. In the past few years, our series of research greatly advance the knowledge of seed germination and seedling emergence out of soil. We identify the novel positive transcription factor and central repressor in mediating light-induced seed germination. Combining the genetics, molecular biology and mathematical modeling methods, we revealed that seeds use a multilevel regulatory circuit of triple feed-forward loops to sensitively and precisely control seed germination in various light conditions (Shi et al., 2013; Shi et al., 2015). In order to study the molecular mechanism underlying seedling emergence from the soil, we design a convenient and highly reproducible soil assay and show that the transcription factor in ethylene signaling pathway EIN3 is essential for the seedling emergence (Zhong et al., 2014). We further demonstrate that the COP1-EBF1/2-EIN3 tandem E3 ligase module channels the light and mechanical pressure signals to elaborately adjust EIN3 protein levels to ensure seedling emergence out of soil (Shi et al., 2016a). After growing out of the soil to reach the sunlight, dark-grown seedlings face dramatic environmental changes. Our recent studies show that photoreceptor phyB manipulates substrate-E3 ligase interactions in a light-dependent manner, thus directly controlling the stability of EIN3. Therefore, the plants adopt the tandem E3 ligase module to gradually adjust EIN3 protein accumulation in the soil, and elicit a rapid degradation of EIN3 to shut down the ethylene responses by a light-dependent “molecular glue” phyB upon emergence (Shi et al., 2016b). Taken together, our findings demonstrate the molecular actions of key factors and regulatory mechanism during seed germination and seedling emergence out of soil, which helps us to understand the natural phenomena and provide the mechanistic basis for crop genetic improvement in future.

Shi, H., Zhong, S., Mo, X., Liu, N., Nezames, C.D., and Deng, X.W. (2013). HFR1 sequesters PIF1 to govern the transcriptional network underlying light-initiated seed germination in Arabidopsis. Plant Cell 25, 3770-3784.

Shi, H., Wang, X., Mo, X., Tang, C., Zhong, S., and Deng, X.W. (2015). Arabidopsis DET1 degrades HFR1 but stabilizes PIF1 to precisely regulate seed germination. Proc Natl Acad Sci U S A 112, 3817-3822.

Shi, H., Liu, R., Xue, C., Shen, X., Wei, N., Deng, X.W., and Zhong, S. (2016a). Seedlings Transduce the Depth and Mechanical Pressure of Covering Soil Using COP1 and Ethylene to Regulate EBF1/EBF2 for Soil Emergence. Curr Biol 26, 139-149.

Shi, H., Shen, X., Liu, R., Xue, C., Wei, N., Deng, X.W., and Zhong, S. (2016b). The Red Light Receptor Phytochrome B Directly Enhances Substrate-E3 Ligase Interactions to Attenuate Ethylene Responses. Dev Cell 39, 597-610.

Zhong, S.W., Shi, H., Xue, C., Wei, N., Guo, H.W., and Deng, X.W. (2014). Ethylene-orchestrated circuitry coordinates a seedling's response to soil cover and etiolated growth. P Natl Acad Sci USA 111, 3913-3920.

Distinct evolutionary dynamics of C4 and CAM photosynthesis

Abstract

CAM and C4 photosynthesis are two carbon-concentrating mechanisms (CCMs) that increase photosynthetic efficiency, and together have evolved hundreds of times in flowering plants over the past 30 million years. Although C4 and CAM share a primary biochemical module, their anatomical specializations are quite distinct, and carry significant ecological repercussions. I'll present the latest ideas on the evolutionary trajectories of both C4 and CAM syndromes, highlighting areas of convergence and divergence. An emerging hypothesis is that anatomical modifications preceeded the emergence of CCM biochemistry during C4 evolution, while the reverse may be true for CAM. I'll discuss the evolutionary implications of this order of events, and suggest that structural innovations may act more generally as key evolutionary "bottlenecks": events that happen relatively rarely, and dramatically alter the adaptive landscape and subsequent evolutionary accessibility of novel phenotypes.

Early angiosperms: Key fossils and extinct diversity

Abstract

Fossil floral structures and other remains of angiosperms recovered from Cretaceous sediments have yielded a wealth of data on the organization and structure of early angiosperms. These discoveries are important in the search for character evolution and systematic diversification in early angiosperms. Results obtained so far from the study of Cretaceous angiosperms corroborates to a large extent patterns of diversification obtained from analyses of extant angiosperms using molecular data. However, the fossils also witness of extensive extinction among early angiosperms that cannot be detected studying extant plants alone. In several cases the fossils possess a suite of distinctive characters that are unknown among extant angiosperms, but that may help bridge morphological splits between extant lineages. In other cases the fossils cannot be place in any existing group. We illustrate extinctions and missing links among Cretaceous angiosperms using a number of exquisite preserved key fossils. Focus will be on fossil members of Chloranthaceae and Laurales, but other groups will also be discussed with examples from early diverging eudicots and core eudicots. It has long been suggested that the Chloranthaceae have an extensive geological history extending back to at least the mid-Early Cretaceous. Fossil flowers, fruits, seeds and stamens with pollen in situ particularly from the Early Cretaceous of Portugal have confirmed this suggestion and show considerable diversification very early in angiosperm history with several extinct forms, but also forms that are closely similar to extant taxa. A key fossil among extinct chloranthoids is Canrightiopsis that includes several different species. The affinity to extant Chloranthaceae is documented by unique seed coat features as well as details of the tiny embryo and nutritive tissue surrounding the embryo. Canrightiopsis is important as a key for understanding character evolution in the Chloranthaceae suggesting an evolutionary link between extinct Canrightia and extant Chloranthus and Sarcandra and a model for the derivation of the tripartite androecium of Chloranthus. Canrightiopsis co-occur with several other chloranthoid taxa, several of them not described earlier. A new fossil genus with three species under description from the Early Cretaceous is significant for understanding structural and systematic diversity among early members of the Laurales. The fossils show a combination of characters that is unknown among extant or fossil members of the group, but phylogenetic analyses clearly places the fossils in the Laurales. Several features are shared with extant core Laurales such as the presence of a single, pendulous seed and valvate anther dehiscence. In gynoecium features it is particularly similar to extant Gomortegaceae. However, other characters such as dicolpate pollen and continuous tectum are shared with extant Calycanthaceae, the earliest branching lineage of Laurales and the new genus thus provide a link between Calycanthaceae and core Laurales.

Another Abominable Mystery: Gene-body Methylation

Abstract

Darwin thought the abrupt origin and rapid diversification of angiosperms to be an abominable mystery.  Here I discuss another ongoing mystery within the genomes of land plants: the evolution and function of DNA methylation in coding genes. Plants methylate both genes and transposable elements (TEs). For the latter, the function is clear: DNA methylation suppresses TE activity. The methylation of TEs has corollary effects on the expression of nearby genes, and thus TE methylation has major consequences for the function and evolution of plant genomes. Just as TEs are methylated in plants, so is a subset of genes. Genic methylation was initially thought to be sporadic, but it is now clear that methylation is a conserved evolutionary property of individual genes. These genes tend to evolve slowly, they are expressed broadly, and their methylation is not a property of their GC content. The cause(s) of conservation remain unclear, as does the function of genic methylation, if indeed it has a function.  I will present current information about evolutionary patterns of genic methylation, a recent idea about the mechanism of genic methylation, and varied evidence that genic DNA methylation correlates with gene expression. The function and evolution of genic methylation remains mysterious, however, because it has been difficult to separate cause from effect.

Genetic basis of complex traits and heterosis in rice

Abstract

Most of agronomically important traits are called complex traits, which are usually controlled by multiple genes and affected by various environmental conditions. Although a lot of QTLs and genes related to rice complex traits have been cloned and functionally characterized, genetic basis and regulatory mechanisms underlying these complex traits are still unclear. We have implemented an integrated approach of genome-wide association study (GWAS) with functional analysis on agronomic traits in a diverse cultivated rice population, which is so called as a CAT-Gs (Catching Agronomic Trait Genes) approach. The associated loci with the agronomic traits such as panicle length, grain sizes, grain weight and grain filling rate can be further characterized through expressional profiling, in-depth genome analysis, transgenic study, genome editing, and population genetic analysis. We believe that allelic genetic variations responsible for the panicle and grain size complex traits can be effectively explored. The genetic basis of these complex traits will be characterized.

Exploitation of heterosis is one of the most important applications of genetics in agriculture. However, the genetic mechanisms of heterosis are only partly understood, and a global view of heterosis from a representative number of hybrid combinations is lacking. We have developed an integrated genomic approach to construct a genome map for elite hybrid rice varieties and their inbred parental lines. We therefore identified that the accumulation of numerous rare superior alleles with positive dominance is an important contributor to the heterotic phenomena. We have further done large-scale genomic mapping for yield related traits and heterotic effects by analyzing over 10,000 rice lines produced from 17 elite rice lines. The large data of genomics and phenomics from the well-designed populations enabled us, for the first time, to identify the genetic contributors comprehensively and find out the exact causes of heterosis. We found that modern rice varieties can be classified into three major types, reflecting the major breeding systems. Within each group a few genomic regions from female parents linked to heterosis effects for improved yields were identified, but these loci varied across the three groups. The key heterosis-related genes often controlled several yield-related components simultaneously, severing as the major contributors of heterosis. For the individual yield components, the heterozygous state of the heterosis-related genes generally acted through the way of dominance complementation. Taking all the components into account, the hybrids with yield heterosis resulted from an optimal combination of multiple yield-related components, meaning better performance of overall yield in crop productions. These results inform on the genomic architecture of heterosis for yield traits in rice, which will be useful information for crop improvement program.

Long-term field experiments and observation data in combination in Inner Mongolia grasslands of China successfully addressed many fundamental questions in ecology

Abstract

The typical steppe ecosystem of China is an important part of the vast Eurasian grasslands in the world. With an area of 0.4 *10⁶ km² in China, these ecosystems not only harbor rich biodiversity resources, but also serve as important bases of livestock production and ecological shelters for northern China. However, Inner Mongolia grassland is experiencing serious degradation resulting from overgrazing and climate change. During the last decades, we have conducted intensive studies focusing on the fundamental questions in ecology with collaborators from home and abroad. Through long-term field monitoring, transect surveys and controlled field experiments, we are trying to address the nature of fundamental concepts and principles in ecology includes 1) formation mechanisms of primary and secondary production, 2) biogeochemistry of major elements (C, N, S, P), 3) Coupled cycling of Carbon, nitrogen and H₂O, 4) stoichiometry of C: N: P ratio and its application. We seek to understand how organisms interact with each other and the abiotic environment, and also apply this knowledge to the management of grassland ecosystem, and the services it provides. Both the science of ecology and researchers on the Inner Mongolia grassland have come a long way over the last decades. Today, it is a dynamic international base for scientists with a focus on studying ecology in natural environments.

Ex situ Cultivated Flora and Germplasm Discovery for Novel Crop Plants

Abstract

There are c. 3000 botanical gardens in the world, distributed widely across different climatic zones and floristic regions. Most importantly they provide habitats for >120,000 vascular plants in ex situ cultivation, accounting 1/3 of known plant species in the world, including many economically important taxa or groups, such Aceraceae, Ericaceae, Fagaceae, Leguminosae, Magnoliaceae, as well as a large number of crop wild relatives, medicinal and aromatic, and horticultural plants. This ex situ cultivated flora contains an enormous amount of plant diversity in many well documented living collections in different botanical gardens and plays a critical role in maintaining the security of plant diversity, and in conservation, sustainable agriculture and other related bio-industries.

China has approximately 33,000 higher plants, of which more than half are endemic to China and encompasses a vast number of species of bryophytes (c. 2200 species), pteridophytes (c. 2600 species), gymnosperms (c. 250 species), and angiosperms (>30000 species), accounting for 9.1%, 22%, 26.7% and 10% of the world total, respectively. The Chinese flora also represents the living remnants of the early Miocene floras of the whole North Temperate regions and is the source of numerous crops and of medicinal and horticultural plants. There are c. 190 Chinese botanical gardens, harboring 22,375 species belonging to 3927 genera and 382 families, of which 20,000 species, 2911 genera and 288 families are native to China, accounting for 91%, 86% and 60% of native families, genera and species, respectively. As an example of initiatives to utilize the ex situ cultivated flora to address plant diversity conservation and germplasm discovery for sustainable agriculture and the bio-industries, the Ex situ Cultivated Flora of China project aims to catalogue and document this mega diversity of plants that are cultivated in the Chinese botanical gardens.

The initiative has three main goals: 1) To enhance taxonomic research on common garden-based living collections: the morphological and biological data collected from these collections should provide adequate and accurate descriptions for the delimitation of difficult taxa in cases when traditional taxonomic revision has been based only on herbarium specimens; 2) To support comparative biology and frontier plant science research: with increasing awareness of environmental and habitat changes in the overall background of climate change on plant distributions in situ, the Ex situ cultivated flora program should provide detailed plant biological information from different gardens across a wide spectrum of different latitudes, climates and habitats for research on adaptive evolution of species, plant migration and distribution shifts and physiological or/and biochemical changes, etc.; 3) To strengthen germlasm discovery and sustainable uses of plant resources, which should enhance our current ongoing efforts in medicinal plants, industrial bio-energy plants, landscaping and ornamental plants, new functional fruits and vegetables, environment-ameliorating plants, etc.

The presentation will provide a comprehensive introduction and well documented case studies. The project of Ex situ Cultivated Flora is planned to be one of the most important initiatives of the plant diversity research platform for sustainable economic and social development in China.

Plant growth in a high CO₂ world

Abstract

Plant growth needs resources and physical environmental conditions that permit acquiring these resources. CO₂ is a central resource (close to 50% of plant biomass is carbon), hence, elevated CO₂ supply is widely held to enhance plant growth and mitigate growth constraints set by resources other than carbon and by environmental stress. I will present theory and evidence that questions such a simple rationale. It is a trivial fact that carbon can only become incorporated into new biomass to the extent soil nutrients permit, because plants are not made of carbon only. Hence, whenever soil nutrients are short, particularly when neighbouring plants compete for the same resources, there is little leeway for more carbon incorporation. Further, when abiotic limitations such as low temperature or low soil moisture cause soil nutrient shortage and a slowing of meristematic activity (tissue formation), it becomes a question of whether carbon uptake limitations or carbon investment limitations weigh more heavily. The two effects (source limitation versus sink limitation) are very hard to separate. At high CO₂, water shortage exerts less of a constraint, for stomatal CO₂ uptake, while at the same time, elevated CO₂ reduces stomatal conductance, thus, causing soil moisture to decline more slowly, also causing nutrients to remain available for a little longer. This non-photosynthetic effect of drought mitigation on growth can be simulated by similarly dosed water addition without any change in CO₂-supply. The effect of such water savings on future plant growth depends on future climate driven moisture regimes. Constraints of growth by low temperature do not seem to get less severe in a high CO₂ world. Alpine and arctic plant growth has been shown to be unresponsive to elevated CO₂. Similar constraints to CO₂ 'fertilization' effects apply to ecosystems that have arrived at a natural steady state of the nutrient cycle and canopy density. In summary, the carbon limitation paradigm of plant growth is ill founded when long-term nutrient shortage, low temperature or drought come into play. The simple reason is that under those three conditions, it is not the photosynthetic machinery that sets the long-term limit to plant growth but sink activity (tissue stoichiometry, meristem functioning). Constraints acting upon sink activity are far more challenging to model than those on source activity. In most cases we simply lack appropriate algorithms and parameters to represent sink activity in a mechanistic way. The problem cannot be solved by tuning the output of source activity driven models, because the actual causality is the reverse: the ability to grow new tissue defines the demand for fresh carbon, a demand set by meristems and their direct stoichiometric and developmental controls, and these demands are communicated to foliage through the phloem pipelines. In other words, in all those cases, photosynthesis (source activity) is driven by the rate of growth (sink activity). Sink control over source activity (CO₂ uptake) can only be eliminated by ample nutrient and water supply, as happens under horticultural growth conditions, which do not represent appropriate test conditions for the likely responses of wild plants to elevated CO₂ concentrations in the atmosphere.

Tropical Plant-Animal Interactions: Coevolution in the Anthropocene

Abstract

The complexity of life on earth is a product of the diversity of species multiplied by the diversity of their interactions.  An understanding of species diversity, which requires correct species identification, is a prerequisite to accurately interpreting and understanding their interactions.  Investigations of plant-herbivore and plant-pollinator interactions have provided classic examples of the interdependent relationships that exist among species within and across ecosystems.  The charismatic tropical Zingiberales, including bananas, birds-of-paradise, heliconias, gingers, and prayer plants, offer illustrative and often surprising insights into the ecology of the animals with which they have coevolved.  Specifically, the ecological interactions between colleopteran herbivores and hummingbird pollinators with their Zingiberalean hosts reveal intricate patterns of their evolutionary history and how they may respond to today’s rapidly changing planet.  The geographic mosaic of these relationships across tropical islands, fragmented landscapes, and elevational gradients suggests that human-caused habitat alterations, biological invasions, and climate change may significantly modify and disrupt through time and space the historical patterns of ecological interactions.  The future of today’s biological complexity in the Age of Humans, in the Anthropocene, remains to be determined.

A Ca²⁺ sensor switch for tolerance to elevated salt stress in Arabidopsis

Abstract

Excessive sodium (Na⁺) in soils inhibits plant growth and development. The Ca²⁺-activated salt overly sensitive (SOS) pathway formed by the Ca²⁺ sensor SOS3/CBL4 interacting with the kinase SOS2/CIPK24 to activate the Na⁺/H⁺ antiporter SOS1, represents a core module for regulating Na⁺ homeostasis and establishing salt tolerance in plants. In natural conditions, the actual soil Na⁺ concentration can vary over a wide range. If and how the intensity of Na⁺ stress is reflected by quantitative parameters of downstream signaling components and adjustment of the SOS remains to be investigated. Here, we identify a Ca²⁺ sensor switch that is specifically activated under highly elevated Na⁺ stress conditions. We report that Na⁺ triggers a primary Ca²⁺ signal specifically localized in root hair differentiation zone of the root from where it expands as a wave. The amplitude of this primary signal rises and the speed of wave propagation accelerates reflecting increasing external Na⁺ concentration, thereby providing quantitative information about stress intensity to the plant. Moreover, by analyzing mutant and over-expression plants, we identified the Ca²⁺ sensor CBL8 as crucial for enhanced salt tolerance in Arabidopsis. Like SOS3/CBL4 also CBL8 interacted with SOS2/CIPK24 and activated SOS1. While the phosphorylation and conformation of SOS3/CBL4 remained largely unaffected by Ca²⁺, CBL8 exhibited conformational changes and enhanced phosphorylation with increasing Ca²⁺ concentrations. Together our data identify a Ca²⁺ sensor switch to optimize plant salt tolerance over a range of stress conditions in which the SOS3-SOS2-SOS1 pathway conveys basal and essential salt tolerance, while in response to intensified Ca²⁺ signals, elicited by highly elevated Na⁺, in addition CBL8-SOS2 complexes are activated to further enhance SOS1 activity for salt extrusion.

Understanding Kranz Anatomy in Maize with a View to Achieving C4 Rice

Abstract

A multi-national effort aimed at introducing components of C₄ photosynthesis into the C₃ plant rice is underway. A fundamental requirement of the ‘C₄ Rice Project’ is the need to understand how Kranz anatomy develops in the leaves of C₄ plants so that leaf anatomy can be manipulated in rice. I will provide an overview of our understanding of Kranz development, discuss recent research aimed at identifying genetic regulators of Kranz anatomy and illustrate how this research fits into the wider C₄ Rice Project.

The quest for the origin and evolution of flowering plants using time-calibrated plastid phylogenomics

Abstract

The angiosperms, i.e., flowering plants, are the most species-rich plant lineage on Earth. Because angiosperms are critical components of nearly all terrestrial habitats, knowledge on their origin and evolution can provide the framework for understanding the history and composition of major terrestrial ecosystems and general patterns of biodiversity. Over the last two decades, molecular phylogenetic studies have greatly advanced our understanding of angiosperm relationships and evolution, as reflected in the latest update  to the Angiosperm Phylogeny Group (APG) classification system (2016). However, the composition and relationships of some clades recognized as orders and families have remained weakly supported, with recent studies often based on either sparse gene sampling or low taxonomic coverage, or both. To address this problem, we assembled a large-scale plastid phylogenomic data set of angiosperms by sampling 80 genes from 2881 plastid genomes representing 2349 angiosperm species, 352 families (85% of the described families), and all 64 orders recognized in APG, with 163 species of gymnosperms comprising the outgroups. Our results yielded the diversification of eight major lineages in the early stages of angiosperm evolution. The ANA grade, i.e., Amborellales, Nymphaeales and Austrobaileyales, was confirmed to be the earliest-diverged set of lineages. However, the relationships of the mesangiosperms, including magnoliids, Chloranthales, monocots, Ceratophyllales and the eudicots, remain poorly resolved.

We estimated the divergence times of major angiosperm clades using 63 carefully verified fossils as calibration points. Our results support the origin of the crown angiosperms in the Rhaetian of the latest Triassic ca. 207 million years ago (mya). A rapid radiation of major lineages and orders of flowering plants occurred in the Middle to earlier Late Jurassic and Early Cretaceous. An early radiation may have occurred at the Callovian in the Middle Jurassic (ca. 165 mya) with the origin of three major lineages of mesangiosperms. Major radiations of the monocot lineages occurred in the Late Jurassic (ca. 157 mya) to the Valanginian in the earliest Cretaceous (ca. 133 mya). Core eudicots began to diverge at the Hauterivian (ca. 131 mya), mainly diversifying from the Aptian (ca. 121 mya) to the Turonian-Coniacian boundary (ca. 90 mya) in the Early Cretaceous, with the Paracryphiales and Dipsacales, the most recently diverged orders, at the mid-Campanian (ca. 79 mya) in the Late Cretaceous. Our divergence time estimates are generally congruent with others based on DNA sequence data and are corroborated by the phylogenomic-based estimate for the origin and diversification of major lineages and orders of holometabolous insects. However, they are significantly earlier than unequivocal fossil records of flowering plants. This may be attributed to the fact that even angiosperm-like pollen records from the Jurassic are spare and are thus difficult to find. The lack of resolution among mesangiosperms in our analysis may result from rapid radiation and extinction in the early stage of angiosperm evolution, particularly during the Jurassic.

Key words: plastomes; angiosperms; dated phylogeny; radiation; co-evolution.

Thirty clues to angiosperm exceptional evolutionary diversification

Abstract

China is World-leading in Cucurbitaceae genomics, having produced the draft genomes of cucumber, Cucumis sativus (Huang et al., Nature Genetics 2009; also Qi et al., Nature Genetics, 2013; Shang et al., Science 2014; Zhou et al., Nature Plants 2016) and watermelon, Citrullus ‘lanatus’ (Guo et al., Nature Genetics 2013). Old-fashioned Sanger sequencing over the past 10 years, however, has revealed numerous misclassifications of material of Cucurbitaceae, from simple misidentification of germplasm to serious misplacements of species in unnatural genera, meaning that names do not reflect evolutionary relationships and cannot be trusted to guide sampling for genomic projects. The family Cucurbitaceae is underrepresented in herbaria because wild cucurbits often are climbers in disturbed habitats or desert plants that are hard to find at the right stage. Fruits of the family are difficult to preserve. Only with DNA barcoding has it become possible to figure out what is what (simply put). In the talk I will illustrate how molecular data are revolutionizing our knowledge about the wild relatives of Cucumis sativus (in India, Thailand, and tropical China), Cucumis melo (in India and Australia), Citrullus lanatus (in West or Northeast Africa), Momordica charantia (in Africa) and Luffa (in India and Australia), using examples of recent and ongoing work in my lab, in collaboration with genomics experts from China.

EXAMPLES:

Renner, S. S., H. Schaefer, and A. Kocyan. 2007. Phylogenetics of Cucumis (Cucurbitaceae): Cucumber (C. sativus) belongs in an Asian/Australian clade far from melon (C. melo). BMC Evolutionary Biology 7:58. DOI: 10.1186/1471-2148-7-58 (“highly accessed”)

Schaefer, H., C. Heibl, and S. S. Renner. 2009. Gourds afloat: A dated phylogeny reveals an Asian origin of the gourd family (Cucurbitaceae) and numerous oversea dispersal events. Proceedings of the Royal Society B 276 (1658): 843-851.

Schaefer, H., and S. S. Renner. 2010. A three-genome phylogeny of Momordica (Cucurbitaceae) suggests seven returns from dioecy to monoecy and recent long-distance dispersal to Asia. Molecular Phylogenetics and Evolution 54(2): 553-560.

Sebastian, P. M., H. Schaefer, I. R. H. Telford, and S. S. Renner. 2010. Cucumber and melon have their wild progenitors in India, and the sister species of Cucumis melo is from Australia. Proceedings of the National Academy of Sciences, USA 107(32): 14269–14273.

Chomicki, G., and S. S. Renner. 2015. Watermelon origin solved with molecular phylogenetics including Linnaean material: Another example of museomics. New Phytologist 205(2): 526-532.

Nuclear phylogenies of angiosperms at both deep and family levels: implications on divergence times, morphological evolution and diversification rates

Abstract

Ministry of Education of Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China

Angiosperms are the most successful plant group, with an estimated total of over 350,000 species.  Angiosperm phylogeny is a foundation for a variety of other studies, including evolutionary biology and ecology, comparative genomics, and translational agriculture and has been examined using chloroplast sequences for many years. Rapid divergences of multiple lineages, frequent whole genome duplications and other factors have posed major challenges to the resolution of angiosperm relationship. Recent advances in DNA sequencing have availed large quantities of nuclear gene sequences, greatly facilitating the acquisition of needed marker information for addressing difficult questions in angiosperm phylogeny. We have used transcriptome sequencing and other approaches to obtain dozens, even hundreds, of nuclear gene sequences, and performed multiple phylogenetic analyses of major deep lineages. These investigations have yielded highly supported relationships that are largely in agreement with chloroplast sequence-based phylogenies; at the same time, the new hypotheses according to nuclear genes support well-resolved relationships for taxa whose relationships were unclear before, illustrating the effectiveness of nuclear genes. Well-resolved relationships include five deep lineages of the mesangiosperm clade representing nearly all angiosperms and several major branches of core eudicots. We have also performed phylogenetic analysis of several groups including Brassicaceae, Asteraceae, and Rosaceae, and will summarize recent results from these analyses, and discuss their implications on the divergence times of relevant groups, reconstruction of ancestral character of key morphological features, and shifts in rates of diversification during angiosperm evolution.

Angiosperm phylogeny; mesangiosperm; core eudicots; Brassicaceae; Asteracea

Mapping Asia Plants

Abstract

Because of the huge population and rapid growth of economy, biodiversity including plants are being seriously threatened in Asia. Both conservation and sustainable use of biodiversity need species distribution data. Asia is the continent with highest diversity of plants. However, the information of plant taxonomy and distribution in Asia are less available and more scattered, compared with other continents such as Europe and America. So, a better infrastructure for plant distribution in Asia is important. In 2015, Asia Biodiversity Conservation and Databases Network (ABCDNet) started a project entitled Mapping Asia Plants for cataloguing species of plants and collecting distribution data from the following aspects: 1) specimens, 2) observations, 3）species checklists, 4) expert maps, 5) inventories, 6) vegetation plots, 7) literatures and 8) on line datasets. Major achievements so far are as follows. 1) for China, national higher plant checklists including 35835 species, 9 million records of occurrence; 2) for Southeast Asia, 120 thousands species names, 1.3 million records of occurrence; 3) for north Asia, 6900 species of higher plants and their distribution in 13 sub-regions. Some of the data collected are shared with the websites of ABCDNet(www.abcdn.org/).

How do plants age and die? - some new insights

Abstract

Angiosperms are the cornerstone of present-day terrestrial biomes, but little is known about the macroevolutionary processes underlying their diversification. A great controversy exists regarding the time when extant angiosperms lineages originated, and many questions remain regarding their evolutionary expansion: What is the phylogenetic position and temporal distribution of radiations leading to extant megadiversity? Are these radiations concentrated in particular phylogenetic regions or times? Are all angiosperm lineages radiating, or are some undergoing evolutionary depletions? Has a limit to angiosperm evolutionary expansion been reached? To investigate the absolute timing of angiosperm crown origin and lineage diversification, we integratively consider molecular sequence data of living species and information from the fossil record. Because sampled extant species with molecular data and fossils that provide absolute times are part of the same evolutionary process, we estimate divergence times and diversification parameters across angiosperms with the Fossilized Birth Death (FBD) Process, a model that estimates the rates of speciation, extinction, fossilization, and sampling probability of extant species, as a prior for divergence time dating. We contrast FBD age estimates for the origin of angiosperms with those derived from relaxed molecular clocks, and from two previous estimates derived from quantitative evaluations of the angiosperm fossil record. As the FBD directly incorporates information from the fossil record, it has a great potential for accurately estimating diversification and relative extinction parameters for angiosperms as a whole. To investigate radiations within angiosperms, we implement a Bayesian method (BAMM) that allows to identify significant diversification shifts across phylogenetic branches and through time. We conduct six alternative analyses that differ in the magnitude of the prior for the expected number of diversification shifts across the tree, and provide both technical and biological results. In all analyses, the posterior distribution of the number of shifts differs substantially from the prior. Moreover, a set of thirty diversification shifts highly supported by the data were congruently identified across the six analyses. Biologically, the placement of core diversification shifts suggests that extant angiosperm diversity is the result of several independent and partially overlapping radiations, interspersed with a few evolutionary depletions. Radiations are phylogenetically scattered and took place over a substantial length of angiosperm evolutionary history. Estimates of their long-term diversification trajectory suggest that angiosperm species accumulation has not reached a limit, but species turnover is increasing. The finding that several diversification shifts are distributed on two or more adjacent phylogenetic branches is congruent with the possibility that underlying causes of diversification may derive from synergic interactions among biological, ecological and physical factors.

Keywords: biodiversity, diversification, evolution, fossil record, phylogenetics, radiation, species-richness,

Phytochrome Photosensory Signaling and Transcriptional Networks

Abstract

Plants constantly monitor the ambient light environment for signals that enable them to adapt to the prevailing conditions. The phytochrome (phy) family of sensory photoreceptors plays a central role in this process. Light absorption induces conversion of the phy molecule to its active Pfr conformer which then migrates rapidly into the nucleus where it induces expression changes in target-genes within minutes. Photoactivated phys signal to their target transcriptional network by binding to, and inducing the phosphorylation and degradation of PIF transcription factors (phy-Interacting Factors), thereby evoking these changes.  We have been examining the mechanisms underlying the signaling transactions at both the phy-PIF and PIF-genome interfaces in this process.  Previously, we have shown that signaling requires direct binding of the phy Pfr conformer to the PIF protein, that this results in multisite phosphorylation of the bHLH factor, and that this in turn leads to polyubiquitination by Cullin3-BTB E3 ubiquitin ligases (called LRBs), and, consequently, proteasomal degradation.  Recently, we have identified a small family of Photoregulatory Protein Kinases (PPKs) that are collectively necessary for normal phy-induced PIF3 phosphorylation in vivo.  These kinases are recruited by photoactivated phyB to a nuclear-localized trimolecular complex with PIF3, where they catalyze multisite PIF3 phosphorylation. This discovery fills a longstanding mechanistic gap in our understanding of the short transduction process from the light-activated photoreceptor to transcriptional regulation. We have also identified a unique negative feedback signaling-attenuation mechanism, directly at the phy-PIF interface, whereby the phy-induced phosphorylation of, and LRB recruitment to, the PIF molecule, results concurrently in ubiquitination and degradation of the interacting phy molecule in a mutually-assured destruction (MAD) configuration.  This coordinated PIF and phy degradation thus results concomitantly in both transcriptional regulation of target genes and immediate feedback attenuation of signaling intensity. Using genome-wide transcriptome analysis, we have identified PIF-regulated genes that respond rapidly to phy photoactivation, and using integrated ChIP-seq and RNA-seq analysis, we have identified a diverse network of these genes that are direct targets of PIF-quartet (PIF1,3,4 and 5)-regulated transcription. Moreover, the evidence unveils an intriguing dual-layered mechanism of regulation, whereby both the level of promoter-binding-site occupancy, and in situ modulation of bound-transcription-factor intrinsic activity, together generate a complex matrix of shared, but quantitatively differential, gene expression patterns, under the control of the phy-PIF signaling pathway.

Endocytosis and the regulation of signaling in plants

Abstract

Receptor-mediated endocytosis is an integral part of signal transduction, because, besides signal attenuation by removal of activated receptors and their bound ligands from the cell surface, it allows the spatial and temporal regulation of the signaling outputs from the endosomes. After receptors have been activated and internalized, they can be separated from their ligands and recycled back to the plasma membrane or transported for degradation. Crucial in the study of the interplay between endocytosis, recycling, and signaling of plant receptor kinases is the development of imaging tools (bioactive fluorescent probes) to visualize membrane-associated signaling events at a high spatiotemporal resolution. Recently, we visualized endocytosis of different receptor kinases in living Arabidopsis thaliana cells using fluorescent small-molecule and peptide ligands. The bioactive fluorescent probes together with genetic, biochemical and pharmacological analyses revealed distinct dynamics of endocytosis and differences in regulation of signaling outputs.

Mobilizing and integrating big data in analyses of phylogenetic and spatial patterns of biodiversity

Abstract

The pace of biological discovery is staggering in this era of “big data.” We are at a crucial juncture when it is more important than ever to mobilize and integrate massive amounts of data to address fundamental issues in the study and preservation of biodiversity. The enormous challenges presently faced in biodiversity science require novel approaches that not only employ massive data sets, but also combine bioinformatics, phylogeny reconstruction at an unprecedented large scale, use enormous amounts of digitized specimen data, as well as large, highly complex, multi-faceted down stream phylogenetic analyses. These post-tree analyses include niche modeling, niche diversification, and ancestral niche reconstruction, as well as other ecological analyses. Recent tool development in multiple disciplines including phylogenetics, ecological niche modeling, combined with rapidly developing, powerful cyberinfrastructure coupled with the availability of multiple new data sources afford unique and powerful opportunities. Together these resources provide novel possibilities for mobilizing and integrating enormous quantities of biological, geological, climatic and other related biodiversity data, ultimately facilitating the discovery of complex patterns and new hypotheses for further study. These multifaceted and interdisciplinary developments are major advances--biodiversity data on the global scale now being collected and analyzed are inherently complex. This tool integration is transforming what we broadly term biodiversity science, enabling numerous new research opportunities that we refer to as “next-generation” investigations in biodiversity science that couple systematics, ecology, and evolution.  The growth in tool building and use also demands new training for our students that integrates domain knowledge in biodiversity as well as data science skills –such connectivity and training is needed to accelerate biodiversity research. This next generation Integrative biodiversity science is of crucial importance--the future of global biodiversity will be greatly impacted by these efforts. We as researchers cannot continue to simply react to continued worldwide threats to biodiversity. In contrast, through the use of integrative, multifaceted research relying on big data, we now have the ability to make biodiversity projections—we can now provide crucial data to scientists, as well as to the public, land managers, policy makers, urban planners, and those in agriculture.

Thinking through the e- in e-Floras; or, Floras old, new, and not-yet

Abstract

When faced with a disruptive new technology such as the World Wide Web, it often takes a lot of work, and time, to escape conventional ways of thinking through a problem and to fully realise the implications of the new. So-called e-Floras are no exception. How much does the e- in the name really reflect a new way of approaching a Flora’s core task (to communicate authoritative, synthesised taxonomic knowledge to as wide an audience as possible in the best way achievable)? If modern taxonomy and systematics were invented, or re-invented, now (in the age of the internet, social media, citizen science and the block chain), rather than in the 18th Century, would we do it all differently? And, what near-future disruptive technologies and paradigms do we need to be aware of when thinking about, or planning, an e-Flora project? Taking the new e-Floras of Australia and New Zealand as starting points, this talk will explore current and future thinking about e-Floras, and map out some ideas for, perhaps, the next wave.

Developing integrative systematics in the informatics and genomic era

Abstract

Systematics is the science of discovering, organizing and interpreting the diversity of all living organisms on Earth. Recent developments in genomics and biodiversity informatics are transforming systematics and have opened up many new opportunities. Major digitization efforts have made available large amounts of biodiversity data.  Developments in biodiversity informatics in the last decade have helped the systematics community explore ways to enhance the efficiency in organizing, publishing, and utilizing systematic information. We are now constructing the tree of life and classifications at various levels using information from hundreds to thousands of genes and sometimes the entire genomes.  The new data and tools are bringing systematics into an exciting age of new discovery and interpretation of biodiversity and its assembly. Integrative systematics in the informatics and genomic era needs to be developed with biological collections continuing to serve as the foundation of the field. Discovering, documenting and analyzing the patterns and processes of biodiversity remain the core of systematics, yet the community needs to enhance the efficiency of systematic research and practices with user-friendly pipelines.  We especially call for new efficient workflows for taxonomic revisions, monographs and floras, that utilize both the traditional strengths of synthesizing diverse collections-based taxonomic data and the capacity of online resources and biodiversity informatics tools. A new global community-wide cyberinfrastructure, Biodiversity Cyberbank, comparable to GenBank for genetic data, needs to be established as the repository of all biodiversity data, as well as the means to effectively organize and disseminate systematic data to biologists and the public, to ensure the long-term sustainability of the vast biodiversity data. Integrative systematics requires the training of the next-generation of systematists with integrative skills, to address grand questions about biodiversity and its assembly at different scales. Finally integrative systematics must proactively educate the public and policy makers on the importance of systematics and collections in the biodiversity crisis of the Anthropocene.

Establishing New Botanic Gardens in Indonesia: An ecoregion approach

Abstract

The development of new botanic gardens has been included in the 2015-2019 National Priority Programs and the Indonesian Biodiversity Strategy and Action Plan (2003-2020). Within international contexts, the development of new botanic gardens is in line with the global commitments such as the Convention on Biological Diversity and the target VIII of the Global Strategy for Plant Conservation. The ecoregion concept has been applied in the new botanic gardens development process in order to save and manage effectively the plant diversity occurred in different ecosystem types. This strategy should not only be valued as a protection effort of plant diversity per se, but also considering the need for empowering local communities. By conserving the plant diversity in their own habitat characteristics we can expect higher success, particularly for endemic, threatened species. This strategy is also less costly because the collected-selected plants are brought to and managed in the closest, most suitable gardens. Since Indonesia consists of 47 different ecoregions, at least one botanic garden should be located in each ecoregion in order to conserve the representatives of the Indonesian plant diversity. By the end of 2016, there have been 30 botanic gardens both developed and developing gardens, located in 17 (out of 47) different ecoregions. The implementation of the Indonesian Presidential Regulation No. 93 in 2011 has strengthened the development phases of the new botanic gardens by engaging the Ministry of Public Works and the Ministry of Internal Affairs. The establishment of new desirable botanic gardens and the relevant roles to conserve plant species ex situ will serve the public needs, provide fruitful visitation, as well as create social and economic benefits. Social welfare is indeed a key factor that must be taken into account if botanic gardens are to succeed in their goals of plant diversity conservation and the sustainable utilization.

Key words: new botanic gardens, ecoregion approach, threatened plants, social benefit, Indonesia.

International developments and responsibilities for the botanical community in plant conservation

Abstract

The development of the Global Strategy for Plant Conservation (GSPC) through the U.N. Convention on Biological Diversity can trace its origins back to a resolution of the International Botanical Congress held in St Louis, Missouri in 1999 and its 2002 adoption by the international community.  Since then the GSPC has been of fundamental importance not only to provide a strategic framework for plant conservation undertaken by the world’s governments, primarily within the context of the U.N.’s Strategic Plan for Biodiversity and its related Aichi targets, but also a guiding document used by numerous botanical institutions worldwide.  The 16 targets of the GSPC are wide-ranging and highlight goals that are due to be achieved by 2020.  These goals relate to understanding and documenting plant diversity, conserving and using plants sustainably, as well as public education and building capacity for plant conservation throughout the world.  The strategy has had a transformative impact on many botanical institutions, particularly botanic gardens, helping to consolidate conservation as a primary purpose for many.

In this presentation, ways in which individual institutions have been contributing towards the achievement of the 2020 goals will be outlined.  Examples from the Missouri Botanical Garden will be included where its most recent strategic plan has made a formal commitment to contributing to the GSPC through research in conservation biology, ecological restoration, community conservation and education programs, horticulture and ex situ conservation, as well as building conservation capacity with institutional partners worldwide.

A widely accessible Flora of all known plant species is a fundamental requirement for plant conservation.  Without it, we have no framework to assess the diversity of plants or the threats they face on a worldwide scale.  The creation of such a Flora was included in the GSPC as its first target.  Subsequently, in response to this target, a World Flora Online (WFO) project was launched in 2012, which is now guided by an international WFO Consortium, involving almost 40 botanical institutions and organisations involved in plant systematics.  The progress in the development of the project since 2012 will be outlined, including the preview of a new WFO portal that is planned to be available at the Congress.

The likely future of plant conservation beyond 2020 will be reviewed when greater integration between biodiversity conservation and sustainable development can be anticipated, within the context of the achievement of the U.N.’s Sustainable Development Goals for 2030.

Big Data in Plant Genomics to Connect Nature-derived Evolutionary Innovations with Future Precision Agriculture

Abstract

DNA is the basic source code of life, connecting nearly all species in this planet during the past billions of years that produced magnificent biodiversity and remarkable innovations. To study the crucial role of plants in ecosystems, medicine development, and resources in food production and nutrition, big data of plant genomics by large-scale species sampling along the entire evolutionary line is an unprecedented but powerful way to understand the fundamental genetics and evolution. To achieve this goal, sampling and digitizing various non-model plants particularly by genome sequencing technology is the key, further to manipulate or edit/synthesize new life forms (or natural products) that are beneficial to human healthcare. From our pilot studies with careful scientific designs in algae, early land plants, and angiosperms that with innovative traits of interest, we have gained extensive novel insights in evolutionary forces that drive genome complexity and adaptation. However, all of these efforts are just the beginning, data is still far from enough, and our understanding to life is still much limited. Sequence most if not all of the species on this planet should be the final approach (every species/data is valuable indeed), just like what we have been working on the ‘plant tree of life’ project and even for the ‘digitize the planet’ project. All of which have been facilitated by the recent development in sequencing technologies (like BGISEQ-500/50 platform), through extensive global collaborations following a Data-Knowledge-Application mode in BGI. Through big data study of plant genomics, we have the opportunity to connect all valuable data/species together, explore biodiversity and gain inspirations from nature, and thus design ‘super species’ that are nutrition-rich and production-effective, and further guide future precision agriculture.

Diversity of tropical forests in South East Asia under the threat of rapid loss

Abstract

In the world, 60,065 species of trees have been recognized (Beech et al. 2017) and tree species richness is the highest in tropical rain forests of Brazil and SE Asia. Tree species richness in SE Asia is, however, largely underscored because taxonomic inventories of trees in SE Asia remain rather incomplete and thus many new species have been described every year. On the other hand, tropical rain forests of SE Asia are rapidly converted to plantations at the rate of 0.36 % per year. Therefore, we need to speed up taxonomic inventories of tropical trees.

To obtain more accurate documentation of species richness in SE Asia, we have carried out a series of field surveys in 35 locations of SE Asia where we placed a total of 136 plots of 100 m x 5 m and collected 32,015 samples of the vascular plant species found in or near each plot even for sterile plants. To identify those collections, we used DNA sequences of three regions widely used for plant DNA barcoding: rbcL, mat K and ITS. However, those regions did not always give sufficient discrimination of closely related species and thus sequencing of three regions for more than 30,000 samples is not cost-effective.

A new DNA barcoding using MIG-seq, a recently developed method of genome-wide SNP genotyping with the next generation sequencing platform (Suyama and Matsuki 2015) enables us to discriminate closely related species more efficiently. We applied this method for some genera of Lauraceae, the most species-rich family in SE Asia. Consequently, we discovered at least the following 104 new species; 7 of Actinodaphne, 20 of Cinnamomum, 10 of Cryptocarya, 42 of Machilus and 25 of Neolitsea. There are more new species, possibly 100 more, in other genera including Alseodaphne, Beilschmiedia, Dehaasia, Lindera, Litsea and Phebe on which taxonomic studies are in progress.

A reliable estimate of the proportion of new species is available in Mt. Bokor, Cambodia where we published the tree flora as a Picture Guide and enumerated 770 species of 108 families. Among the 770 total, 65 species (8.4%) were undescribed; the family having the richest new species was Lauraceae in which 11 of 33 species (33.3%) was undescribed. Our 32,015 specimens from 35 locations of SE Asia include approximately 24,000 species among which ca. 2,000 species (24,000 x 0.084 =2016) would be undescribed. Because the cumulative number of species we collected are still linearly increasing, this is likely to be underestimated.

New species are often found as one or a few individuals in disturbed and fragmented stands of lowland forest. Considering the rapid loss of tropical forest in SE Asia, many species may be becoming extinct before those are collected and described. We need more intensive efforts to discover and describe species in tropical forest of SE Asia and the method we employed provide an efficient way of responding to this need.

Sequence assembly, evolution and functional application of the cotton genomes

Abstract

We used the highly homozygous G. hirsutum (AtDt, 2n = 52) genetic standard line TM-1 for DNA sequencing. We crossed a tetraploid G. barbadense cv. 3-79 with TM-1 to obtain 167 RIL individuals to construct the high-density genetic map. To successfully assemble the genome, we combined 180-fold whole-genome shotgun (WGS) sequences with a total of 100,187 BAC end sequences. Repeat sequences accounted for 57% of the D genome, 68.5% of the A genome and 67.2% of the AtDt genome. The AtDt genome displayed high degrees of conserved gene orders with the two diploids. Insertions of long terminal repeats (LTR), especially Gypsy-type retrotransposons, seems responsible for the two-fold size differences between the D (775.2 Mb) and A (1,694 Mb) genomes. Transposable elements (TEs) originated from Dt are more active than those from At. In-depth genome-wide analysis helped to resolve the puzzle with regard to gossypol biosynthesis and ethylene production in various cottons. The expression patterns of a large number of functional genes, especially both primary cell wall-specific and secondary cell wall-specific CesA or CesA-like (CSL) genes, are significantly different in the two subgenomes, suggesting that genome variation, caused likely by TE, especially by retrotransposon insertion, may play a crucial role during the concerted cotton genome evolution.

Key words: cotton geneomes, allotetraploid, retrotransposons, functional studies