De-Zhu Li

Kunming Institute of Botany CAS · Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species

Polyploidization is a major driver of speciation and its importance to plant evolution has been well recognized. Bamboos comprise of one diploid herbaceous and three polyploid woody lineages, and are the only major subfamily in grasses which diversified in forests with tree-like lignified culm for its woody members. Here we generated four draft gen...

Rapid evolutionary radiations are among the most challenging phylogenetic problems, wherein different types of data (e.g., morphology, molecular) or genetic markers (e.g., nuclear, organelle) often yield inconsistent results. The tribe Arundinarieae i.e., the temperate bamboos, is a clade of tetraploid originated 22 million years ago and subsequent...

The grass family (Poaceae) includes all commercial cereal crops and is a major contributor to biomass in various terrestrial ecosystems. The ancestry of all grass genomes includes a shared whole-genome duplication (WGD), named rho (ρ) WGD, but the evolutionary significance of ρ-WGD remains elusive. We sequenced the genome of Pharus latifolius, a gr...

Background Flowering plants (angiosperms) are dominant components of global terrestrial ecosystems, but phylogenetic relationships at the familial level and above remain only partially resolved, greatly impeding our full understanding of their evolution and early diversification. The plastome, typically mapped as a circular genome, has been the mos...

Geographical names and the entities they represent act as a fundamental cornerstone across numerous disciplines. However, inconsistent geographical names and arbitrarily defined regional geographical scales are common, hindering cross-disciplinary communication and synthesis. The Pan-Tibetan Highlands, comprising the Tibetan Plateau, Himalaya, Heng...

Cymbidium is an orchid genus with rapid radiation and high ornamental, economic, ecological and cultural importance, but its classification is controversial based on morphology. The plastid genome (plastome), as an extension of plant standard DNA barcodes, has been widely used as a potential molecular marker for identificating the recently diverged...

Polyploids are common in Camellia sect. Paracamellia, which contain many important oil crop species. However, their complex evolutionary history is largely unclear. In this study, 22 transcriptomes and 19 plastomes of related species of Camellia were sequenced and assembled, providing the most completed taxa sampling of C. sect. Oleifera and C. sec...

Mycorrhiza play key roles for ecosystem structure and functioning in forests. However, how different mycorrhizal types influence mountain forest biodiversity–ecosystem functioning (BEF) relationships are largely unknown. We evaluate how the diversity of distinct mycorrhiza‐associated fungi and trees shapes forest carbon storage along elevational gr...

The advances accelerated by next‐generation sequencing and long‐read sequencing technologies continue to provide an impetus for plant phylogenetic study. In the past decade, a large number of phylogenetic studies adopting hundreds to thousands of genes across a wealth of clades have emerged and ushered plant phylogenetics and evolution into a new e...

Species are fundamental biological units, but their discovery and delimitation requires appropriate data and methods. To better circumscribe species, we must improve our species concepts and bolster the underlying data resources necessary to enact them. Here, we provide six prescriptions for better collecting and synergizing our knowledge on specie...

Species are fundamental biological units, but their discovery and delimitation requires appropriate data and methods. To better circumscribe species, we must improve our species concepts and bolster the underlying data resources necessary to enact them. Here, we provide six prescriptions for better collecting and synergizing our knowledge on specie...

The taxonomy of the Sino-Himalayan alpine bamboos is controversial due to their complex evolutionary history and further complicated by the scarcity of inflorescence. Here, we supplement the description of the inflorescence of Fargesia angustissima T.P. Yi and Yushania pauciramificans T.P. Yi, which shed light on the taxonomy of Fargesia Franchet,...

Long-distance dispersal (LDD) beyond the range of a species is an important driver of ecological and evolutionary patterns, but insufficient attention has been given to postdispersal establishment. In this review, we summarize current knowledge of the post-LDD establishment phase in plant colonization, identify six key determinants of establishment...

Introduction East Asia (EA), which falls within the region of the Asian monsoon that is composed of the East Asia monsoon (EAM) and the Indian monsoon (IM), is known for its high species diversity and endemism. This has been attributed to extreme physiographical heterogeneity in conjunction with climate and sea-level changes during the Pleistocene,...

Identification of the evolution history and genetic diversity of a species is important in the utilization of novel genetic variation in this species, as well as for its conservation. Pistacia chinensis is an important biodiesel tree crop in China, due to the high oil content of its fruit. The aim of this study was to uncover the genetic structure...

Background: Polypodiales suborder Dennstaedtiineae contain a single family Dennstaedtiaceae, eleven genera, and about 270 species, and include some groups that were previously placed in Dennstaedtiaceae, Hypolepidaceae, Monachosoraceae, and Pteridaceae. The classification and phylogenetic relationships among these eleven genera have been poorly und...

The evolution of subtropical evergreen broadleaved forests (EBLFs) in East Asia is interesting while complicated. Genus-level phylogenies indicate that the origins of EBLFs could trace back to the Oligocene–Miocene boundary or even the Eocene, while population-level phylogeographic evidence suggests that they diversified after the Miocene, particul...

The Convolvulaceae is a pantropical family with high morphological diversity and economic values. To date, however, the phylogenetic relationships among the major lineages or tribes in the family have not been fully resolved. In order to resolve these relationships, we sampled the complete plastome sequences from 40 species, representing eight reco...

Understanding the mechanisms that shape the geographic distribution of plant species is a central theme of biogeography. Although seed mass, seed dispersal mode and phylogeny have long been suspected to affect species distribution, the link between the sources of variation in these attributes and their effects on the distribution of seed plants are...

Mountainous regions can promote complex speciation scenarios, including hybridization leading to chloroplast capture, revealed by incongruent phylogenetic trees. Four allopatric Taxus lineages from the Hengduan Mountains, southwestern China, exhibit cytonuclear phylogenetic discordance. We use multi-omic data at the population level to investigate...

Quercus variabilis (Fagaceae) is an ecologically and economically important deciduous broadleaved tree species native to and widespread in East Asia. It is a valuable woody species and an indicator of local forest health, and occupies a dominant position in forest ecosystems in East Asia. However, genomic resources from Q. variabilis are still lack...

Background and aims: Rhododendron is a species-rich and taxonomically challenging genus due to recent adaptive radiation and frequent hybridization. A well resolved phylogenetic tree is conducive to understanding the diverse history of Rhododendron in the Himalaya-Hengduan Mountains where the genus is most diverse. Methods: We reconstructed the...

The millions of herbarium specimens in collections around the world provide historical resources for phylogenomics and evolutionary studies. Many rare and endangered species exist only as historical specimens. Here, we report a case study of the monotypic Pseudobartsia yunnanensis (= Pseudobartsia glandulosa: Orobanchaceae) known from a single Chin...

Sexual dimorphism in dioecious plants often occurs as a consequence of the different resource requirements of females and males, especially during reproduction. The contrasting reproductive roles of the sexes can influence the phenology of growth, plant size and flowering time, with implications for the intensity of competitive interactions within...

Biodiversity across multiple trophic levels is required to maintain multiple ecosystem functions. Yet, it remains unclear how multitrophic diversity and species interactions regulate ecosystem multifunctionality. Here, combining data from nine different trophic groups (including trees, shrubs, herbs, leaf mites, small mammals, bacteria, pathogenic...

Main conclusion CG and CHG methylation levels in the rapid shoot growth stages (ST2–ST4) of woody bamboos were obviously decreased, which might regulate the internode elongation during rapid shoot growth, while CHH methylation was strongly associated with shoot developmental time or age. Abstract DNA methylation plays a critical role in the regula...

Fagus L. is a key component in temperate deciduous broadleaf forests of the Northern Hemisphere. However, its biogeographic history has not been examined under the framework of a fully resolved and reasonably time‐calibrated phylogeny. In this study, we sequenced 28 nuclear single/low‐copy loci (18,555 bp in total) of 11 Fagus species/segregates an...

Three woody bamboo species collected in Hainan, China in 1940 have been described as Dinochloa based on vegetative specimens. However, the identity of these species has long been in doubt, largely because the vegetative phase in species of Dinochloa is morphologically similar to that in species of Melocalamus, a climbing or scrambling bamboo genus...

Plant mitochondrial DNA has been described as evolving rapidly in structure but slowly in sequence. However, many of the noncoding portions of plant mitogenomes are not homologous among species, raising questions about the rate and spectrum of mutations in noncoding regions. Recent studies suggested that the lack of homology in noncoding regions co...

Understanding the mechanisms that shape the geographic distribution of plant species is a central theme of biogeography. Although seed mass, seed dispersal mode and phylogeny have long been suspected to affect species distribution, the link between the sources of variation of these attributes and their effects to the distribution of seed plants are...

Climate change and geological events have long been known to shape biodiversity, implying that these can likewise be viewed from a biological perspective. To study whether plants can shed light on this, and how they responded to climate change there, we examined Oreocnide, a genus widely distributed in SE Asia. Based on broad geographic sampling wi...

Background and Aims The Araceae are one of the most diverse monocot families with numerous morphological and ecological novelties. Plastid and mitochondrial genes have been used to investigate the phylogeny, and interpret shifts in the pollination biology and biogeography of the Araceae. In contrast, the role of whole-genome duplication (WGD) in th...

The Hickeliinae (Poaceae: Bambusoideae) is an ecologically and economically significant subtribe of tropical bamboos restricted to Madagascar, Comoros, Reunion Island, and a small part of continental Africa (Tanzania). Because these bamboos rarely flower, field identification is challenging, and inferring the evolutionary history of Hickeliinae fro...

Background and Aims The Araceae are one of the most diverse monocot families with numerous morphological and ecological novelties. Plastid and mitochondrial genes have been used to investigate the phylogeny, and interpret shifts in the pollination biology and biogeography of the Araceae. In contrast, the role of whole-genome duplication (WGD) in th...

Species of Cephalotaxus have great economic and ecological values. However, the taxonomy and interspecific phylogenetic relationships within the genus have been controversial and remained not fully resolved until now. To date, no study examined the efficiency of the complete plastome as super-barcode across Cephalotaxus species with multiple sample...

Structural variation of plastid genomes (plastomes), particularly large inversions and gene losses, can provide key evidence for the deep phylogeny of plants. In this study, we investigated the structural variation of fern plastomes in a phylogenetic context. A total of 127 plastomes representing all 50 recognized families and 11 orders of ferns we...

Grasses are widespread on every continent and are found in all terrestrial biomes. The dominance and spread of grasses and grassland ecosystems have led to significant changes in Earth’s climate, geochemistry, and biodiversity. The abundance of DNA sequence data, particularly chloroplast sequences, and advances in placing grass fossils within the f...

Intra-specific genetic diversity is a fundamental component of biodiversity, and is key to species adaptation and persistence. However, significant knowledge gaps still exist in our understanding of the patterns of genetic diversity and their key determinants. Most previous investigations mainly utilized single-species and/or a limited number of ex...

Urticeae s.l, a tribe of Urticaceae well-known for their stinging trichomes, consists of more than 10 genera and approximately 220 species. Relationships within this tribe remain poorly known due to the limited molecular and taxonomic sampling of previous studies, and chloroplast genome (CP genome/plastome) evolution is still largely unaddressed. T...

Poaceae (the grasses) includes rice, maize, wheat and other crops and is the most economically important angiosperm family. Poaceae is also one of the largest plant families, consisting of over 11,000 species with a global distribution and contributing to diverse ecosystems. Poaceae species are classified into twelve subfamilies with generally stro...

Fargesia, the largest genus within the temperate bamboo tribe Arundinarieae, has more than 90 species mainly distributed in the mountains of Southwest China. The Fargesia bamboos are important components of the subalpine forest ecosystems that provide food and habitat for many endangered animals, including the giant panda. However, species-level id...

Morphological approaches often fail to delimit species in recently derived species complexes. This can be exacerbated in historical collections which may have lost key features in specimen preparation and preservation. Here, we examine the Pedicularis siphonantha complex, endemic to the Mountains of Southwest China. This complex is characterized by...

Melocanninae is sister to other subtribes of Paleotropical woody bamboos with some 90 species mainly concentrated in Asia. However, phylogenetic relationships within the subtribe are poorly known. Here, we filled the gaps in complete plastome data of Melocanninae, reconstructed the phylogeny of Melocanninae, and further estimated divergence time an...

Background Understanding the processes governing angiosperm seed growth and development is essential both for fundamental plant biology and for agronomic purposes. Master regulators of angiosperm seed development are expressed in a seed-specific manner. However, it is unclear how this seed specificity of transcription is established. In some verteb...

We present an updated worldwide phylogenetic classification of Poaceae with 11,783 species in 12 subfamilies, seven supertribes, 54 tribes, five supersubtribes, 109 subtribes, and 789 accepted genera. The subfamilies (in descending order based on the number of species) are Pooideae with 4126 species in 219 genera, 15 tribes, and 34 subtribes; Panic...

Dryopteris sukungiana, a new tetraploid fern species of Dryopteridaceae in Yunnan, Southwest China, is described and illustrated. Morphologically, D. sukungiana belongs to the D. sparsa complex but is unique in spreading blackish brown scales on the stipe, glandular hairs and small fibrillose scales on the abaxial surface of the lamina. Phylogeneti...

Gene duplication is increasingly recognized as an important mechanism for the origination of new genes, as revealed by comparative genomic analysis. However, how new duplicate genes contribute to phenotypic evolution remains largely unknown, especially in plants. Here, we identified the new gene EXOV, derived from a partial gene duplication of its...

The rapid Cretaceous diversification of flowering plants remains Darwin’s ‘abominable mystery’ despite numerous fossil flowers discovered in recent years. Wildfires were frequent in the Cretaceous and many such early flower fossils are represented by charcoalified fragments, lacking complete delicate structures and surface textures, making their si...

The Poales is one of the largest orders of flowering plants with significant economic and ecological values. Reconstructing the phylogeny of the Poales is important for understanding its evolutionary history that forms the basis for biological studies. However, due to sparse taxon sampling and limited molecular data, previous studies have resulted...

Phylogenetic analyses supported that four traditionally defined families Sterculiaceae, Tiliaceae, Bombacaceae and Malvaceae were subsumed into Malvaceae s.l. and nine subfamilies had been recognized within Malvaceae s.l. However, phylogenetic relationships among the nine subfamilies were not well resolved. Moreover, phylogenetic relationships amon...

Morphological trait-matching and species abundance are thought to be the main factors affecting the frequency and strength of mutualistic interactions. However, the relative importance of trait-matching and species abundance in shaping species interactions across environmental gradients remains poorly understood, especially for plant–insect mutuali...

Standard plant DNA barcodes based on 2-3 plastid regions, and nrDNA ITS show variable levels of resolution, and fail to discriminate among species in many plant groups. Genome skimming to recover complete plastid genome sequences and nrDNA arrays has been proposed as a solution to address these resolution limitations. However, few studies have empi...

Two new species of Yushania (Poaceae, Bambusoideae, Arundinarieae) are described and illustrated from Hunan, China. Yushania longshanensis D.Z. Li & X.Y. Ye is distinguished from related species (Y. confusa, Y. angustifolia and Y. pachyclada) by having a thinner culm (0.2-0.3 cm in diameter), glabrous sheath scar, no oral setae, a large glabrous le...

Prickles act against herbivores, pathogens or mechanical injury, while also prevent water loss. However, whether prickles have new function and the molecular genetics of prickle patterning remains poorly explored. Here, we generated a high-quality reference genome assembly for ‘Basye’s Thornless’ (BT), a prickle-free cultivar of Rosa wichuraiana, t...

Reticulate evolution is a common and important driving force in angiosperm evolution. In this study, we analyzed the phylogenetic signals of genomic regions with different inheritance patterns to understand the evolutionary process of organisms using species‐rich Himalaya‐Hengduan taxa of bamboos (Fargesia and Yushania). We constructed phylogenetic...

The Adiantum pedatum complex is disjunctly distributed in North America and eastern Asia. In this study, we carried out a detailed morphological study based on 137 specimens representing the biogeographic diversity of this complex. The sequences of eight chloroplast markers of 35 samples were analyzed with maximum likelihood and Bayesian inference....

Dryopteris sect. Diclisodon is a small section of ferns with about 12 species mainly distributed in East Asia. Here, we carried out morphological and phylogenetic analyses of this section. A new species from southwest China, D. gaoligongensis, is described and illustrated. Dryopteris gaoligongensis resembles D. indonesiana and D. sparsa, but differ...

As drivers of evolutionary innovations, new genes allow organisms to explore new niches. However, clear examples of this process remain scarce. Bamboos, the unique grass lineage diversifying into the forest, have evolved with a key innovation of fast growth of woody stem, reaching up to 1 m per day. Here, we identify 1,622 bamboo-specific orphan ge...

Posttranscriptional modifications, including intron splicing and RNA editing, are common processes during regulation of gene expression in plant organelle genomes. However, the intermediate products of intron-splicing, and the interplay between intron-splicing and RNA-editing were not well studied. Most organelle transcriptome analyses were based o...

Saururus chinensis is a core member of Saururaceae, an ancient, perianthless (lacking petals or sepals) family of the magnoliids in the Mesangiospermae, which is important for understanding the origin and evolution of early flowers due to its unusual floral composition and petaloid bracts. To compare their transcriptomes, RNA-seq abundance analysis...

Walnuts are highly valued for their rich nutritional profile and wide medicinal applications. This demand has led to the intensification of breeding activities in major walnut production areas such as southwest China, in order to develop more superior cultivars. With the increasing number of cultivars, accurate identification becomes fundamental to...

Inferring the intrinsic and extrinsic drivers of species diversification and phenotypic disparity across the tree of life is a major challenge in evolutionary biology. In green plants, polyploidy (or whole-genome duplication, WGD) is known to play a major role in microevolution and speciation, but the extent to which WGD has shaped macroevolutionar...