De-Zhu Li

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

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...

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...

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...

Polyploidy (genome duplication) is a pivotal force in evolution. However, the interactions between parental genomes in a polyploid nucleus, frequently involving subgenome dominance, are poorly understood. Here we showcase analyses of a bamboo system (Poaceae: Bambusoideae) comprising a series of lineages from diploid (herbaceous) to tetraploid and...

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...

The c. 270 endemic species of Pedicularis in the Himalaya-Hengduan Mountains (HHM) region exhibit high diversity in geographic distribution, elevational range and floral morphology. Many of these, including the species with the longest corolla tubes and beaked galeas, are monophyletic and represent a putative in situ radiation. In this study, we fo...

Conservation of endangered plants is crucial for maintenance of biodiversity and uninterrupted provision of ecosystem services in a changing world. However, the lack of comprehensive phylogeographic information for most of the endangered species significantly hampers effective conservation action, especially for species distributed across national...

Grasses (Poaceae) comprise c . 11 800 species and are central to human livelihoods and terrestrial ecosystems. Knowing their relationships and evolutionary history is key to comparative research and crop breeding. Advances in genome‐scale sequencing allow for increased breadth and depth of phylogenomic analyses, making it possible to infer a new re...

In the Mountains of Southwest China (MSC), accelerated diversification triggered by mountain uplift and monsoon intensification in the Miocene is widely revealed, but less is known about the stage after the Pliocene. Thus, the tempo-spatial evolution of the endemism of Gaoligong Shan (GLGS), a young and isolated mountain with the highest biodiversi...

Rapid growth is an innovative trait of woody bamboos that has been widely studied. However, the genetic basis and evolution of this trait are poorly understood. Taking advantage of genomic resources of 11 representative bamboos at different ploidal levels, we integrated morphological, physiological, and transcriptomic datasets to investigate rapid...

Woody bamboo (Bambusoideae) is renowned for its polyploidy and rare flowering. Bambusa odashimae is one of the bamboo species with the highest chromosome count (104) in the subfamily and has the highest heterozygosity of all sequenced bamboo genomes so far. Compared with other bamboo species, it can efficiently utilize exogenous hormones to regulat...

Evolutionary transitions from sexual to asexual reproduction should have significant influences on ge-netic divergence and polymorphism at the genome level. Plant lineages with diverse reproductive sys-tems provide opportunities to investigate this question using comparative approaches and studies ofmolecular evolution. We investigated evidence for...

The woody bamboos (Bambusoideae) exhibit distinctive biological traits within Poaceae, such as highly lignified culms, rapid shoot growth, monocarpic mass flowering and nutlike or fleshy caryopses. Much of the remarkable morphological diversity across the subfamily exists within a single hexaploid clade, the paleotropical woody bamboos (PWB), makin...

Vascular plants are crucial to global biodiversity, so their systematic taxonomy, origin and evolution are important topics. With the rapid development of sequencing technology, numerous vascular plant plastomes have been sequenced and published, offering significant insights into these issues. This study aims to present the basic characteristics a...

Feralization is an important evolutionary process, but the mechanisms behind it remain poorly understood. Here, we use the ancient fiber crop, ramie (Boehmeria nivea (L.) Gaudich.) as a model to investigate genomic changes associated with both domestication and fertilization. We first produced a chromosome-scale de novo genome assembly of feral ram...

Mycorrhizal associations are key mutualisms that shape the structure of forest communities and multiple ecosystem functions. However, we lack a framework for predicting the varying dominance of distinct mycorrhizal associations in an integrated proxy of multifunctionality across ecosystems. Here, we used the datasets containing diversity of mycorrh...

Many examples of phenotypic modifications resulting from high‐elevation adaptation have been documented, however, the underlying processes responsible for these modifications and whether the continuity of the adaptation process remain elusive, particularly in plants. The alpine plants distributed along wide elevational gradients provide an ideal sy...

Plant life-history is determined by two transitions, the germination and the flowering times, in which the phosphatidylethanolamine-binding proteins (PEBP) FLOWERING LOCUS T (FT) and TERMINAL FLOWER1 (TFL1) play key regulatory roles. Compared to the highly conserved TFL1-likes, FT-like genes vary in copy numbers significantly in gymnosperms and mon...

Brassicaceae represents an important plant family from both a scientific and economic perspective. However, genomic features related to the early diversification of this family have not been fully characterized, especially upon the uplift of the Tibetan Plateau, which was followed by increasing aridity in the Asian interior, intensifying monsoons i...

全球马先蒿属植物约有600 ～ 700 种，主要分布于北温带高山地区，中国记录390 余种。本书收录中国马先蒿属植物253 种，书中对每个种的形态特征、生境、分布等信息进行了记述，并配有彩色照片。本书编写参考《中国植物志》及Flora of China，根据形态特征将马先蒿属植物划分为5 个大类和5 个亚类，在此基础上编制了检索表，用于物种快速鉴定；根据形态－地理原则，对于一些形态相近的种绘制了地理分布图，以辅助物种的准确鉴别。 本书可供植物分类学、进化生物学、保护生物学、生态学和植物资源学等领域的研究人员和相关专业师生使用，也可供自然保护区的工作人员和植物爱好者阅读。

Grasses (Poaceae) comprise around 11,800 species and are central for human livelihoods and terrestrial ecosystems. Knowing their relationships and evolutionary history is key to comparative research and crop breeding. Advances in genome-scale sequencing allow for increased breadth and depth of phylogenomic analyses, making it possible to infer a ne...

Niche convergence or conservatism have been proposed as essential mechanisms underlying elevational plant community assembly in tropical mountain ecosystems. Subtropical mountains, compared to tropical mountains, are likely to be shaped by a mixing of different geographic affinities of species and remain somehow unclear. Here, we used 31 0.1-ha per...

BambooBase provides a comprehensive collection of 18 genomes, 476 transcriptomes, 16 epigenomes, and taxonomic resources of all 135 currently recognized genera of bamboos (Figure 1A). Notably, it provides valuable information on subgenome-scale sequence similarity- and collinearity-based homologous groups (Figure 1B). A diverse range of versatile a...

The adaptive significance of phenotypic differences between females and males can provide insights into sex-specific selection and the evolution of sexual dimorphism. Dioecious plants commonly exhibit sexual dimorphism in height, although its ecological and evolutionary significance have rarely been examined experimentally. Here, we investigate the...

Pseudosasa gracilis (Poaceae: Bambusoideae) is a temperate woody bamboo species endemic to Southcentral China with a narrow distribution. Previous phylogenetic studies revealed an unexpected, isolated phylogenetic position of Ps. gracilis. Here we conducted phylogenomic analysis by sampling populations of Ps. gracilis and its sympatric species Ps....

Background The plastid is the photosynthetic organelle in plant cell, and the plastid genomes (plastomes) are generally conserved in evolution. As one of the most economically and ecologically important order of angiosperms, Poales was previously documented to exhibit great plastomic variation as an order of photoautotrophic plants. Results We acq...

Angiosperms are the cornerstone of most terrestrial ecosystems and human livelihoods1,2. A robust understanding of angiosperm evolution is required to explain their rise to ecological dominance. So far, the angiosperm tree of life has been determined primarily by means of analyses of the plastid genome3,4. Many studies have drawn on this foundation...

The Millettioid/Phaseoloid (or the Millettioid) clade is a major lineage of the subfamily Papilionoideae (Fabaceae) that is poorly understood in terms of its diversification and biogeographic history. To fill this gap, we generated a time‐calibrated phylogeny for 749 species representing c . 80% of the genera of this clade using nrDNA ITS, plastid...

Poaceae members shared a whole-genome duplication called rho. However, little is known about the evolutionary pattern of the rho-derived duplicates among Poaceae lineages and implications in adaptive evolution. Here we present phylogenomic/phylotranscriptomic analyses of 363 grasses covering all 12 subfamilies and report nine previously unknown who...

Parasitic lifestyle can often relax the constraint on the plastome, leading to gene pseudogenization and loss, and resulting in diverse genomic structures and rampant genome degradation. Although several plastomes of parasitic Cuscuta have been reported, the evolution of parasitism in the family Convolvulaceae which is linked to structural variatio...

Dryopteris jinpingensis, a new species of diploid, sexually reproductive ferns of Dryopteridaceae from Yunnan, southwestern China, is described and illustrated. Morphologically, D. jinpingensis is similar to D. gaoligongensis but unique in elongated lanceolate laminae, sessile or subsessile pinna stalks, and overlapping membranous scales adnate to...

Chinese Assam tea (Camellia sinensis var. assamica) is an important tea crop with a long history of cultivation in Yunnan, China. Despite its potential value as a genetic resource, its genetic diversity and domestication/breeding history remain unclear. To address this issue, we genotyped 469 ancient tea plant trees representing 26 C. sinensis var....

An improved understanding of biodiversity-productivity relationships (BPRs) along environmental gradients is crucial for effective ecosystem management and biodiversity conservation. The stress-gradient hypothesis suggests that BPRs are stronger in stressful environments compared to more favorable conditions. However, there is limited knowledge reg...

Sex-biased genes offer insights into the evolution of sexual dimorphism. Sex-biased genes, especially those with male bias, show elevated evolutionary rates of protein sequences driven by positive selection and relaxed purifying selection in animals. Although rapid sequence evolution of sex-biased genes and evolutionary forces have been investigate...

Predicting species extinction is challenging in the context of climate change. The International Union for Conservation of Nature (IUCN) Red List of Threatened Species assesses species extinction risk by accounting for population size and global range of taxa, but this approach neglects the importance of genetic variability. Here, we propose a life...

Polyploidy, or whole genome duplication (WGD) is widely regarded as key innovation promoting species diversification in plants. However, the hypothesis still remains controversial. Here, we tested the hypothesis by analyzing the association between polyploidy and the diversification of Araceae. Using 1081 single/low copy orthologous clusters from 9...

Boehmeria nivea var. strigosa Zeng Y. Wu & Y. Zhao, a new variety of B. nivea (Urticaceae) from southwest China, is here described and illustrated based on evidence from morphology and molecular phylogeny. This new variety is mainly characterized by its green abaxial leaf blade, partly connate stipules, and densely patent strigose hairs. The phylog...

Sex-biased genes offer insights into the evolution of sexual dimorphism. Sex-biased genes, especially those with male bias, show elevated evolutionary rates of protein sequences driven by positive selection and relaxed purifying selection in animals. Although rapid sequence evolution of sex-biased genes and evolutionary forces have been investigate...

Evolutionary transitions from outcrossing to selfing in flowering plants have convergent morphological and genomic signatures and can involve parallel evolution within related lineages. Adaptive evolution of morphological traits is often assumed to evolve faster than nonadaptive features of the genomic selfing syndrome. We investigated phenotypic a...

Aims A comprehensive understanding of the genetic variation of walnuts (Juglans regia and J. sigillata) in the Himalaya and its potential drivers are essential for the conservation and sustainable utilization of these plant genetic resources. In this study, we aimed to uncover the genetic landscape of walnuts and potential drivers in the Himalaya f...

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...

The powerhouse, mitochondria, in plants feature high levels of structural variation, while the encoded genes are normally conserved. However, the substitution rates and spectra of mitochondria DNA within the Brassicaceae, a family with substantial scientific and economic importance, have not been adequately deciphered. Here, by analyzing three newl...

Background Quercus aliena is a major montane tree species of subtropical and temperate forests in China, with important ecological and economic value. In order to reveal the species’ population dynamics, genetic diversity, genetic structure, and association with mountain habitats during the evolutionary process, we re-sequenced the genomes of 72 Q....

Evergreen broad‐leaved forests (EBLFs) are dominated by a monsoon climate and form a distinct biome in East Asia with notably high biodiversity. However, the origin and evolution of East Asian EBLFs (EAEBLFs) remain elusive despite the estimation of divergence times for various representative lineages. Using 72 selected generic‐level characteristic...

Sex-biased genes offer insights into the evolution of sexual dimorphism. Sex-biased genes, especially those with male bias, show elevated evolutionary rates of protein sequences driven by positive selection and relaxed purifying selection in animals. Although rapid sequence evolution of sex-biased genes and evolutionary forces have been investigate...

Background Independent origins of carnivory in multiple angiosperm families are fabulous examples of convergent evolution using a diverse array of life forms and habitats. Previous studies have indicated that carnivorous plants have distinct evolutionary trajectories of plastid genome (plastome) compared to their non-carnivorous relatives, yet the...

Current biodiversity loss is generally considered to have been caused by anthropogenic disturbance, but it is unclear when anthropogenic activities began to affect biodiversity loss. One hypothesis suggests it began with the Industrial Revolution, whereas others propose that anthropogenic disturbance has been associated with biodiversity decline si...

Five new orchid species from southwestern China’s Yunnan Province and the Tibetan Autonomous Region, Neottia lihengiae, Neottia chawalongensis, Papilionanthe motuoensis, Gastrochilus lihengiae, and Gastrochilus bernhardtianus, are described and illustrated. To confirm their identities, and to resolve phylogenetic relationships, we sequenced the com...

Genomic imprinting refers to parent‐of‐origin‐dependent gene expression and primarily occurs in the endosperm of flowering plants, but its functions and epigenetic mechanisms remain to be elucidated in eudicots. Castor bean, a eudicot with large and persistent endosperm, provides an excellent system for studying the imprinting. Here, we identified...

Perennial monocarpic mass flowering represents as a key developmental innovation in flowering time diversity in several biological and economical essential families, such as the woody bamboos and the shrubby Strobilanthes. However, molecular and genetic mechanisms underlying this important biodiversity remain poorly investigated. Here, we generated...

Mountainous regions provide a multitude of habitats and opportunities for complex speciation scenarios. Hybridization leading to chloroplast capture, which can be revealed by incongruent phylogenetic trees, is one possible outcome. Four allopatric Taxus lineages (three species and an undescribed lineage) from the Hengduan Mountains, southwest China...

Sex-biased genes offer insights into the evolution of sexual dimorphism. Sex-biased genes, especially those with male bias, show elevated evolutionary rates of protein sequences driven by positive selection and relaxed purifying selection in animals. Although rapid sequence evolution of sex-biased genes and evolutionary forces have been investigate...

Sex-biased genes offer insights into the evolution of sexual dimorphism. Sex-biased genes, especially those with male bias, show elevated evolutionary rates of protein sequences driven by positive selection and relaxed purifying selection in animals. Although rapid sequence evolution of sex-biased genes and evolutionary forces have been investigate...

reference trascriptome, orthology data, and alignments (Positive selection and relaxed purifying selection contribute to rapid evolution of male-biased genes in a dioecious flowering plant)

Epiphytes with crassulacean acid metabolism (CAM) photosynthesis are widespread in vascular plants, and repeated evolution of CAM photosynthesis is a key innovation for micro-ecosystem adaptation. However, our understanding of the molecular regulation of CAM photosynthesis in epiphytes remains elusive. Here, we report a high-quality chromosomal-lev...

Sex-biased genes offer insights into the evolution of sexual dimorphism. Sex-biased genes, especially those with male bias, show elevated evolutionary rates of protein sequences driven by positive selection and relaxed purifying selection in animals. Although rapid sequence evolution of sex-biased genes and evolutionary forces have been investigate...

Flowering plant lineages display remarkable diversity in life history and morphological form. However our understanding of how this phenotypic diversity or disparity, arises and what, if any, relation there is to processes such as gene and genome duplication remains unlcear. Here we investigate the relationship between phenotypic and genomic evolut...

The evergreen versus deciduous leaf habit is an important functional trait for adaptation of forest trees and has been hypothesized to be related to the evolutionary processes of the component species under paleoclimatic change, and potentially reflected in the dynamic history of evergreen broadleaved forests (EBLFs) in East Asia. However, knowledg...

Standard barcodes and ultra-barcodes face challenges in delimitation and discrimination of closely related species with deep coalescence, hybrid speciation, gene flow or low sequence-variation. Single copy orthologs (SCOs) have been recommended as standardized nuclear markers in metazoan DNA taxonomy. Here, we assessed the performance of SCOs in id...

Information about smoke cues for seed germination is fundamental to understanding fire adaptation. Recently, lignin-derived syringaldehyde (SAL) was identified as a new smoke cue for seed germination, which challenges the assumption that cellulose-derived karrikins are the primary smoke cues. We highlight the overlooked association between lignin a...

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...

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...

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...