Genomic analyses of agronomic traits in tea plants and related species.

The genus contains three types of domesticates that meet various needs of ancient humans: the ornamental , the edible oil-producing , and the beverage-purposed tea plant . The genomic drivers of the functional diversification of domesticates remain unknown. Here, we present the genomic variations of 625 accessions based on a new genome assembly of var.

Genetic analyses of ancient tea trees provide insights into the breeding history and dissemination of Chinese Assam tea ( var. ).

Chinese Assam tea ( var. ) 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.

Niche convergence and biogeographic history shape elevational tree community assembly in a subtropical mountain forest.

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.

A leading-edge scenario in the phylogeography and evolutionary history of East Asian insular in Taiwan and the Philippines.

The cool temperate origin of gymnosperm species in East Asia is specifically diverse and widespread. Certain lineages have managed to extend their distribution further south to subtropical and tropical islands such as Taiwan and the Philippines. To address questions including whether these insular lineages, recently identified as , have become genetically distinct from each other and from their continental relatives, and when and how they colonized their residing islands, we sampled over 11 populations, covering 179 individuals from Taiwan and the Philippines.

Nuclear phylogenomics of Asteraceae with increased sampling provides new insights into convergent morphological and molecular evolution.

Convergent morphological evolution is widespread in flowering plants, and understanding this phenomenon relies on well-resolved phylogenies. Nuclear phylogenetic reconstruction using transcriptome datasets has been successful in various angiosperm groups, but it is limited to taxa with available fresh materials. Asteraceae, which are one of the two largest angiosperm families and are important for both ecosystems and human livelihood, show multiple examples of convergent evolution.

Distinctive plastome evolution in carnivorous angiosperms.

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 extent and general characteristics remain elusive.

Results: We compared plastomes from 9 out of 13 carnivorous families and their non-carnivorous relatives to assess carnivory-associated evolutionary patterns.

Phylogenetic Relationships and Next-Generation Barcodes in the Genus Reveal a High Proportion of Misidentified Cultivated Plants.

Accurate species identification is key to conservation and phylogenetic inference. Living plant collections from botanical gardens/arboretum are important resources for the purpose of scientific research, but the proportion of cultivated plant misidentification are un-tested using DNA barcodes. Here, we assembled the next-generation barcode (complete plastid genome and complete nrDNA cistron) and mitochondrial genes from genome skimming data of species with multiple accessions for each species to test the species discrimination and the misidentification proportion of cultivated plants used in studies.

 (Taxaceae), a new natural hybrid from southeast Yunnan province, China.

During floristic surveys of Taxaceae in Hekou County, Yunnan Province, China, a putative natural hybrid between H.L. Li and L.

Variation in gene expression along an elevation gradient of var. assessed in a comparative transcriptomic analysis.

Selection along environmental gradients may play a vital role in driving adaptive evolution. Nevertheless, genomic variation and genetic adaptation along environmental clines remains largely unknown in plants in alpine ecosystems. To close this knowledge gap, we assayed transcriptomic profiles of late flower bud and early leaf bud of var.

Phylogenomics and morphological evolution of the mega-diverse genus Artemisia (Asteraceae: Anthemideae): implications for its circumscription and infrageneric taxonomy.

Background And Aims: Artemisia is a mega-diverse genus consisting of ~400 species. Despite its medicinal importance and ecological significance, a well-resolved phylogeny for global Artemisia, a natural generic delimitation and infrageneric taxonomy remain missing, owing to the obstructions from limited taxon sampling and insufficient information on DNA markers. Its morphological characters, such as capitulum, life form and leaf, show marked variations and are widely used in its infrageneric taxonomy.

Phylogenomics and the flowering plant tree of life.

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 era. In the meantime, a roadmap for researchers when making decisions across different approaches for their phylogenomic research design is imminent.

Plastome sequences fail to resolve shallow level relationships within the rapidly radiated genus (Lamiaceae).

As one of the largest genera of Lamiaceae and of great medicinal importance, is also phylogenetically and taxonomically recalcitrant largely ascribed to its recent rapid radiation in the Hengduan Mountains. Previous molecular phylogenetic studies using limited loci have only successfully resolved the backbone topology of the genus, but the interspecific relationships suffered from low resolution, especially within the largest clade (Clade IV) which comprises over 80% species. In this study, we attempted to further elucidate the phylogenetic relationships within especially Clade IV using plastome sequences with a broad taxon sampling of ca.

Recent advances on phylogenomics of gymnosperms and a new classification.

Living gymnosperms comprise four major groups: cycads, , conifers, and gnetophytes. Relationships among/within these lineages have not been fully resolved. Next generation sequencing has made available a large number of sequences, including both plastomes and single-copy nuclear genes, for reconstruction of solid phylogenetic trees.

Testing the Complete Plastome for Species Discrimination, Cryptic Species Discovery and Phylogenetic Resolution in (Cephalotaxaceae).

Species of 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 species with multiple samples per taxon.

Determinants of Genetic Structure in a Highly Heterogeneous Landscape in Southwest China.

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 explanatory variables; so here we mapped the patterns of plastid genetic diversity within 15 plant species, and explored the key determinants shaping these patterns using a wide range of variables.

Multitrophic diversity and biotic associations influence subalpine forest ecosystem multifunctionality.

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 9 different trophic groups (including trees, shrubs, herbs, leaf mites, small mammals, bacteria, pathogenic fungi, saprophytic fungi, and symbiotic fungi) and 13 ecosystem functions related to supporting, provisioning, and regulating services, we used a multitrophic perspective to evaluate the effects of elevation, diversity, and network complexity on scale-dependent subalpine forest multifunctionality.

Phylotranscriptomics of Theaceae: generic-level relationships, reticulation and whole-genome duplication.

Background And Aims: Theaceae, with three tribes, nine genera and more than 200 species, are of great economic and ecological importance. Recent phylogenetic analyses based on plastomic data resolved the relationships among the three tribes and the intergeneric relationships within two of those tribes. However, generic-level relationships within the largest tribe, Theeae, were not fully resolved.