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

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.assamica populations,plus two of its wild relatives(six and three populations of C.taliensis and C.crassicolumna,respectively)using 16 nuclear microsatellite loci.Results showed that Chinese Assam tea has a relatively high,but comparatively lower gene diversity(H_(S)=0.638)than the wild relative C.crassicolumna(H_S=0.658).Clustering in STRUCTURE indicated that Chinese Assam tea and its two wild relatives formed distinct genetic groups,with considerable interspecific introgression.The Chinese Assam tea accessions clustered into three gene pools,corresponding well with their geographic distribution.However,New Hybrids analysis indicated that 68.48%of ancient Chinese Assam tea plants from Xishuangbanna were genetic intermediates between the Puer and Lincang gene pools.In addition,10%of the ancient Chinese Assam tea individuals were found to be hybrids between Chinese Assam tea and C.taliensis.Our results suggest that Chinese Assam tea was domesticated separately in three gene pools(Puer,Lincang and Xishuangbanna)in the Mekong River valley and that the hybrids were subsequently selected during the domestication process.Although the domestication history of Chinese Assam tea in southwestern Yunnan remains complex,our results will help to identify valuable genetic resources that may be useful in future tea breeding programs.

Recent advances on phylogenomics of gymnosperms and a new classification

Living gymnosperms comprise four major groups:cycads,Ginkgo,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.Recent advances in gymnosperm phylogenomic studies have updated our knowledge of gymnosperm systematics.Here,we review major advances of gymnosperm phylogeny over the past 10 years and propose an updated classification of extant gymnosperms.This new classification includes three classes(Cycadopsida,Ginkgoopsida,and Pinopsida),five subclasses(Cycadidae,Ginkgoidae,Cupressidae,Pinidae,and Gnetidae),eight orders(Cycadales,Ginkgoales,Araucariales,Cupressales,Pinales,Ephedrales,Gnetales,and Welwitschiales),13 families,and 86 genera.We also described six new tribes including Acmopyleae Y.Yang,Austrocedreae Y.Yang,Chamaecyparideae Y.Yang,Microcachrydeae Y.Yang,Papuacedreae Y.Yang,and Prumnopityeae Y.Yang,and made 27 new combinations in the genus Sabina.

Distributional responses to climate change for alpine species of Cyananthus and Primula endemic to the Himalaya-Hengduan Mountains

Global warming increases the vulnerability of plants, especially alpine herbaceous species, to local extinction. In this study, we collected species distribution information from herbarium specimens for ten selected Cyananthus and Primula alpine species endemic to the Himalaya-Hengduan Mountains(HHM).Combined with climate data from WorldClim, we used Maximum Entropy Modeling(MaxEnt) to project distributional changes from the current time period to 2070. Our predictions indicate that, under a wide range of climate change scenarios, the distributions of all species will shift upward in elevation and northward in latitude; furthermore, under these scenarios, species will expand the size of their range. For the majority of the species in this study, habitats are available to mitigate upward and northward shifts that are projected to be induced by changing climate. If current climate projections, however, increase in magnitude or continue to increase past our projection dates, suitable habitat for future occupation by alpine species will be limited as we predict range contraction or less range expansion for some of the species under more intensified climate scenarios. Our study not only underscores the value of herbarium source information for future climate model projections but also suggests that future studies on the effects of climate change on alpine species should include additional biotic and abiotic factors to provide greater resolution of the local dynamics associated with species persistence under a warming climate.

Genetic analysis of walnut cultivars from southwest China:Implications for germplasm improvement

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 selecting the right cultivar for grafting,industrial processing or development of new cultivars.To ensure proper identification of cultivars and understand the genetic structure of wild and cultivated material,we genotyped 362 cultivated and wild individuals of walnut trees from southwest China(with two additional populations from Xinjiang,plus three cultivars from Canada,France and Belgium) using 36 polymorphic microsatellite loci.We found relatively low indices of genetic diversity(H_(O)=0.570,H_(E)=0.404,N_(A)=2.345) as well as a high level of clonality(>85% of cultivars),indicating reliance on genetically narrow sources of parental material for breeding.Our STRUCTURE and PCoA analyses generally delineated the two species,though considerable levels of introgression were also evident.More significantly,we detected a distinct genetic group of cultivated Juglans sigillata,which mainly comprised individuals of the popular ’Yangbidapao’ landrace.Finally,a core set of 18 SSR loci was selected,which was capable of identifying 32 cultivars.In a nutshell,our results call for more utilization of genetically disparate material,including wild walnut trees,as parental sources to breed for more cultivars.The data reported herein will significantly contribute towards the genetic improvement and conservation of the walnut germplasm in southwest China.

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.Nuclear Asteraceae phylogenies have resolved relationships among most subfamilies and many tribes,but many phylogenetic and evolutionary questions regarding subtribes and genera remain,owing to limited sampling.Here,we increased the sampling for Asteraceae phylogenetic reconstruction using transcriptomes and genome-skimming datasets and produced nuclear phylogenetic trees with 706 species representing two-thirds of recognized subtribes.Ancestral character reconstruction supports multiple convergent evolutionary events in Asteraceae,with gains and losses of bilateral floral symmetry correlated with diversification of some subfamilies and smaller groups,respectively.Presence of the calyx-related pappus may have been especially important for the success of some subtribes and genera.Molecular evolutionary analyses support the likely contribution of duplications of MADS-box and TCP floral regulatory genes to innovations in floral morphology,including capitulum inflorescences and bilaterally symmetric flowers,potentially promoting the diversification of Asteraceae.Subsequent divergences and reductions in CYC2 gene expression are related to the gain and loss of zygomorphic flowers.This phylogenomic work with greater taxon sampling through inclusion of genome-skimming datasets reveals the feasibility of expanded evolutionary analyses using DNA samples for understanding convergent evolution.

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.This review focuses on the utility of genomic data(from organelle genomes,to both reduced representation sequencing and whole-genome sequencing) in phylogenetic and evolutionary investigations,describes the baseline methodology of experimental and analytical procedures,and summarizes recent progress in flowering plant phylogenomics at the ordinal,familial,tribal,and lower levels.We also discuss the challenges,such as the adverse impact on orthology inference and phylogenetic reconstruction raised from systematic errors,and underlying biological factors,such as whole-genome duplication,hybridization/introgression,and incomplete lineage sorting,together suggesting that a bifurcating tree may not be the best model for the tree of life.Finally,we discuss promising avenues for future plant phylogenomic studies.

Incomplete reproductive isolation between Rhododendron taxa enables hybrid formation and persistence

The evolutionary consequences of hybridization ultimately depend on the magnitude of reproductive isolation between hybrids and their parents. We evaluated the relative contributions of pre-and post-zygotic barriers to reproduction for hybrid formation, hybrid persistence and potential for reproductive isolation of hybrids formed between two Rhododendron species,R. spiciferum and R. spinuliferum. Our study established that incomplete reproductive isolation promotes hybrid formation and persistence and delays hybrid speciation.All pre-zygotic barriers to reproduction leading to hybrid formation are incomplete: parental species have overlapping flowering; they share the same pollinators;reciprocal assessments of pollen tube germination and growth do not differ among parents. The absence of post-zygotic barriers between parental taxa indicates that the persistence of hybrids is likely. Reproductive isolation was incomplete between hybrids and parents in all cases studied, although asymmetric differences in reproductive fitness were prevalent and possibly explain the genetic structure of natural hybrid swarms where hybridization is known to be bidirectional but asymmetric. Introgression, rather than speciation, is a probable evolutionary outcome of hybridization between the two Rhododendron taxa. Our study provides insights into understanding the evolutionary implications of natural hybridization in woody plants.

Phylogeny and Evolution of Bracts and Bracteoles in Tacca (Dioscoreaceae)

Most species in the genus Tacca （Dioscoreaceae） feature green to black purple, conspicuous inflorescence involucral bracts with variable shapes, motile filiform appendages （bracteoles）, and diverse types of inflorescence morphology. To infer the evolution of these inflorescence traits, we reconstructed the molecular phylogeny of the genus, using DNA sequences from one nuclear, one mitochondrial, and three plastid loci （Internal Transcribed Spacer （ITS）, atpA, rbcL, trnL-F, and trnH-psbA）. Involucres and bracteoles characters were mapped onto the phylogeny to analyze the sequence of inflorescence trait evolution. In all analyses, species with showy involucres and bracteoles formed the most derived clade, while ancestral Tacca had small and plain involucres and short bracteoles, namely less conspicuous inflorescence structures. Two of the species with the most elaborate inflorescence morphologies （T. chantrieri in southeast China and T. integrifolia in Tibet）, are predominantly self-pollinated, indicating that these conspicuous floral displays have other functions rather than pollinator attraction. We hypothesize that the motile bracteoles and involucres may facilitate selfing; display photosynthesis in the dim understory, and protect flowers from herbivory.