Angiosperms(flowering plants) are by far the most diverse land plant group with over 300,000 species. The sudden appearance of diverse angiosperms in the fossil record was referred to by Darwin as the “abominable mystery,”hence contributing to the heightened interest in angiosperm evolution. Angiosperms display wide ranges of morphological, physiological,and ecological characters, some of which have probably influenced their species richness. The evolutionary analyses of these characteristics help to address questions of angiosperm diversification and require well resolved phylogeny. Following the great successes of phylogenetic analyses using plastid sequences,dozens to thousands of nuclear genes from next-generation sequencing have been used in angiosperm phylogenomic analyses, providing well resolved phylogenies and new insights into the evolution of angiosperms. In this review we focus on recent nuclear phylogenomic analyses of large angiosperm clades, orders, families,and subdivisions of some families and provide a summarized Nuclear Phylogenetic Tree of Angiosperm Families. The newly established nuclear phylogenetic relationships are highlighted and compared with previous phylogenetic results. The sequenced genomes of Amborella,Nymphaea, Chloranthus, Ceratophyllum, and species of monocots, Magnoliids, and basal eudicots, have facilitated the phylogenomics of relationships among five major angiosperms clades. All but one of the 64 angiosperm orders were included in nuclear phylogenomics with well resolved relationships except the placements of several orders. Most families have been included with robust and highly supported placements, especially for relationships within several large and important orders and families.Additionally, we examine the divergence time estimation and biogeographic analyses of angiosperm on the basis of the nuclear phylogenomic frameworks and discuss the differences compared with previous analyses. Furthermore,we discuss the implications of nuclear phylogenomic analyses on ances
Plant root-nodule symbiosis(RNS)with mutualistic nitrogen-fixing bacteria is restricted to a single clade of angiosperms,the Nitrogen-Fixing Nodulation Clade(NFNC),and is best understood in the legume family.Nodulating species share many commonalities,explained either by divergence from a common ancestor over 100 million years ago or by convergence following independent origins over that same time period.Regardless,comparative analyses of diverse nodulation syndromes can provide insights into constraints on nodulation—what must be acquired or cannot be lost for a functional symbiosis—and the latitude for Plant Communications Genomic landscape of nodulation variation in the symbiosis.However,much remains to be learned about nodulation,especially outside of legumes.Here,we employed a large-scale phylogenomic analysis across 88 species,complemented by 151 RNA-seq libraries,to elucidate the evolution of RNS.Our phylogenomic analyses further emphasize the uniqueness of the transcription factor NIN as a master regulator of nodulation and identify key muta-tions that affect its function across the NFNC.Comparative transcriptomic assessment revealed nodule-specific upregulated genes across diverse nodulating plants,while also identifying nodule-specific and nitrogen-response genes.Approximately 70%of symbiosis-related genes are highly conserved in the four representative species,whereas defense-related and host-range restriction genes tend to be lineage specific.Our study also identified over 900000 conserved non-coding elements(CNEs),over 300000 of which are unique to sampled NFNC species.NFNC-specific CNEs are enriched with the active H3K9ac mark and are correlated with accessible chromatin regions,thus representing a pool of candidate regula-tory elements for genes involved in RNS.Collectively,our results provide novel insights into the evolution of nodulation and lay a foundation for engineering of RNS traits in agriculturally important crops.
Here, we infer the historical biogeography and evolutionary diversification of the genus Lilium. For this purpose, we used the complete plastomes of 64 currently accepted species in the genus Lilium(14plastomes were newly sequenced) to recover the phylogenetic backbone of the genus and a timecalibrated phylogenetic framework to estimate biogeographical history scenarios and evolutionary diversification rates of Lilium. Our results suggest that ancient climatic changes and geological tectonic activities jointly shaped the distribution range and drove evolutionary radiation of Lilium, including the Middle Miocene Climate Optimum(MMCO), the late Miocene global cooling, as well as the successive uplift of the Qinghai-Tibet Plateau(QTP) and the strengthening of the monsoon climate in East Asia during the late Miocene and the Pliocene. This case study suggests that the unique geological and climatic events in the Neogene of East Asia, in particular the uplift of QTP and the enhancement of monsoonal climate, may have played an essential role in formation of uneven distribution of plant diversity in the Northern Hemisphere.
Nian ZhouKe MiaoChangkun LiuLinbo JiaJinjin HuYongjiang HuangYunheng Ji
The angiosperm family Elaeagnaceae comprises three genera and ca.100 species distributed mainly in Eurasia and North America.Little family-wide phylogenetic and biogeographic research on Elaeagnaceae has been conducted,limiting the application and preservation of natural genetic resources.Here,we reconstructed a strongly supported phylogenetic framework of Elaeagnaceae to better understand interand intrageneric relationships,as well as the origin and biogeographical history of the family.For this purpose,we used both nuclear and plastid sequences from Hyb-Seq and genome skimming approaches to reconstruct a well-supported phylogeny and,along with current distributional data,infer historical biogeographical processes.Our phylogenetic analyses of both nuclear and plastid data strongly support the monophyly of Elaeagnaceae and each of the three genera.Elaeagnus was resolved as sister to the well-supported clade of Hippophae and Shepherdia.The intrageneric relationships of Elaeagnus and Hippophae were also well resolved.High levels of nuclear gene tree conflict and cytonuclear discordance were detected within Elaeagnus,and our analyses suggest putative ancient and recent hybridization.We inferred that Elaeagnaceae originated at ca.90.48 Ma(95%CI?89.91e91.05 Ma),and long-distance dispersal likely played a major role in shaping its intercontinentally disjunct distribution.This work presents the most comprehensive phylogenetic framework for Elaeagnaceae to date,offers new insights into previously unresolved relationships in Elaeagnus,and provides a foundation for further studies on classification,evolution,biogeography,and conservation of Elaeagnaceae.
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.
Guojin ZhangJunbo YangCaifei ZhangBohan JiaoJoséL.PaneroJie CaiZhi-Rong ZhangLian-Ming GaoTiangang GaoHong Ma
Cymbidium(Orchidaceae:Epidendroideae),with around 60 species,is widely-distributed across Southeast Asia,providing a nice system for studying the processes that underlie patterns of biodiversity in the region.However,phylogenetic relationships of Cymbidium have not been well resolved,hampering investigations of species diversification and the biogeographical history of this genus.In this study,we construct a plastome phylogeny of 56 Cymbidium species,with four well-resolved major clades,which provides a framework for biogeographical and diversification rate analyses.Molecular dating and biogeographical analyses show that Cymbidium likely originated in the region spanning northern IndoBurma to the eastern Himalayas during the early Miocene(~21.10 Ma).It then rapidly diversified into four major clades in East Asia within approximately a million years during the middle Miocene.Cymbidium spp.migration to the adjacent regions(Borneo,Philippines,and Sulawesi)primarily occurred during the Pliocene-Pleistocene period.Our analyses indicate that the net diversification rate of Cymbidium has decreased since its origin,and is positively associated with changes in temperature and monsoon intensity.Favorable hydrothermal conditions brought by monsoon intensification in the early Miocene possibly contributed to the initial rapid diversification,after which the net diversification rate was reduced with the cooling climate after the middle Miocene.The transition from epiphytic to terrestrial habits may have enabled adaptation to cooler environments and colonization of northern niches,yet without a significant effect on diversification rates.This study provides new insights into how monsoon activity and temperature changes affected the diversification dynamics of plants in Southeast Asia.
Until now the genus Amana(Liliaceae),known as ’East Asian tulips’,has contained just seven species.In this study,a phylogenomic and integrative taxonomic approach was used to reveal two new species,Amana nanyueensis from Central China and A.tianmuensis from East China.A.nanyueensis resembles Amana edulis in possessing a densely villous-woolly bulb tunic and two opposite bracts,but differs in its leaves and anthers.Amana tianmuensis resembles Amana erythronioides in possessing three verticillate bracts and yellow anthers,but differs in aspects of its leaves and bulbs.These four species are clearly separated from each other in principal components analysis based on morphology.Phylogenomic analyses based on plastid CDS further support the species delimitation of A.nanyueensis and A.tianmuensis and suggests they are closely related to A.edulis.Cytological analysis shows that A.nanyueensis and A tianmuensis are both diploid(2n=2x=24),different from A edulis,which is either diploid(northern populations) or tetraploid(southern populations,2n=4x=48).The pollen morphology of A.nanyueensis is similar to other Amana species(single-groove germination aperture),but A.tianmuensis is quite different because of the presence of a sulcus membrane,which creates the illusion of double grooves.Ecological niche modelling also revealed a niche differentiation between A.edulis,A.nanyueensis and A.tianmuensis.
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.
Cen GuoYang LuoLian-Ming GaoTing-Shuang YiHong-Tao LiJun-Bo YangDe-Zhu Li
