Deep genome skimming reveals the hybrid origin of Pseudosasa gracilis (Poaceae: Bambusoideae)

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.nanunica and Sinosasa polytricha reflecting different genomic signals,by deep genome skimming.Integrating molecular evidence from chloroplast genes and genome-wide SNPs,we deciphered the phylogenetic relationships of Ps.gracilis.Both plastid and nuclear data indicate that Ps.gracilis is more closely related to Sinosasa,which is discordant with the taxonomic treatment.To further explore this molecular-morphological conflict,we screened 411“perfect-copy”syntenic genes to reconstruct phylogenies using both the concatenation and coalescent methods.We observed extensive discordance between gene trees and the putative species tree.A significant hybridization event was detected based on 411 genes from the D subgenome,showing Ps.gracilis was a hybrid descendant between Sinosasa longiligulata and Ps.nanunica,with 63.56%and 36.44%inheritance probabilities of each parent.Moreover,introgression events were detected in the C subgenome between Ps.gracilis and S.polytricha in the same distribution region.Our findings suggest that sympatric hybridization and introgression play a crucial role in the origin of Ps.gracilis.By providing an empirical example of bamboo of hybrid origin using comprehensive analyses based on genomic data from different inheritance systems and morphological characters,our study represents a step forward in understanding of reticulate evolution of bamboos.

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.

New insights into intergeneric relationships of Hickeliinae(Poaceae:Bambusoideae) revealed by complete plastid genomes

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 from herbarium specimens is even more so.Molecular phylogenetic work is critical to understanding this group of bamboos.Here,comparative analysis of 22 newly sequenced plastid genomes showed that members of all genera of Hickeliinae share evolutionarily conserved plastome structures.We also determined that Hickeliinae plastome sequences are informative for phylogenetic reconstructions.Phylogenetic analysis showed that all genera of Hickeliinae are monophyletic,except for Nastus,which is paraphyletic and forms two distant clades.The type species of Nastus(Clade Ⅱ) is endemic to Reunion Island and is not closely related to other sampled species of Nastus endemic to Madagascar(Clade Ⅵ).Clade Ⅵ(Malagasy Nastus) is sister to the Sokinochloa+Hitchcockella clade(Clade Ⅴ),and both clades have a clumping habit with short-necked pachymorph rhizomes.The monotypic Decaryochloa is remarkable in having the longest floret in Bambuseae and forms a distinct Clade Ⅳ.Clade Ⅲ,which has the highest generic diversity,consists of Cathariostachys,Perrierbambus,Sirochloa,and Valiha,which are also morphologically diverse.This work provides significant resources for further genetic and phylogenomic studies of Hickeliinae,an understudied subtribe of bamboo.

Plastid phylogenomics provides new insights into the systematics,diversification,and biogeography of Cymbidium(Orchidaceae)

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.

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.

A revision of Dryopteris sect.Diclisodon(Dryopteridaceae)based on morphological and molecular evidence with description of a new species

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 differs by having a creeping rhizome and large 4-pinnate fronds.We also show that D.glabrior Ching&Z.Y.Liu is a distinct species;however,because it is a later homonym of D.glabrior Copel.,it should be renamed D.renchangiana.We conclude that a species previously known as D.nitidula,also an illegitimate homonym,should be recognized with a new name,D.sinonepalensis.We resolve the phylogenetic position of D.yoroii as sister to other sampled species of D.sect Diclisodon.Our phylogenetic analyses confirm the distinctiveness of D.gaoligongensis,D.renchangiana,and D.sinonepalensis.A key to species of D.sect Diclisodon in China is provided.

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.

Testing complete plastomes and nuclear ribosomal DNA sequences for species identification in a taxonomically difficult bamboo genus Fargesia

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 identification of Fargesia is difficult.Moreover,the rapid radiation and slow molecular evolutionary rate of Fargesia pose a significant challenge to using DNA barcoding with standard plant barcodes(rbcL,matK,and ITS) in bamboos.With progress in the sequencing technologies,complete plastid genomes(plastomes) and nuclear ribosomal DNA(nrDNA)sequences have been proposed as organelle barcodes for species identification;however,these have not been tested in bamboos.We collected 196 individuals representing 62 species of Fargesia to comprehensively evaluate the discriminatory power of plastomes and nrDNA sequences compared to standard barcodes.Our analysis indicates that complete plastomes have substantially higher discriminatory power(28.6%) than standard barcodes(5.7%),whereas nrDNA sequences show a moderate improvement(65.4%) compared to ITS(47.2%).We also found that nuclear markers performed better than plastid markers,and ITS alone had higher discriminatory power than complete plastomes.The study also demonstrated that plastomes and nrDNA sequences can contribute to intrageneric phylogenetic resolution in Fargesia.However,neither of these sequences were able to discriminate all the sampled species,and therefore,more nuclear markers need to be identified.

The identity of Dinochloa species and enumeration of Melocalamus(Poaceae:Bambusoideae) in China

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 of the paleotropical woody bamboos(Poaceae:Bambusoideae)that consists of about 15 species and one variety.To determine the phylogenetic affinity of the three Dinochloa species from Hainan,we sampled almost all recognized Chinese species of Melocalamus and representative species of Dinochloa as well as other closely related genera,performed molecular phylogenetic analysis,and compared their morphology based on herbarium and fieldwork investigation.Our ddRAD data indicate that the three species from Hainan are closely related to Melocalamus,not Dinochloa.Morphological analysis showed that these three species have a climbing habit but do not grow spirally,their culm leaves have smooth bases,and there is a ring of powder and/or tomenta above and below the nodes.Taken together our findings indicate that the three species from Hainan originally published in Dinochloa should be transferred to Melocalamus,i.e.,Melocalamus orenudus(McClure) D.Z.Li& J.X.Liu,Melocalamus puberulus(McClure) D.Z.Li & J.X.Liu,and Melocalamus utilis(McClure) D.Z.Li &J.X.Liu,respectively.This study concludes with an enumeration of Chinese species of Melocalamus,with a key to nine recognized species and one variety,and a lectotypification for M. compatiflorus.

Genomes of Meniocus linifolius and Tetracme quadricornis reveal the ancestral karyotype and genomic features of core Brassicaceae

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 in Eastern Asia,and significantly fluctuating daily temperatures.Here,we reveal the genomic architecture that accompanied early Brassicaceae diversification by analyzing two high-quality chromosome-level genomes for Meniocus linifolius(Arabodae;clade D)and Tetracme quadricornis(Hesperodae;clade E),together with genomes representing all major Brassicaceae clades and the basal Aethionemeae.We reconstructed an ancestral core Brassicaceae karyotype(CBK)containing 9 pseudochromosomes with 65 conserved syntenic genomic blocks and identified 9702 conserved genes in Brassicaceae.We detected pervasive conflicting phylogenomic signals accompanied by widespread ancient hybridization events,which correlate well with the early divergence of core Brassicaceae.We identified a successive Brassicaceae-specific expansion of the class I TREHALOSE-6-PHOSPHATE SYNTHASE 1(TPS1)gene family,which encodes enzymes with essential regulatory roles in flowering time and embryo development.The TPS1s were mainly randomly amplified,followed by expression divergence.Our results provide fresh insights into historical genomic features coupled with Brassicaceae evolution and offer a potential model for broad-scale studies of adaptive radiation under an ever-changing environment.

Genomic variation,environmental adaptation,and feralization in ramie,an ancient fiber crop

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 feralization.We first produced a chromosome-scale de novo genome assembly of feral ramie and investigated structural variations between feral and domesticated ramie genomes.Next,we gathered 915 accessions from 23 countries,comprising cultivars,major landraces,feral populations,and the wild progenitor.Based on whole-genome resequencing of these accessions,we constructed the most comprehensive ramie genomic variation map to date.Phylogenetic,demographic,and admixture signal detection analyses indicated that feral ramie is of exoferal or exo-endo origin,i.e.,descended from hybridization between domesticated ramie and the wild progenitor or ancient landraces.Feral ramie has higher genetic diversity than wild or domesticated ramie,and genomic regions affected by natural selection during feralization differ from those under selection during domestication.Ecological analyses showed that feral and domesticated ramie have similar ecological niches that differ substantially from the niche of the wild progenitor,and three environmental variables are associated with habitat-specific adaptation in feral ramie.These findings advance our understanding of feralization,providing a scientific basis for the excavation of new crop germplasm resources and offering novel insights into the evolution of feralization in nature.

A new subtribal classification of Arundinarieae(Poaceae,Bambusoideae)with the description of a new genus

A new subtribal classification of the woody bamboo tribe Arundinarieae is proposed based on recent phylogenomic studies.Five subtribes,corresponding to the five major lineages of the ddRAD-seq based phylogenomic trees,are recognised:Arundinariinae(the leptomorph lineage),Ampelocalaminae(the ADH lineage),Gaoligongshaniinae(represented by Gaoligongshania),Hsuehochloinae(represented by Hsuehochloa) and Thamnocalaminae(the pachymorph lineage,i.e.,alpine bamboos).Subtribes Ampelocalaminae,Gaoligongshaniinae and Hsuehochloinae are newly established,while the circumscriptions of subtribes Arundinariinae and Thamnocalaminae differ from the traditional classification.Subtribe Arundinariinae also includes those taxa that were previous members of the subtribe Shibataeinae.Thus,among the five redefined subtribes,Arundinariinae is the most heterogenous in terms of morphology.In Arundinarieae,rhizome type has greater implications for classification than other vegetative and reproductive characters at the subtribal level.In addition,the new monotypic genus Ravenochloa is described on the basis of its mo rphological characteristics and geographical distribution to accommodate the unique phylogenetic entity of Indocalamus wilsonii.

Diversity in seed oil content and fatty acid composition in Acer species with potential as sources of nervonic acid

Nervonic acid(NA,cis-15-tetracosenoic acid)is a very long-chain monounsaturated fatty acid that has been shown to be a core component of nerve fibers and nerve cells.It can be used to treat and prevent many neurological diseases.At present,commercially available NA is mainly derived from Acer truncatum seeds,which contain about 5%e6%NA in their seed oil.The aim of this study were to identify and analyze NA-containing Acer species that could be used as NA resource plants.For this purpose,46 Acer species seeds were collected in China and in some or all of the seed oils from these species 15 fatty acids were detected,including linoleic acid,oleic acid(C18:1D9,C18:1D11),erucic acid,palmitic acid,NA,linolenic acid(C18:3D6,9,12,C18:3D9,12,15),eicosenoic acid(C20:1D11,C20:1D13),stearic acid,behenic acid,tetracosanoic acid,arachidic acid,and docosadienoic acid.Nervonic acid was detected in all samples,but the content was highly variable among species.NA content over 9%was detected in eleven species,of which Acer elegantulum had the highest levels(13.90%).The seed oil content,seed weight,and fatty acid profiles varied among species,but the comprehensive evaluation value(W)showed that A.coriaceifolium could be a new potential NA resources plant.The results also showed that NA was significantly negatively correlated with palmitic acid,oleic acid,and eicosenoic acid,but positively correlated with eicosadienoic acid,behenic acid,erucic acid,and tetracosanoic acid,which indicate the probable pathway for NA biosynthesis in Acer plants.This study has identified Acer species that may serve as NA resources and will help guide subsequent species breeding programs.

Phylogenomic analyses reveal intractable evolutionary history of a temperate bamboo genus (Poaceae: Bambusoideae)

Shibataea is a genus of temperate bamboos(Poaceae:Bambusoideae)endemic to China,but little is known about its phylogenetic position and interspecific relationships.To elucidate the phylogenetic relationship of the bamboo genus Shibataea,we performed genome-scale phylogenetic analysis of all seven species and one variety of the genus using double digest restriction-site associated DNA sequencing(dd RAD-seq)and whole plastid genomes generated using genome skimming.Our phylogenomic analyses based on dd RAD-seq and plastome data congruently recovered Shibataea as monophyletic.The nuclear data resolved S.hispida as the earliest diverged species,followed by S.chinensis,while the rest of Shibataea can be further divided into two clades.However,the plastid and nuclear topologies conflict significantly.By comparing the results of network analysis and topologies reconstructed from different datasets,we identify S.kumasasa as the most admixed species,which may be caused by incomplete lineage sorting(ILS)or interspecific gene flow with four sympatric species.This study highlights the power of dd RAD and plastome data in resolving complex relationships in the intractable bamboo genus.

Comparative plastomic analysis and insights into the phylogeny of Salvia (Lamiaceae)

Salvia is the largest genus of Lamiaceae,with almost 1000 species,and has been divided into 11 subgenera.Salvia subg.Glutinaria,native to East Asia,is particularly important because of its potential medicinal value.However,the interspecific relationships of this subgenus have not been resolved and the plastomes of Salvia have rarely been studied.In the current study,we compared plastid genome structure and organization of 19 species of Salvia(14 newly sequenced and 5 previously published).Our comparative analysis showed that all Salvia plastomes examined have a quadripartite structure typical of most angiosperms and contain an identical set of 114 unique genes(80 protein-coding genes,4 rRNA genes,and 30 tRNA genes).The plastome structure of all Salvia species is highly conserved like other Lamiaceae plastomes.Gene content,gene order,and GC content were highly similar in these plastomes.The inverted repeats/single copy region(IR/SC)boundaries of Salvia are highly conserved,and IR contraction only occurred in two species(Salvia mekongensis and S.rosmarinus).In Salvia,sequence divergence was higher in non-coding regions than in coding regions.We found that using large single copy(LSC)and small single copy regions(SSC)with exclusion of the rapidly evolving sites produced the highest resolution in phylogenetic analysis of Salvia,suggesting that using suitable informative sites to build trees is more conducive in phylogenetic research.This study assembled a powerful matrix data set for studying the phylogeny of Salvia,resolving the interspecific relationship of Salvia subg.Glutinaria.The newly sequenced plastid genomes will also enrich the plastome database of Salvia,providing the scientific basis for the development and utilization of germplasm resources of this large and important genus.

Two new species of Yushania(Poaceae:Bambusoideae)from South China,with a taxonomic revision of related species

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(0.2e0.3 cm in diameter),glabrous sheath scar,no oral setae,a large glabrous leaf blade(10e200.9e1.3 cm)and 3e4 pairs of secondary veins.Yushania stoloniforma D.Z.Li&X.Y.Ye has a distinctive scrambling habit,which differs from its putative close allies.Both of these two new species have a solitary branch at the basal nodes and can be assigned to Yushania sect.Yushania based on morphological features.Additionally,we treated Yushania gigantea T.P.Yi&L.Yang as a new synonym of Y.elevata T.P.Yi and renamed Y.microphylla T.P.Yi&L.Yang as Y.weiningensis D.Z.Li&X.Y.Ye.

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.

Extreme plastid RNA editing may confound phylogenetic reconstruction:A case study of Selaginella(lycophytes)

Cytidine-to-uridine(C-to-U)RNA editing is common in coding regions of organellar genomes throughout land plants.In most cases RNA editing alters translated amino acids or creates new start codons,potentially confounds phylogenetic reconstructions.In this study,we used the spike moss genus Selaginella(lycophytes),which has the highest frequency of RNA editing,as a model to test the effects of extreme RNA editing on phylogenetic reconstruction.We predicted the C-to-U RNA editing sites in coding regions of 18 Selaginella plastomes,and reconstructed the phylogenetic relationships within Selaginella based on three data set pairs consisted of plastome or RNA-edited coding sequences,first and second codon positions,and translated amino acid sequences,respectively.We predicted between 400 and 3100 RNA editing sites of 18 Selaginella plastomes.The numbers of RNA editing sites in plastomes were highly correlated with the GC content of first and second codon positions,but not correlated with the GC content of plastomes as a whole.Contrast phylogenetic analyses showed that there were substantial differences(e.g.,the placement of clade B in Selaginella)between the phylogenies generated by the plastome and RNA-edited data sets.This empirical study provides evidence that extreme C-to-U RNA editing in the coding regions of organellar genomes alters the sequences used for phylogenetic reconstruction,and might even confound phylogenetic reconstruction.Therefore,RNA editing sites should be corrected when plastid or mitochondrial genes are used for phylogenetic studies,particularly in those lineages with abundant organellar RNA editing sites,such as hornworts,quillworts,spike mosses,and some seed plants.

High-quality Cymbidium mannii genome and multifaceted regulation of crassulacean acid metabolism in epiphytes

Epiphytes with crassulacean acid metabolism(CAM)photosynthesis are widespread among vascular plants,and repeated evolution of CAM photosynthesis is a key innovation for micro-ecosystem adaptation.However,we lack a complete understanding of the molecular regulation of CAM photosynthesis in epiphytes.Here,we report a high-quality chromosome-level genome assembly of a CAM epiphyte,Cymbidium mannii(Orchidaceae).The 2.88-Gb orchid genome with a contig N50 of 22.7 Mb and 27192 annotated genes was organized into 20 pseudochromosomes,82.8%of which consisted of repetitive elements.Recent expansions of long terminal repeat retrotransposon families have made a major contribution to the evolution of genome size in Cymbidium orchids.We reveal a holistic scenario of molecular regulation of metabolic physiology using high-resolution transcriptomics,proteomics,and metabolomics data collected across a CAM diel cycle.Patterns of rhythmically oscillating metabolites,especially CAM-related products,reveal circadian rhythmicity in metabolite accumulation in epiphytes.Genomewide analysis of transcript and protein level regulation revealed phase shifts during the multifaceted regulation of circadian metabolism.Notably,we observed diurnal expression of several core CAM genes(especially bCA and PPC)that may be involved in temporal fixation of carbon sources.Our study provides a valuable resource for investigating post-transcription and translation scenarios in C.mannii,an Orchidaceae model for understanding the evolution of innovative traits in epiphytes.

BambooBase:A comprehensive database of bamboo omics and systematics

Dear Editor,Bamboos(Bambusoideae,Poaceae)are of significant economic and ecological importance,supporting billions of people and contributing to international trade(Wu et al.,2023).They play a crucial role in carbon fixation and support a multitude of other species including the giant panda(Clark et al.,2015).Since the release of the first draft genome of moso bamboo(Phyllostachys edulis)(Peng et al.,2013),there has been a notable increase in the sequencing,assembly,and annotation of diverse bamboo genomes(Guo et al.,2019;Zheng et al.,2022;Ma et al.,2024).An existing resource for bamboo genomics,BambooGDB(Zhao et al.,2014),provides information based on the individual draft reference genome of moso bamboo.What is needed,however,is a resource reinforcing multiple genome assemblies in Bambusoideae to enable researchers to unravel the evolutionary history of chromosomes and genes through cladespecific comparative genomic investigations.Here,we present BambooBase(https://bamboo.genobank.org/),a newly developed web-based database designed to provide a seamless user experience for bamboo omics and systematics.