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.

Central Asia revealed as a key area in evolution of Eremurus (Asphodelaceae)

Eremurus was described at the beginning of the 19th century.However,due to limited sampling and the small number of gene markers to date,its phylogeny and evolution are largely unknown.In this study,we analyzed plastomes from 27 species belonging to 2 subgenera and 3 sections of Eremurus,which are found in Central Asia(its center of diversity)and China.We also analyzed nuclear DNA ITS of 33 species,encompassing all subgenera and sections of the genus in Central Asia,southwest Asia and China.Our findings revealed that the genus was monophyletic,although both subgenera Eremurus and Henningia were found to be paraphyletic.Both plastome and nrDNA-based phylogenetic trees had three clades that did not reflect the current taxonomy of the genus.Our biogeographical and time-calibrated trees suggest that Eremurus originated in the ancient Tethyan area in the second half of the Eocene.Diversification of Eremurus occurred from the early Oligocene to the late Miocene.Paratethys Sea retreat and several orogenetic events,such as the progressive uplift of the Qinghai-Tibet Plateau and surrounding mountain belts(Altai,Pamir,Tian Shan),caused serious topographic and climate(aridification)changes in Central Asia that may have triggered a split of clades and speciation.In this transformed Central Asia,speciation proceeded rapidly driven mainly by vicariance caused by numerous mountain chains and specialization to a variety of climatic,topographic and soil conditions that exist in this region.

Cryptic diversity and rampant hybridization in annual gentians on the Qinghai-Tibet Plateau revealed by population genomic analysis

Understanding the evolutionary and ecological processes involved in population differentiation and speciation provides critical insights into biodiversity formation. In this study, we employed 29,865 single nucleotide polymorphisms(SNPs) and complete plastomes to examine genomic divergence and hybridization in Gentiana aristata, which is endemic to the Qinghai-Tibet Plateau(QTP) region. Genetic clustering revealed that G. aristata is characterized by geographic genetic structures with five clusters(West, East, Central, South and North). The West cluster has a specific morphological character(i.e., blue corolla) and higher values of FSTcompared to the remaining clusters, likely the result of the geological barrier formed by the Yangtze River. The West cluster diverged from the other clusters in the Early Pliocene;these remaining clusters diverged from one another in the Early Quaternary. Phylogenetic reconstructions based on SNPs and plastid data revealed substantial cyto-nuclear conflicts. Genetic clustering and D-statistics demonstrated rampant hybridization between the Central and North clusters,along the Bayankala Mountains, which form the geological barrier between the Central and North clusters. Species distribution modeling demonstrated the range of G. aristata expanded since the Last Interglacial period. Our findings provide genetic and morphological evidence of cryptic diversity in G. aristata, and identified rampant hybridization between genetic clusters along a geological barrier.These findings suggest that geological barriers and climatic fluctuations have an important role in triggering diversification as well as hybridization, indicating that cryptic diversity and hybridization are essential factors in biodiversity formation within the QTP region.

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.

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.

Morphological and genomic evidence for a new species of Corallorhiza(Orchidaceae:Epidendroideae)from SW China

Corallorhiza sinensis,a new species of mycoheterotrophic orchid from western Sichuan,China,is described and illustrated based on molecular and morphological evidence.It is morphologically similar to Corallorhiza trifida,but can be distinguished by bigger flowers,both sepals and petals with 3 veins,and longer lateral lobes of lip.To distinguish the new Corallorhiza species and explore its phylogenetic position within subtribe Calypsoinae,this study employed sequences of the nuclear ribosomal DNA(nrDNA)and whole plastome assembled from the genome skimming approach.The plastome is 148,124 bp in length,including a pair of inverted repeats(IRs)of 26,165 bp,a large single-copy region(LSC)of 82,207 bp,and a small single-copy region(SSC)of 13,587 bp.Further,phylogenetic analyses were performed using nrDNA sequence and 79 coding sequences(CDSs)from 26 complete plastomes of subtribe Calypsoinae.The phylogenetic tree based on nrDNA sequence suggested that Corallorhiza is a monophyletic group,and strongly support C.sinensis as sister to the rest species of Corallorhiza.The plastid tree showed that 10 Corallorhiza species grouped into two clades and C.sinensis is most closely related to the North American C.striata and C.bentleyi instead of Oreorchis foliosa and O.angustata in the same clade.The plastid tree and nrDNA tree indicate Oreorchis is a paraphyletic.Although the topological conflicts are displayed between plastome and nrDNA phylogenies of C.sinensis,it is still the most closely related to Corallorhiza.Comparative analysis showed that C.sinensis populations are characteristic of the intermediate morphological traits between Corallorhiza and Oreorchis.The finding of this new species from China shed new light on the phylogeny of Oreorchis and Corallorhiza.

Phoenix phylogeny, and analysis of genetic variation in a diverse collection of date palm(Phoenix dactylifera) and related species

Date palm(Phoenix dactylifera),one of the most ancient crops,is grown commercially in>30 countries.Using whole plastome assemblies,phylogenetic analyses revealed that cultivated date palm accessions share the same clade with Phoenix sylvestris,Phoenix pusilla and Phoenix acaulis,which are native to the Indian subcontinent,and Phoenix caespitosa that is native to the Arabian Peninsula and the deserts of Somalia.Analysis of genetic diversity and genetic relationships among date palm accessions from 13 producing countries involved 195 date palm accessions that were genotyped at 19 microsatellite loci.Extensive genetic diversity was observed,with many accessions heterozygous for most markers in this clonally propagated crop.The average number of alleles per locus(42.1),expected heterozygosity(0.8),observed heterozygosity(0.47)and fixation indices(FST=0.42)demonstrated substantial genetic diversity and population structure.Iraqi accessions were found to have the richest allelic diversity,and the most private alleles.The model-based Bayesian method indicated that these accessions could be broadly divided into two structure groups,one group with predominantly African accessions and another predominantly Asian.Some germplasm,especially from Tunisia and Iraq,deviated from this generalization.Many accessions in the STRUCTURE-derived groups were found to be genetic admixtures,with gene flow between Asian and African groups.Indian and Pakistani date palms were found to be most closely related to North African germplasm.

Plastome and phylogenetic relationship of the woody buckwheat Fagopyrum tibeticum in the Qinghai-Tibet Plateau

The phylogenetic position of the monotypic woody Parapteropyrum(Polygonaceae)remains controversial.Parapteropyrum has been thought to be closely related to the woody genera of the tribe Atraphaxideae,although some evidence indicates that it nests within the herbal buckwheat genus Fagopyrum of tribe Polygoneae.In this study,we used plastome data to determine the phylogenetic position of Parapteropyrum(Fagopyrum)tibeticum.Different reference species were used to assemble plastomes of three species currently placed in the tribe Ataphaxideae:Parapteropyrum(Fagopyrum)tibeticum,Atraphaxis bracteata and Calligonum ebinuricum.Once assembled,plastomes were characterized and compared to plastomes of 12 species across the family Polygonaceae.Phylogenetic analyses of Polygonaceae were performed using whole plastome,all plastome genes,and single-copy genes.Plastomes assembled using different reference plastomes did not differ;however,annotations showed small variation.Plastomes of Parapteropyrum(Fagopyrum)tibeticum,A.bracteata and C.ebinuricum have the typical quadripartite structure with lengths between 159,265 bp and 164,270 bp,and a total number of plastome genes of about 130.Plastome microsatellites(SSR)ranged in number from 48 to 77.Maximum Likelihood and Bayesian analyses of three plastome data sets consistently nested Parapteropyrum within the genus Fagopyrum.Furthermore,our analyses indicated that sampled woody genera of the family Polygonaceae are polyphyletic.Our study provides strong evidence that the woody Parapteropyrum tibeticum,which is distantly related to woody genera sampled here,should be taxonomically placed under Fagopyrum as Fagopyrum tibeticum.

Plastid phylogenomic insights into the evolution of subfamily Dialioideae (Leguminosae)

The subfamily Dialioideae(Leguminosae)consists of 17 genera and about 85 species.Previous studies have detected significant plastid genome(plastome)structure variations in legumes,particularly in subfamilies Papilionoideae and Caesalpinioideae.Hence it is important to investigate plastomes from the newly recognized Dialioideae to better understand the plastome variation across the whole family.Here,we used nine plastomes representing nine genera of Dialioideae to explore plastome structural variation and intergeneric relationships in this subfamily.All plastomes of Dialioideae exhibited a typical quadripartite structure,and had relatively conserved structure compared with other legume subfamilies.However,the genome size ranged from 154,124 bp to 165,973 bp and gene numbers ranged from 129 to132,mainly due to the expansion and contraction of the inverted repeat(IR)regions.The IR of Distemonanthus benthamianus has experienced two separate expansions into the large single copy(LSC)region and the small single copy(SSC)region,and one contraction from SSC.Poeppigia procera has experienced two separate IR expansions into LSC,while Dicorynia paraensis has experienced an IR contraction from LSC.Highly divergent regions or genes(ndhC-trnV^(UAC),psbK-trnQ^(UUG),rps19-rps3,rpl33-rps18,accD-psaI,trnG^(UCC)-trnS^(GCU),psbI-trnS^(GCU),5'rps16-trnQ^(UUG)and ycf1)were identified as potential molecular markers for further species delimitation and population genetics analysis in legumes.Phylogenetic analysis based on 77 protein-coding sequences fully resolved the intergeneric relationships among nine genera except a moderately supported sister relationship between Petalostylis labicheoides and Labichea lanceolata.Our study reveals new insights into the structural variations of plastomes in subfamily Dialioideae and advances our understanding of the evolutionary trajectories of legume plastomes.

The complete plastome of Panax stipuleanatus: Comparative and phylogenetic analyses of the genus Panax(Araliaceae)

Panax stipuleanatus(Araliaceae) is an endangered and medicinally important plant endemic to China.However, phylogenetic relationships within the genus Panax have remained unclear. In this study, we sequenced the complete plastome of P. stipuleanatus and included previously reported Panax plastomes to better understand the relationships between species and plastome evolution within the genus Panax.The plastome of P. stipuleanatus is 156,069 base pairs(bp) in length, consisting of a pair of inverted repeats(IRs, each 25,887 bp) that divide the plastome into a large single copy region(LSC, 86,126 bp) and a small single copy region(SSC, 8169 bp). The plastome contains 114 unigenes(80 protein-coding genes,30 tRNA genes, and 4 r RNA genes). Comparative analyses indicated that the plastome gene content and order, as well as the expansion/contraction of the IR regions, are all highly conserved within Panax. No significant positive selection in the plastid protein-coding genes was observed across the eight Panax species, suggesting the Panax plastomes may have undergone a strong purifying selection. Our phylogenomic analyses resulted in a phylogeny with high resolution and supports for Panax. Nine proteincoding genes and 10 non-coding regions presented high sequence divergence, which could be useful for identifying different Panax species.

Plastome characteristics of Cannabaceae

Cannabaceae is an economically important family that includes ten genera and ca. 117 accepted species.To explore the structure and size variation of their plastomes, we sequenced ten plastomes representing all ten genera of Cannabaceae. Each plastome possessed the typical angiosperm quadripartite structure and contained a total of 128 genes. The Inverted Repeat(IR) regions in five plastomes had experienced small expansions(330 e983 bp) into the Large Single-Copy(LSC) region. The plastome of Chaetachme aristata has experienced a 942-bp IR contraction and lost rpl22 and rps19 in its IRs. The substitution rates of rps19 and rpl22 decreased after they shifted from the LSC to IR. A 270-bp inversion was detected in the Parasponia rugosa plastome, which might have been mediated by 18-bp inverted repeats. Repeat sequences, simple sequence repeats, and nucleotide substitution rates varied among these plastomes.Molecular markers with more than 13% variable sites and 5% parsimony-informative sites were identified, which may be useful for further phylogenetic analysis and species identification. Our results show strong support for a sister relationship between Gironniera and Lozanell(BS ? 100). Celtis, CannabisHumulus, Chaetachme-Pteroceltis, and Trema-Parasponia formed a strongly supported clade, and their relationships were well resolved with strong support(BS ? 100). The availability of these ten plastomes provides valuable genetic information for accurately identifying species, clarifying taxonomy and reconstructing the intergeneric phylogeny of Cannabaceae.

Molecular phylogenetic analyses based on the complete plastid genomes and nuclear sequences reveal Daphne(Thymelaeaceae)to be non-monophyletic as current circumscription

The diverse members of the genus Daphne are prized for their fragrant flowers.Despite being promising ornamental plants in many countries,genetic information of Daphne is scarce.In this study,the plastomes of four species and one variety of Daphne were sequenced and analyzed.The plastomes were typical and contained a pair of inverted repeat(IR)regions that separated the large single-copy(LSC)region from the small single-copy(SSC)region.With a length ranging from 132,869 bp(D.genkwa)to 174,773 bp(D.championii),106 to 141 genes were predicted.Comparative plastome analysis of the newly sequenced plastomes with four publicly available Daphne plastomes identified an expansion of the IRs,sequence variations,and mutational hotspots.Phylogenetic analyses indicated that the genus Daphne in its current circumscription is polyphyletic.Daphne genkwa was nested within the genus Wikstroemia,while D.championii was well resolved as sister to Edgeworthia.These findings concurred with results from our study that used nuclear ribosomal internal transcribed spacer sequence data.The conflicts on the molecular placement of D.championii and D.genkwa and the present taxonomic classification in Daphne suggest that a new intergeneric classification system of Daphneae warrants consideration.

Development of genomic resources for the genus Celtis (Cannabaceae) based on genome skimming data

Celtis is a Cannabaceae genus of 60e70 species of trees,or rarely shrubs,commonly known as hackberries.This woody genus consists of very valuable forest plants that provide important wildlife habitat for birds and mammals.Although previous studies have identified its phylogenetic position,interspecific relationships within Celtis remain unclear.In this study,we generated genome skimming data from five Celtis species to analyze phylogenetic relationships within the genus and develop genome resources.The plastomes of Celtis ranged in length from 158,989 bp to 159,082 bp,with a typical angiosperm quadripartite structure,and encoded a total of 132 genes with 20 duplicated in the IRs.Comparative analyses showed that plastome content and structure were relatively conserved.Whole plastomes showed no signs of gene loss,translocations,inversions,or genome rearrangement.Six plastid hotspot regions(trnH-psbA,psbA-trnK,trnG-trnR,psbC-trnS,cemA-petA and rps8-rpl14),4097 polymorphic nuclear SSRs,as well as 62 low or single-copy gene fragments were identified within Celtis.Moreover,the phylogenetic relationships based on the complete plastome sequences strongly endorse the placement of C.biondii as sister to the((((C.koraiensis,C.sinensis),C.tetrandra),C.julianae),C.cerasifera)clade.These findings and the genetic resources developed here will be conducive to further studies on the genus Celtis involving phylogeny,population genetics,and conservation biology.

Plastome sequencing of Myripnois dioica and comparison within Asteraceae

Myripnois is a monotypic shrub genus in the daisy family constricted to northern China.Although wild populations of Myripnois dioica are relatively rare,this plant may potentially be cultured as a fine ornamental.In the present study,we sequenced the complete plastome of M.dioica,generating the first plastome sequences of the subfamily Pertyoideae.The plastome of M.dioica has a typical quadripartite circular structure.A large^20-kb and a small^3-kb inversion were detected in the large single copy(LSC)region and shared by other Asteraceae species.Plastome phylogenomic analyses based on 78 Asteraceae species and three outgroups revealed four groups,corresponding to four Asteraceae subfamilies:Asteroideae,Cichorioideae,Pertyoideae and Carduoideae.Among these four subfamilies,Pertyoideae is sister to Asteroideae+Cichorioideae;Carduoideae is the most basal clade.In addition,we characterized 13 simple sequence repeats(SSRs)that may be useful in future studies on population genetics.

Plastid RNA editing reduction accompanied with genetic variations in Cymbidium,a genus with diverse lifestyle modes

Recent sequencing efforts have broadly uncovered the evolutionary trajectory of plastid genomes(plastomes)of flowering plants in diverse habitats,yet our knowledge of the evolution of plastid posttranscriptional modifications is limited.In this study,we generated 11 complete plastomes and performed ultra-deep transcriptome sequencing to investigate the co-evolution of plastid RNA editing and genetic variation in Cymbidium,a genus with diverse trophic lifestyles.Genome size and gene content is reduced in terrestrial and green mycoheterotrophic orchids relative to their epiphytic relatives.This could be partly due to extensive losses and pseudogenization of ndh genes for the plastid NADH dehydrogenase-like complex,but independent pseudogenization of ndh genes has also occurred in the epiphyte C.mannii,which was reported to use strong crassulacean acid metabolism photosynthesis.RNA editing sites are abundant but variable in number among Cymbidium plastomes.The nearly twofold variation in editing abundance is mainly due to extensive reduction of ancestral editing sites in ndh transcripts of terrestrial,mycoheterotrophic,and C.mannii plastomes.The co-occurrence of editing reduction and pseudogenization in ndh genes suggests functional constraints on editing machinery may be relaxed,leading to nonrandom loss of ancestral edited sites via reduced editing efficiency.This study represents the first systematic examination of RNA editing evolution linked to plastid genome variation in a single genus.We also propose an explanation for how genomic and posttranscriptional variations might be affected by lifestyle-associated ecological adaptation strategies in Cymbidium.

Taxonomic synopsis of Berberis(Berberidaceae)from the northern Hengduan mountains region in China,with descriptions of seven new species

Though Berberis(Berberidaceae)is widely distributed across the Eurasian landmass it is most diverse in the Himalaya-Hengduan Mountain(HHM)region.There are more than 200 species in China where it is one of the most common mountain shrubs.The study on the taxonomy and evolution of Berberis in this region can thus provide an important insight into the origin and diversification of its flora.A prerequisite to this is mapping and describing the various species of Berberis in the region-a task that despite recent progress is by no means complete.It is clear that in China there may be a significant number of species still to be described and that even with published species much about their distribution remains to be discovered.As a contribution to the first of these tasks seven new species from the northern Hengduan Mountain of N.Sichuan and S.Qinghai:Berberis chinduensis,Berberis degexianensis,Berberis jiajinshanensis,Berberis jinwu,Berberis litangensis,Berberis longquensis and Berberis riparia,are described here.Differences in overall morphology and especially in floral structures with each other and with similar species of Berberis in the same region are presented.The report is the result of phylogenetic analyses based on plastome and partial nrDNA sequences of both the seven proposed new species and a significant number of similar species already published.Provisional conclusions as to the insights provides on the history of the genetic divergence are discussed.

Plastome characteristics and species identification of Chinese medicinal wintergreens(Gaultheria,Ericaceae)

Wintergreen oil is a folk medicine widely used in foods,pesticides,cosmetics and drugs.In China,nine out of 47 species within Gaultheria(Ericaceae)are traditionally used as Chinese medicinal wintergreens;however,phylogenetic approaches currently used to discriminating these species remain unsatisfactory.In this study,we sequenced and characterized plastomes from nine Chinese wintergreen species and identified candidate DNA barcoding regions for Gaultheria.Each Gaultheria plastome contained 110 unique genes(76 protein-coding,30 tRNA,and four rRNA genes).Duplication of trnfM,rps14,and rpl23 genes were detected,while all plastomes lacked ycf1 and ycf2 genes.Gaultheria plastomes shared substantially contracted SSC regions that contained only the ndhF gene.Moreover,plastomes of Gaultheria leucocarpa var.yunnanensis contained an inversion in the LSC region and an IR expansion to cover the ndhF gene.Multiple rearrangement events apparently occurred between the Gaultheria plastomes and those from several previously reported families in Ericales.Our phylogenetic reconstruction using 42 plastomes revealed well-supported relationships within all nine Gaultheria species.Additionally,seven mutational hotspot regions were identified as potential DNA barcodes for Chinese medicinal wintergreens.Our study is the first to generate complete plastomes and describe the structural variations of the complicated genus Gaultheria.In addition,our findings provide important resources for identification of Chinese medicinal wintergreens.

Comparative analysis of plastomes in Oxalidaceae:Phylogenetic relationships and potential molecular markers

The wood sorrel family,Oxalidaceae,is mainly composed of annual or perennial herbs,a few shrubs,and trees distributed from temperate to tropical zones.Members of Oxalidaceae are of high medicinal,ornamental,and economic value.Despite the rich diversity and value of Oxalidaceae,few molecular markers or plastomes are available for phylogenetic analysis of the family.Here,we reported four new whole plastomes of Oxalidaceae and compared them with plastomes of three species in the family,as well as the plastome of Rourea microphylla in the closely related family Connaraceae.The eight plastomes ranged in length from 150,673 bp(Biophytum sensitivum)to 156,609 bp(R.microphylla).Genome annotations revealed a total of 129e131 genes,including 83e84 protein-coding genes,eight rRNA genes,37 tRNA genes,and two to three pseudogenes.Comparative analyses showed that the plastomes of these species have minor variations at the gene level.The smaller plastomes of herbs B.sensitivum and three Oxalis species are associated with variations in IR region sizes,intergenic region variation,and gene or intron loss.We identified sequences with high variation that may serve as molecular markers in taxonomic studies of Oxalidaceae.The phylogenetic trees of selected superrosid representatives based on 76 protein-coding genes corroborated the Oxalidaceae position in Oxalidales and supported it as a sister to Connaraceae.Our research also supported the monophyly of the COM(Celastrales,Oxalidales,and Malpighiales)clade.

Accurate authentication of Dendrobium officinale and its closely related species by comparative analysis of complete plastomes

Owing to its great medicinal and ornamental values, Dendrobium officinale is frequently adulterated with other Dendrobium species on the market. Unfortunately, the utilization of the common DNA markers ITS,ITS2, and mat Ktrbc L is unable to distinguish D. officinale from 5 closely related species of it(D. tosaense, D.shixingense, D. flexicaule, D. scoriarum and D. aduncum). Here, we compared 63 Dendrobium plastomes comprising 40 newly sequenced plastomes of the 6 species and 23 previously published plastomes. The plastomes of D. officinale and its closely related species were shown to have conserved genome structure and gene content. Comparative analyses revealed that small single copy region contained higher variation than large single copy and inverted repeat regions, which was mainly attributed to the loss/retention of ndh genes.Furthermore, the intraspecific sequence variability among different Dendrobium species was shown to be diversified, which necessitates a cautious evaluation of genetic markers specific for different Dendrobium species.By evaluating the maximum likelihood trees inferred from different datasets, we found that the complete plastome sequence dataset had the highest discriminatory power for D. officinale and its closely related species,indicating that complete plastome sequences can be used to accurately authenticate Dendrobium species.& 2018 Chinese Pharmaceutical Association and Institute of Materia Medica, Chinese Academy of Medical Sciences. Production and hosting by Elsevier B.V. This is an open access article under the CC BY-NC-ND license(http://creativecommons.org/licenses/by-nc-nd/4.0/).

The large single-copy(LSC) region functions as a highly effective and efficient molecular marker for accurate authentication of medicinal Dendrobium species

Having great medicinal values,Dendrobium species of"Fengdou"(DSFs)are a taxonomically complex group in Dendrobium genus including many closely related and recently diverged species.Traditionally used DNA markers have been proved to be insufficient in authenticating many species of this group.Here,we investigated 101 complete plastomes from 23 DSFs,comprising 72 newly sequenced and 29 documented,which all exhibited well-conserved genomic organization and gene order.Plastomewide comparison showed the co-occurrence of single nucleotide polymorphisms(SNPs)and insertions/deletions(indels),which can be explained by both the repeat-associated and indel-associated mutation hypotheses.Moreover,guanine-cytosine(GC)content was found to be negatively correlated with the three divergence variables(SNPs,indels and repeats),indicating that GC content may reflect the level of the local sequence divergence.Our species authentication analyses revealed that the relaxed filtering strategies of sequence alignment had no negative impact on species identification.By assessing the maximum likelihood(ML)trees inferred from different datasets,we found that the complete plastome and large single-copy(LSC)datasets both successfully identified all 23 DSFs with the maximum bootstrap values.However,owing to the high efficiency of LSC in species identification,we recommend using LSC for accurate authentication of DSFs.