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.Ho...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.展开更多
Elucidating the origins and mechanisms of polyploidization requires tracing the evolutionary history of polyploid species,particularly those with complex origins.Agropyron cristatum,traditionally regarded as an autopo...Elucidating the origins and mechanisms of polyploidization requires tracing the evolutionary history of polyploid species,particularly those with complex origins.Agropyron cristatum,traditionally regarded as an autopolyploid,exhibits characteristics indicative of a segmental allopolyploid.Here,we used phylogenetic analysis based on a low-copy nuclear gene(i.e.,Pgk1),SLAF-seq,and plastome data from 20 diploid and 120 tetraploid Agropyron individuals to determine whether tetraploid A.cristatum arose from an allopolyploid or autopolyploid event.Phylogenetic analyses based on Pgk1 and SLAF-seq data identified two distinct A.cristatum lineages that corresponded to the two main Agropyron habitats in Central Asia–Europe and East Asia–Qinghai-Tibet Plateau.These findings,taken together with molecular dating and gene flow analyses,suggest that the East Asian tetraploid A.cristatum originated via both autopolyploidy from A.cristatum and hybridization between diploid A.cristatum and A.mongolicum,with each diploid cytotype acting as a maternal donor.Furthermore,the Central Asia–Europe tetraploid A.cristatum originated solely via autopolyploidy of diploid A.cristatum.Our findings also indicate that rapid diversification of Agropyron was likely driven by climate oscillations,geographic isolation,introgressive hybridization,and chloroplast capture.These findings challenge simplistic views of autopolyploids and underscore substantial potential for achieving high levels of genetic and adaptive diversity through recurrent hybridization and reticulate evolution.展开更多
Plastome variation,including single spontaneous nucleotide substitutions and single insertions/deletions,is the major source of leaf variegation in plants.Additionally,one recent study has showed that a simple plastom...Plastome variation,including single spontaneous nucleotide substitutions and single insertions/deletions,is the major source of leaf variegation in plants.Additionally,one recent study has showed that a simple plastome structural variation,which is induced by one pair of small inverted repeats,can also result in leaf variegation.Here we show a complex plastome structural variation caused by intermolecular and intramolecular recombination across three pairs of small inverted repeats accounts for leaf variegation in a widely cultivated shrub Heptapleurum ellipticum(Araliaceae).This plastome structural variation contains two deletions and two duplications,resulting in dramatic expansion of IRs,substantial contraction of LSC and loss of 11 genes that essential for photosynthesis.Plastome heteroplasmy was detected in both green and albino sectors of variegated leaves.Relative to green sectors,albino sectors in the variegated leaves exhibit significantly reduced expression for the 11 genes lost in the mutated plastome as well as 26 other genes,but significantly increased expression for one gene related to translation apparatus.Optical and transmission electron microscopy observations showed that mesophyll cells of albino sectors possess plastids lacking grana lamellae,which likely carry the mutated plastome and contribute to albinism.In both sectors,the first layer of spongy mesophyll cells beneath the lower epidermis contains normal chloroplasts,suggesting periclinal division of the lower epidermis during development.Our study demonstrates that multiple small repeats can collectively mediate intra-and inter-molecular recombination in plastome and offers a new mechanism accounting for leaf variegation in plants.展开更多
Stephanodiscaceae is one of the most diverse family of the freshwater centric diatoms.However,the scarcity of whole plastome data poses a significant challenge to the undertaking of genomic studies on this taxonomic g...Stephanodiscaceae is one of the most diverse family of the freshwater centric diatoms.However,the scarcity of whole plastome data poses a significant challenge to the undertaking of genomic studies on this taxonomic group.We collected data on the plastid genomes from 33 members of the Stephanodiscaceae and its close relatives,including 12 newly-sequenced genomes and 21 deposited in National Center for Biotechnology Information(NCBI).Phylogenetic trees are yielded five major clades based on homologous genes.The features of the plastid genomes,including repeat sequences,codon usage,and selection pressure for each clade,are analyzed.The paper makes a contribution to the field of diatom genomics by describing the structural characteristics of the plastid genomes in the Stephanodiscaceae and its closely related species,complemented by related analyses.It provides crucial data that will serve as indispensable references for future research.展开更多
The sugarcane subtribe Saccharinae(Andropogoneae,Poaceae)was established in 1846,but its delimitation has long been debated.Moreover,the relationships among the genera of Saccharinae remain unclear,and there is no con...The sugarcane subtribe Saccharinae(Andropogoneae,Poaceae)was established in 1846,but its delimitation has long been debated.Moreover,the relationships among the genera of Saccharinae remain unclear,and there is no consensus on whether Pseudosorghum,a small genus in tropical Asia with only two species,should be included.Here,we performed phylogenomic analyses using whole plastomes(69 of them newly sequenced)from 132 individuals,representing 65 species in 19 related genera.We also built trees with nuclear ribosomal DNA sequences.Our results justify the inclusion of Pseudosorghum,likely also the Eulalia Clade III,in Saccharinae.Furthermore,both morphological and molecular analyses support merging the two Pseudosorghum species.The backbone relationships of the Saccharinae phylogeny were highly supported with four polyphyletic clades of Miscanthus and the inclusion of Narenga and Tripidium rufipilum in Saccharum.Pseudosorghum is moderately supported as sister to the Miscanthus Clade I,while the remaining Tripidium species could be excluded from the subtribe.Saccharinae is estimated to have originated~3.73 million years ago in East Asia,followed by intercontinental dispersals.Our study provides a comprehensive phylogenetic framework for future taxonomic revisions of this economically important subtribe.展开更多
Integrative data from plastid and nuclear loci are increasingly utilized to resolve species boundaries and phylogenetic relationships within major angiosperm clades.Debregeasia(Urticaceae),an economically important ge...Integrative data from plastid and nuclear loci are increasingly utilized to resolve species boundaries and phylogenetic relationships within major angiosperm clades.Debregeasia(Urticaceae),an economically important genus,presents challenges in species delimitation due to its overlapping morphological traits and unstable taxonomic assignments.Here,we analyzed 14 morphological traits and generated 12 data matrices from the plastomes and nrDNA using genome skimming from the nine recognized morphospecies to clarify species boundaries and assess barcode performance in Debregeasia.We also used a universal set of 353 nuclear genes to explore reticulate evolution and biogeographic history of Debregeasia.Plastomes of Debregeasia exhibited the typical quadripartite structure with conserved gene content and marginal independent variations in the SC/IR boundary at inter-and intra-specific levels.Three Debregeasia species were non-monophyletic and could not be discerned by any barcode;however,ultra-barcodes identified the remaining six(67%),outperforming standard barcodes(56%).Our phylogenetic analyses placed Debregeasia wallichiana outside the genus and suggested six monophyletic clades in Debregeasia,although the placement between Debregeasia hekouensis and Debregeasia libera varied.There was extensive trait overlap in key morphologically diagnostic characters,with reticulation analysis showing potentially pervasive hybridization,likely influenced by speciation patterns and overlaps between species ranges.We inferred that Debregeasia crown diversification began at ca.12.82 Ma(95%HPD:11.54-14.63 Ma)in the mid-Miocene within Australia,followed by vicariance and later longdistance dispersal,mainly out of southern China.Our findings highlight the utility of genomic data with integrative lines of evidence to refine species delimitation and explore evolutionary relationships in complex plant lineages.展开更多
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 ...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.展开更多
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...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.展开更多
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 trifi...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.展开更多
基金supported by the Large-scale Scientific Facilities of the Chinese Academy of Sciences(Grant No:2017eLSFGBOWSe02)。
文摘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.
基金funded by the following projects:the National Natural Science Foundation of China(Nos.31870360 and 32171603)Xining Science and Technology Major Project(2023-Z-13)+2 种基金Qinghai Provincial Science and Technology Major Project(2023-SF-A5)Youth Innovation Promotion Association(Chinese Academy of Sciences,Grant/Award Number:Y2023116)the Qinghai Provincial central guide local science and technology development funds project(2025ZY002).
文摘Elucidating the origins and mechanisms of polyploidization requires tracing the evolutionary history of polyploid species,particularly those with complex origins.Agropyron cristatum,traditionally regarded as an autopolyploid,exhibits characteristics indicative of a segmental allopolyploid.Here,we used phylogenetic analysis based on a low-copy nuclear gene(i.e.,Pgk1),SLAF-seq,and plastome data from 20 diploid and 120 tetraploid Agropyron individuals to determine whether tetraploid A.cristatum arose from an allopolyploid or autopolyploid event.Phylogenetic analyses based on Pgk1 and SLAF-seq data identified two distinct A.cristatum lineages that corresponded to the two main Agropyron habitats in Central Asia–Europe and East Asia–Qinghai-Tibet Plateau.These findings,taken together with molecular dating and gene flow analyses,suggest that the East Asian tetraploid A.cristatum originated via both autopolyploidy from A.cristatum and hybridization between diploid A.cristatum and A.mongolicum,with each diploid cytotype acting as a maternal donor.Furthermore,the Central Asia–Europe tetraploid A.cristatum originated solely via autopolyploidy of diploid A.cristatum.Our findings also indicate that rapid diversification of Agropyron was likely driven by climate oscillations,geographic isolation,introgressive hybridization,and chloroplast capture.These findings challenge simplistic views of autopolyploids and underscore substantial potential for achieving high levels of genetic and adaptive diversity through recurrent hybridization and reticulate evolution.
基金supported financially by the National Natural Science Foundation of China(31811530297 and 32170217).
文摘Plastome variation,including single spontaneous nucleotide substitutions and single insertions/deletions,is the major source of leaf variegation in plants.Additionally,one recent study has showed that a simple plastome structural variation,which is induced by one pair of small inverted repeats,can also result in leaf variegation.Here we show a complex plastome structural variation caused by intermolecular and intramolecular recombination across three pairs of small inverted repeats accounts for leaf variegation in a widely cultivated shrub Heptapleurum ellipticum(Araliaceae).This plastome structural variation contains two deletions and two duplications,resulting in dramatic expansion of IRs,substantial contraction of LSC and loss of 11 genes that essential for photosynthesis.Plastome heteroplasmy was detected in both green and albino sectors of variegated leaves.Relative to green sectors,albino sectors in the variegated leaves exhibit significantly reduced expression for the 11 genes lost in the mutated plastome as well as 26 other genes,but significantly increased expression for one gene related to translation apparatus.Optical and transmission electron microscopy observations showed that mesophyll cells of albino sectors possess plastids lacking grana lamellae,which likely carry the mutated plastome and contribute to albinism.In both sectors,the first layer of spongy mesophyll cells beneath the lower epidermis contains normal chloroplasts,suggesting periclinal division of the lower epidermis during development.Our study demonstrates that multiple small repeats can collectively mediate intra-and inter-molecular recombination in plastome and offers a new mechanism accounting for leaf variegation in plants.
基金Supported by the National Natural Science Foundation of China(No.31970217)the Scientific and Technological Innovation Programs of Higher Education Institution in Shanxi(No.2019L0070)。
文摘Stephanodiscaceae is one of the most diverse family of the freshwater centric diatoms.However,the scarcity of whole plastome data poses a significant challenge to the undertaking of genomic studies on this taxonomic group.We collected data on the plastid genomes from 33 members of the Stephanodiscaceae and its close relatives,including 12 newly-sequenced genomes and 21 deposited in National Center for Biotechnology Information(NCBI).Phylogenetic trees are yielded five major clades based on homologous genes.The features of the plastid genomes,including repeat sequences,codon usage,and selection pressure for each clade,are analyzed.The paper makes a contribution to the field of diatom genomics by describing the structural characteristics of the plastid genomes in the Stephanodiscaceae and its closely related species,complemented by related analyses.It provides crucial data that will serve as indispensable references for future research.
基金supported by Yunnan Fundamental Research Project(202401BC070001)a research project of the Germplasm Bank of Wild Species,Kunming Institute of Botany,CAS,and the Project of Science and Technology Commission of Shanghai Municipality(23DZ1204601).
文摘The sugarcane subtribe Saccharinae(Andropogoneae,Poaceae)was established in 1846,but its delimitation has long been debated.Moreover,the relationships among the genera of Saccharinae remain unclear,and there is no consensus on whether Pseudosorghum,a small genus in tropical Asia with only two species,should be included.Here,we performed phylogenomic analyses using whole plastomes(69 of them newly sequenced)from 132 individuals,representing 65 species in 19 related genera.We also built trees with nuclear ribosomal DNA sequences.Our results justify the inclusion of Pseudosorghum,likely also the Eulalia Clade III,in Saccharinae.Furthermore,both morphological and molecular analyses support merging the two Pseudosorghum species.The backbone relationships of the Saccharinae phylogeny were highly supported with four polyphyletic clades of Miscanthus and the inclusion of Narenga and Tripidium rufipilum in Saccharum.Pseudosorghum is moderately supported as sister to the Miscanthus Clade I,while the remaining Tripidium species could be excluded from the subtribe.Saccharinae is estimated to have originated~3.73 million years ago in East Asia,followed by intercontinental dispersals.Our study provides a comprehensive phylogenetic framework for future taxonomic revisions of this economically important subtribe.
基金funded by the National Natural Science Foundation of China(42171071,42211540718)Key Research Program of Frontier Sciences,CAS(ZDBS-LY-7001)+3 种基金Yunnan Fundamental Research Projects(202401AT070190,202201BC070001)Top-notch Young Talents Project of Yunnan Provincial“Ten Thousand Talents Program”(YNWR-QNBJ-2018-146,YNWR-QNBJ-2020-293)CAS“Light of West China”Programsupported by the China Scholarship Council(202304910135 and 202304910138)for a one-year study at the University of Toronto.
文摘Integrative data from plastid and nuclear loci are increasingly utilized to resolve species boundaries and phylogenetic relationships within major angiosperm clades.Debregeasia(Urticaceae),an economically important genus,presents challenges in species delimitation due to its overlapping morphological traits and unstable taxonomic assignments.Here,we analyzed 14 morphological traits and generated 12 data matrices from the plastomes and nrDNA using genome skimming from the nine recognized morphospecies to clarify species boundaries and assess barcode performance in Debregeasia.We also used a universal set of 353 nuclear genes to explore reticulate evolution and biogeographic history of Debregeasia.Plastomes of Debregeasia exhibited the typical quadripartite structure with conserved gene content and marginal independent variations in the SC/IR boundary at inter-and intra-specific levels.Three Debregeasia species were non-monophyletic and could not be discerned by any barcode;however,ultra-barcodes identified the remaining six(67%),outperforming standard barcodes(56%).Our phylogenetic analyses placed Debregeasia wallichiana outside the genus and suggested six monophyletic clades in Debregeasia,although the placement between Debregeasia hekouensis and Debregeasia libera varied.There was extensive trait overlap in key morphologically diagnostic characters,with reticulation analysis showing potentially pervasive hybridization,likely influenced by speciation patterns and overlaps between species ranges.We inferred that Debregeasia crown diversification began at ca.12.82 Ma(95%HPD:11.54-14.63 Ma)in the mid-Miocene within Australia,followed by vicariance and later longdistance dispersal,mainly out of southern China.Our findings highlight the utility of genomic data with integrative lines of evidence to refine species delimitation and explore evolutionary relationships in complex plant lineages.
基金funded by endowment funds from the University of Georgia Giles Professorship and the Georgia Research Alliance
文摘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.
基金supported by grants from CAS' Largescale Scientific Facilities (Grant No.2017-LSF-GBOWS-02)the Key R & D Program of Yunnan Province,China (Grant No.20210 3AC100003)Ten Thousand Talent Program of Yunnan Province (Grant No.YNWR-QNBJ-2020-297)。
文摘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.
基金Project of Orchid Biodiversity Survey of China from National Forestry and Grassland AdministrationNational Wild Plant Germplasm Resource Center for all kinds of support+1 种基金supported by the grants from the Second Tibetan Plateau Scientific Expedition and Research(STEP)program(2019QZKK0502)the National Natural Science Foundation of China(31970211)。
文摘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.
