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
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 econom...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.展开更多
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 m...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/).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
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 t...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.展开更多
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 modif...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.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
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
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the Disciplinary Professional Construction Project of College of Art&College of Landscape Architecture,Fujian Agriculture and Forestry University(YSYL-bdpy-2,YSYL-bdpy-1).
文摘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.
基金supported by the National Natural Science Foundation of China (Grant Nos. 31170300 and 31670330)the Priority Academic Program Development of Jiangsu Higher Education Institutions to Xiaoyu Ding (Grant No. 2015-SWYY-014)
文摘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/).
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supported by the Strategic Priority Research Program of Chinese Academy of Sciences (XDA20050203)the National Key R&D Program of China (2017YFC0505200)+1 种基金the Major Program of the National Natural Science Foundation of China (31590823)the National Natural Science Foundation of China (31570213)
文摘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.
基金supported by the Strategic Priority Research Program of the Chinese Academy of Sciences(grant no.XDB31010000)by the Large-scale Scientific Facilities of the Chinese Academy of Sciences(grant no.2017-LSF-GBOWS-02)+1 种基金by an open research project for“Cross-Cooperative Team”of the Germplasm Bank of Wild Species,Kunming Institute of Botany,Chinese Academy of Sciencesby the CAS Pioneer Hundred Talents Program(to A.Z.).
文摘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.
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.
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.
