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

Plant Diversity 2024年第3期46卷 333-343页

作者： Dilmurod Makhmudjanov Sergei Volis Ziyoviddin Yusupov Inom Juramurodov Komiljon Tojibaev Tao Deng Hang Sun CAS Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of BotanyChinese Academy of SciencesKunming 650201YunnanChina Yunnan International Joint Laboratory for Biodiversity of Central Asia Kunming Institute of BotanyChinese Academy of SciencesKunming 650201YunnanChina Institute of Botany Academy Sciences of UzbekistanTashkent 100125Uzbekistan University of Chinese Academy of Sciences Beijing 100864China

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.

关键词： Asphodelaceae Asphodeloideae plastome Central Asia Qinghai-Tibet Plateau

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

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Plant Diversity 2024年第2期46卷 194-205页

作者： Peng-Cheng Fu Qiao-Qiao Guo Di Chang Qing-Bo Gao Shan-Shan Sun School of Life Science Luoyang Normal UniversityLuoyang 471934PR China Key Laboratory of Adaptation and Evolution of Plateau Biota Northwest Institute of Plateau BiologyChinese Academy of SciencesXining 810001PR China

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.

关键词： Gentiana aristata Hybrid zone Qinghai-Tibet Plateau plastome Nuclear SNPs

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

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Plant Diversity 2022年第6期44卷 519-529页

作者： Yan-Ling Xu Hao-Hua Shen Xin-Yu Du Lu Lu School of Pharmaceutical Sciences and Yunnan Key Laboratory of Pharmacology for Natural Products Kunming Medical UniversityKunmingYunnanChina Germplasm Bank of Wild Species Kunming Institute of BotanyChinese Academy of SciencesKunmingYunnanChina

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.

关键词： DNA barcodes Gene duplication plastome Repeat sequences Structural variation

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plastome-wide comparison reveals new SNV resources for the authentication of Dendrobium huoshanense and its corresponding medicinal slice(Huoshan Fengdou)

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Acta Pharmaceutica Sinica B 2018年第3期8卷 466-477页

作者： Zhitao Niu Jiajia Pan Qingyun Xue Shuying Zhu Wei Liu Xiaoyu Ding College of Life Sciences Nanjing Normal University

Dendrobium species and their corresponding medicinal slices have been extensively used as traditional Chinese medicine(TCM) in many Asian countries. However, it is extremely difficult to identify Dendrobium species based on their morphological and chemical features. In this study, the plastomes of D. huoshanense were used as a model system to investigate the hypothesis that plastomic mutational hotspot regions could provide a useful single nucleotide variants(SNVs) resource for authentication studies. We surveyed the plastomes of 17 Dendrobium species, including the newly sequenced plastome of D. huoshanense. A total of 19 SNVs that could be used for the authentication of D. huoshanense were detected. On the basis of this comprehensive comparison, we identified the four most informative hotspot regions in the Dendrobium plastome that encompass ccsA to ndhF, matK to 3′trnG, rpoB to psbD, and trnT to rbcL. Furthermore, to established a simple and accurate method for the authentication of D. huoshanense and its medicinal slices, a total of 127 samples from 20 Dendrobium species including their corresponding medicinal slices(Fengdous) were used in this study. Our results suggest that D. huoshanense and its medicinal slices can be rapidly and unequivocally identified using this method that combines real-time PCR with the amplification refractory mutation system(ARMS).

关键词： Dendrobium huoshanense plastome Slices Single nucleotide variants RT-ARMS Authentication

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plastome characteristics of Cannabaceae

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Plant Diversity 2018年第3期40卷 127-137页

作者： Huanlei Zhang Jianjun Jin Michael J.Moore Tingshuang Yi Dezhu Li Germplasm Bank of Wild Species Kunming Institute of Botany Chinese Academy of Sciences Kunming College of Life Sciences University of Chinese Academy of Sciences Department of Biology Oberlin College

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.

关键词： plastome IR expansion/contraction Repeats SSR Sequence divergence Phylogenomics

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

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Plant Diversity 2021年第3期43卷 198-205页

作者： Bibo Yang Liangda Li Jianquan Liu Lushui Zhang Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education College of Life SciencesSichuan UniversityChengdu610065China

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.

关键词： Woody buckwheat Atraphaxideae plastome Phylogeny Woodiness

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

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Plant Diversity 2018年第6期40卷 265-276页

作者： Changkun Liu Zhenyan Yang Lifang Yang Junbo Yang Yunheng Ji Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of Botany Chinese Academy of Sciences School of Life Science Yunnan University Germplasm Bank of Wild Species Kunming Institute of Botany Chinese Academy of Sciences

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.

关键词： Araliaceae plastome Comparative genomics Panax stipuleanatus Phylogenomics

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

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Plant Diversity 2023年第2期45卷 125-132页

作者： Rivontsoa A.Rakotonasolo Soejatmi Dransfield Thomas Haevermans Helene Ralimanana Maria S.Vorontsova Meng-Yuan Zhou De-Zhu Li Germplasm Bank of Wild Species Kunming Institute of BotanyChinese Academy of SciencesKunmingYunnan650201China Department Flore Parc Botanique et Zoologique de TsimbazazaAntananarivo101Madagascar Kew Madagascar Conservation Center Antananarivo101Madagascar Comparative Plant and Fungal Biology Royal Botanic Gardens KewRichmondSurreyUK Institut de Systématiqueévolution Biodiversité(ISYEB) Muséum National d'Histoire NaturelleCentre National de La Recherche Scientifiqueécole Pratique des HautesétudesUniversitédes AntillesSorbonne Université45 Rue BuffonCP 5075005ParisFrance University of Chinese Academy of Sciences Beijing100049China

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.

关键词： Bamboo Hickeliinae Madagascar Paleotropical Phylogenomics plastome

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

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Plant Diversity 2023年第2期45卷 147-155页

作者： Shi-Yu Lv Xia-Ying Ye Zhong-Hu Li Peng-Fei Ma De-Zhu Li School of Life Science Northwest UniversityXi'anShaanxi710069China Germplasm Bank of Wild Species Kunming Institute of BotanyChinese Academy of SciencesKunmingYunnan650201China Agronomy and Life Science Department Zhaotong UniversityZhaotongYunnan657000China Kunming College of Life Science University of Chinese Academy of SciencesKunmingYunnan650201China

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.

关键词： Fargesia Genome-skimming DNA barcoding plastome Ribosomal DNA

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

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Plant Diversity 2019年第5期41卷 330-339页

作者： Srinivasa R.Chaluvadi Porter Young Kentrez Thompson Bochra Amina Bahri Bhavesh Gajera Subhash Narayanan Robert Krueger Jeffrey L.Bennetzen Department of Genetics University of GeorgiaAthensGAUSA Institute of Plant Breeding Genetics and Genomics(Department of Crop and Soil Sciences)and Department of Plant BiologyUniversity of GeorgiaAthensGA 30602USA Laboratory of Bioaggressors and Integrated Protection in Agriculture The National Agronomic Institute of TunisiaUniversity of Carthage43 Avenue Charles-NicolleTunis 1082Tunisia Anand Agricultural University AnandIndia USDA-ARS National Clonal Germplasm Repository for Citrus and Dates RiversideCAUSA

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.

关键词： Date palm improvement Germplasm dissemination plastome Simple sequence repeats

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