{"title":"基于源自新转录组的EST-SSR标记的Diospyrosmun A.Chev. ex Lecomte(Ebenaceae)种群遗传学分析。","authors":"Xuan Thi Tuyet Bui, Duy Dinh Vu","doi":"10.3897/BDJ.12.e130385","DOIUrl":null,"url":null,"abstract":"<p><p><i>Diospyrosmun</i> A.Chev. ex Lecomte (Ebenaceae), a native evergreen tree in Vietnam, has important economic and ecological values. The absence of effective and reliable molecular markers has hampered the study of <i>D.mun's</i> genetic diversity and population structure, even though it is an endemic and endangered species. Therefore, significant enrichment of genomic resources is urgently needed to uncover and better understand the genetic architecture of <i>D.mun</i>. This study aims to demonstrate an efficient and reliable tool to explore the polymorphism within <i>D.mun</i> germplasm. It provides a valuable platform for the breeding and conservation of this species and other endangered species worldwide. The Illumina HiSeq™ 4000 sequencing technology was applied for the transcriptomic analysis, genetic differentiation and population structure of <i>D.mun</i> in Vietnam. In this study, the transcriptomes of <i>D.mun</i> were analysed using the Illumina HiSeq<sup>TM</sup> 4000 sequencing system and a total of 5,588,615,700 base pairs were generated. <i>De novo</i> assembly indicated that 91,134 unigenes were generated (average length = 645.55 bp, N50 = 957 bp, Q20 = 98.08% and Q30 = 94.51%). A total of 92,798 and 21,134 unigenes had significant similarities amongst Nr and Swiss-Prot, respectively. In the GO database, 19,929 unigenes were annotated and these genes were divided into three major categories and 50 subcategories. In the KOG analysis, 18,499 unigenes were annotated and divided into 25 gene function categories. In the KEGG analysis, 12,017 unigenes were annotated. According to the related pathways involved, they could be classified into 56 subclasses. In this study, we have identified a total of 9,391 EST-SSR markers. Ten microsatellite loci were employed to assess the genetic diversity and structure of 82 adult <i>D.mun</i> trees across three populations in Vietnam. The results indicated moderate levels of genetic diversity with <i>PIC</i> = 0.77, <i>N<sub>A</sub></i> = 3.9, <i>N<sub>E</sub></i> = 2.8, <i>Ho</i> = 0.56 and <i>H<sub>E</sub></i> = 0.58 and the fixation index value was recorded as positive for three populations (NS, NH and CP). Genetic differentiation among populations was low (F<sub>ST</sub> = 0.045), suggesting limited gene flow (Nm = 5.34). This result indicates gene exchange between the populations of ancient <i>D.mun</i> from different geographical areas and regions. The analysis of molecular variance (AMOVA) showed that high genetic variation existed within individuals (91%) compared to amongst populations (4%). Genetic structure analysis, DAPC and the NJ tree indicated that the three populations were divided into three main clusters. With this study, we provide a molecular resoureces for the breeding and conservation of <i>D.mun</i>.</p>","PeriodicalId":55994,"journal":{"name":"Biodiversity Data Journal","volume":null,"pages":null},"PeriodicalIF":1.0000,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11424986/pdf/","citationCount":"0","resultStr":"{\"title\":\"Population genetics analysis of <i>Diospyrosmun</i> A.Chev. ex Lecomte (Ebenaceae) based on EST-SSR markers derived from a novel transcriptome.\",\"authors\":\"Xuan Thi Tuyet Bui, Duy Dinh Vu\",\"doi\":\"10.3897/BDJ.12.e130385\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p><i>Diospyrosmun</i> A.Chev. ex Lecomte (Ebenaceae), a native evergreen tree in Vietnam, has important economic and ecological values. The absence of effective and reliable molecular markers has hampered the study of <i>D.mun's</i> genetic diversity and population structure, even though it is an endemic and endangered species. Therefore, significant enrichment of genomic resources is urgently needed to uncover and better understand the genetic architecture of <i>D.mun</i>. This study aims to demonstrate an efficient and reliable tool to explore the polymorphism within <i>D.mun</i> germplasm. It provides a valuable platform for the breeding and conservation of this species and other endangered species worldwide. The Illumina HiSeq™ 4000 sequencing technology was applied for the transcriptomic analysis, genetic differentiation and population structure of <i>D.mun</i> in Vietnam. In this study, the transcriptomes of <i>D.mun</i> were analysed using the Illumina HiSeq<sup>TM</sup> 4000 sequencing system and a total of 5,588,615,700 base pairs were generated. <i>De novo</i> assembly indicated that 91,134 unigenes were generated (average length = 645.55 bp, N50 = 957 bp, Q20 = 98.08% and Q30 = 94.51%). A total of 92,798 and 21,134 unigenes had significant similarities amongst Nr and Swiss-Prot, respectively. In the GO database, 19,929 unigenes were annotated and these genes were divided into three major categories and 50 subcategories. In the KOG analysis, 18,499 unigenes were annotated and divided into 25 gene function categories. In the KEGG analysis, 12,017 unigenes were annotated. According to the related pathways involved, they could be classified into 56 subclasses. In this study, we have identified a total of 9,391 EST-SSR markers. Ten microsatellite loci were employed to assess the genetic diversity and structure of 82 adult <i>D.mun</i> trees across three populations in Vietnam. The results indicated moderate levels of genetic diversity with <i>PIC</i> = 0.77, <i>N<sub>A</sub></i> = 3.9, <i>N<sub>E</sub></i> = 2.8, <i>Ho</i> = 0.56 and <i>H<sub>E</sub></i> = 0.58 and the fixation index value was recorded as positive for three populations (NS, NH and CP). Genetic differentiation among populations was low (F<sub>ST</sub> = 0.045), suggesting limited gene flow (Nm = 5.34). This result indicates gene exchange between the populations of ancient <i>D.mun</i> from different geographical areas and regions. The analysis of molecular variance (AMOVA) showed that high genetic variation existed within individuals (91%) compared to amongst populations (4%). Genetic structure analysis, DAPC and the NJ tree indicated that the three populations were divided into three main clusters. With this study, we provide a molecular resoureces for the breeding and conservation of <i>D.mun</i>.</p>\",\"PeriodicalId\":55994,\"journal\":{\"name\":\"Biodiversity Data Journal\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":1.0000,\"publicationDate\":\"2024-09-18\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11424986/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Biodiversity Data Journal\",\"FirstCategoryId\":\"93\",\"ListUrlMain\":\"https://doi.org/10.3897/BDJ.12.e130385\",\"RegionNum\":4,\"RegionCategory\":\"环境科学与生态学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2024/1/1 0:00:00\",\"PubModel\":\"eCollection\",\"JCR\":\"Q3\",\"JCRName\":\"BIODIVERSITY CONSERVATION\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Biodiversity Data Journal","FirstCategoryId":"93","ListUrlMain":"https://doi.org/10.3897/BDJ.12.e130385","RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2024/1/1 0:00:00","PubModel":"eCollection","JCR":"Q3","JCRName":"BIODIVERSITY CONSERVATION","Score":null,"Total":0}
Population genetics analysis of Diospyrosmun A.Chev. ex Lecomte (Ebenaceae) based on EST-SSR markers derived from a novel transcriptome.
Diospyrosmun A.Chev. ex Lecomte (Ebenaceae), a native evergreen tree in Vietnam, has important economic and ecological values. The absence of effective and reliable molecular markers has hampered the study of D.mun's genetic diversity and population structure, even though it is an endemic and endangered species. Therefore, significant enrichment of genomic resources is urgently needed to uncover and better understand the genetic architecture of D.mun. This study aims to demonstrate an efficient and reliable tool to explore the polymorphism within D.mun germplasm. It provides a valuable platform for the breeding and conservation of this species and other endangered species worldwide. The Illumina HiSeq™ 4000 sequencing technology was applied for the transcriptomic analysis, genetic differentiation and population structure of D.mun in Vietnam. In this study, the transcriptomes of D.mun were analysed using the Illumina HiSeqTM 4000 sequencing system and a total of 5,588,615,700 base pairs were generated. De novo assembly indicated that 91,134 unigenes were generated (average length = 645.55 bp, N50 = 957 bp, Q20 = 98.08% and Q30 = 94.51%). A total of 92,798 and 21,134 unigenes had significant similarities amongst Nr and Swiss-Prot, respectively. In the GO database, 19,929 unigenes were annotated and these genes were divided into three major categories and 50 subcategories. In the KOG analysis, 18,499 unigenes were annotated and divided into 25 gene function categories. In the KEGG analysis, 12,017 unigenes were annotated. According to the related pathways involved, they could be classified into 56 subclasses. In this study, we have identified a total of 9,391 EST-SSR markers. Ten microsatellite loci were employed to assess the genetic diversity and structure of 82 adult D.mun trees across three populations in Vietnam. The results indicated moderate levels of genetic diversity with PIC = 0.77, NA = 3.9, NE = 2.8, Ho = 0.56 and HE = 0.58 and the fixation index value was recorded as positive for three populations (NS, NH and CP). Genetic differentiation among populations was low (FST = 0.045), suggesting limited gene flow (Nm = 5.34). This result indicates gene exchange between the populations of ancient D.mun from different geographical areas and regions. The analysis of molecular variance (AMOVA) showed that high genetic variation existed within individuals (91%) compared to amongst populations (4%). Genetic structure analysis, DAPC and the NJ tree indicated that the three populations were divided into three main clusters. With this study, we provide a molecular resoureces for the breeding and conservation of D.mun.
Biodiversity Data JournalAgricultural and Biological Sciences-Ecology, Evolution, Behavior and Systematics
CiteScore
2.20
自引率
7.70%
发文量
283
审稿时长
6 weeks
期刊介绍:
Biodiversity Data Journal (BDJ) is a community peer-reviewed, open-access, comprehensive online platform, designed to accelerate publishing, dissemination and sharing of biodiversity-related data of any kind. All structural elements of the articles – text, morphological descriptions, occurrences, data tables, etc. – will be treated and stored as DATA, in accordance with the Data Publishing Policies and Guidelines of Pensoft Publishers.
The journal will publish papers in biodiversity science containing taxonomic, floristic/faunistic, morphological, genomic, phylogenetic, ecological or environmental data on any taxon of any geological age from any part of the world with no lower or upper limit to manuscript size.