Full-length transcriptome sequencing analysis and development of EST-SSR markers for the endangered species Populus wulianensis.
Identifieur interne : 000390 ( Main/Exploration ); précédent : 000389; suivant : 000391Full-length transcriptome sequencing analysis and development of EST-SSR markers for the endangered species Populus wulianensis.
Auteurs : Qichao Wu [République populaire de Chine] ; Fengqi Zang [République populaire de Chine] ; Xiaoman Xie [République populaire de Chine] ; Yan Ma [République populaire de Chine] ; Yongqi Zheng [République populaire de Chine] ; Dekui Zang [République populaire de Chine]Source :
- Scientific reports [ 2045-2322 ] ; 2020.
Abstract
Populus wulianensis is an endangered species endemic to Shandong Province, China. Despite the economic and ornamental value of this species, few genomics and genetic studies have been performed. In this study, we performed a relevant analysis of the full-length transcriptome sequencing data of P. wulianensis and obtained expressed sequence tag (EST)-simple sequence repeat (SSR) markers with polymorphisms that can be used for further genetic research. In total, 8.18 Gb (3,521,665) clean reads with an average GC content of 42.12% were obtained. From the corrected 64,737 high-quality isoforms, 42,323 transcript sequences were obtained after redundancy analysis with CD-HIT. Among these transcript sequences, 41,876 sequences were annotated successfully. A total of 23,539 potential EST-SSRs were identified from 16,057 sequences. Excluding mononucleotides, the most abundant motifs were trinucleotide SSRs (47.80%), followed by di- (46.80%), tetra- (2.98%), hexa- (1.58%) and pentanucleotide SSRs (0.84%). Among the 100 designed EST-SSRs, 18 were polymorphic with high PIC values (0.721 and 0.683) and could be used for analyses of the genetic diversity and population structure of P. wulianensis. These full-length transcriptome sequencing data will facilitate gene discovery and functional genomics research in P. wulianensis, and the novel EST-SSRs developed in our study will promote molecular-assisted breeding, genetic diversity and conservation biology research in this species.
DOI: 10.1038/s41598-020-73289-5
PubMed: 33004908
PubMed Central: PMC7530656
Affiliations:
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Ma</name><affiliation wicri:level="1"><nlm:affiliation>College of Forestry, Key Laboratory of State Forestry Administration for Silviculture of the Lower Yellow River, Shandong Agricultural University, Tai'an, 271018, People's Republic of China. myiris@sina.com.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Forestry, Key Laboratory of State Forestry Administration for Silviculture of the Lower Yellow River, Shandong Agricultural University, Tai'an, 271018</wicri:regionArea><wicri:noRegion>271018</wicri:noRegion></affiliation></author><author><name sortKey="Zheng, Yongqi" sort="Zheng, Yongqi" uniqKey="Zheng Y" first="Yongqi" last="Zheng">Yongqi Zheng</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, People's Republic of China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Forestry, Chinese 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xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Forestry, Key Laboratory of State Forestry Administration for Silviculture of the Lower Yellow River, Shandong Agricultural University, Tai'an, 271018</wicri:regionArea><wicri:noRegion>271018</wicri:noRegion></affiliation></author><author><name sortKey="Zang, Fengqi" sort="Zang, Fengqi" uniqKey="Zang F" first="Fengqi" last="Zang">Fengqi Zang</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, People's Republic of China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091</wicri:regionArea><wicri:noRegion>100091</wicri:noRegion></affiliation></author><author><name sortKey="Xie, Xiaoman" sort="Xie, Xiaoman" uniqKey="Xie X" first="Xiaoman" last="Xie">Xiaoman Xie</name><affiliation wicri:level="1"><nlm:affiliation>Center for Forest Genetic Resources of Shandong Province, Jinan, 250014, People's Republic of China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Center for Forest Genetic Resources of Shandong Province, Jinan, 250014</wicri:regionArea><wicri:noRegion>250014</wicri:noRegion></affiliation></author><author><name sortKey="Ma, Yan" sort="Ma, Yan" uniqKey="Ma Y" first="Yan" last="Ma">Yan Ma</name><affiliation wicri:level="1"><nlm:affiliation>College of Forestry, Key Laboratory of State Forestry Administration for Silviculture of the Lower Yellow River, Shandong Agricultural University, Tai'an, 271018, People's Republic of China. myiris@sina.com.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Forestry, Key Laboratory of State Forestry Administration for Silviculture of the Lower Yellow River, Shandong Agricultural University, Tai'an, 271018</wicri:regionArea><wicri:noRegion>271018</wicri:noRegion></affiliation></author><author><name sortKey="Zheng, Yongqi" sort="Zheng, Yongqi" uniqKey="Zheng Y" first="Yongqi" last="Zheng">Yongqi Zheng</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, People's Republic of China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091</wicri:regionArea><wicri:noRegion>100091</wicri:noRegion></affiliation></author><author><name sortKey="Zang, Dekui" sort="Zang, Dekui" uniqKey="Zang D" first="Dekui" last="Zang">Dekui Zang</name><affiliation wicri:level="1"><nlm:affiliation>College of Forestry, Key Laboratory of State Forestry Administration for Silviculture of the Lower Yellow River, Shandong Agricultural University, Tai'an, 271018, People's Republic of China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Forestry, Key Laboratory of State Forestry Administration for Silviculture of the Lower Yellow River, Shandong Agricultural University, Tai'an, 271018</wicri:regionArea><wicri:noRegion>271018</wicri:noRegion></affiliation></author></analytic><series><title level="j">Scientific reports</title><idno type="eISSN">2045-2322</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Populus wulianensis is an endangered species endemic to Shandong Province, China. Despite the economic and ornamental value of this species, few genomics and genetic studies have been performed. In this study, we performed a relevant analysis of the full-length transcriptome sequencing data of P. wulianensis and obtained expressed sequence tag (EST)-simple sequence repeat (SSR) markers with polymorphisms that can be used for further genetic research. In total, 8.18 Gb (3,521,665) clean reads with an average GC content of 42.12% were obtained. From the corrected 64,737 high-quality isoforms, 42,323 transcript sequences were obtained after redundancy analysis with CD-HIT. Among these transcript sequences, 41,876 sequences were annotated successfully. A total of 23,539 potential EST-SSRs were identified from 16,057 sequences. Excluding mononucleotides, the most abundant motifs were trinucleotide SSRs (47.80%), followed by di- (46.80%), tetra- (2.98%), hexa- (1.58%) and pentanucleotide SSRs (0.84%). Among the 100 designed EST-SSRs, 18 were polymorphic with high PIC values (0.721 and 0.683) and could be used for analyses of the genetic diversity and population structure of P. wulianensis. These full-length transcriptome sequencing data will facilitate gene discovery and functional genomics research in P. wulianensis, and the novel EST-SSRs developed in our study will promote molecular-assisted breeding, genetic diversity and conservation biology research in this species.</div></front></TEI><pubmed><MedlineCitation Status="In-Process" Owner="NLM"><PMID Version="1">33004908</PMID><DateRevised><Year>2020</Year><Month>11</Month><Day>03</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">2045-2322</ISSN><JournalIssue CitedMedium="Internet"><Volume>10</Volume><Issue>1</Issue><PubDate><Year>2020</Year><Month>10</Month><Day>01</Day></PubDate></JournalIssue><Title>Scientific reports</Title><ISOAbbreviation>Sci Rep</ISOAbbreviation></Journal><ArticleTitle>Full-length transcriptome sequencing analysis and development of EST-SSR markers for the endangered species Populus wulianensis.</ArticleTitle><Pagination><MedlinePgn>16249</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1038/s41598-020-73289-5</ELocationID><Abstract><AbstractText>Populus wulianensis is an endangered species endemic to Shandong Province, China. Despite the economic and ornamental value of this species, few genomics and genetic studies have been performed. In this study, we performed a relevant analysis of the full-length transcriptome sequencing data of P. wulianensis and obtained expressed sequence tag (EST)-simple sequence repeat (SSR) markers with polymorphisms that can be used for further genetic research. In total, 8.18 Gb (3,521,665) clean reads with an average GC content of 42.12% were obtained. From the corrected 64,737 high-quality isoforms, 42,323 transcript sequences were obtained after redundancy analysis with CD-HIT. Among these transcript sequences, 41,876 sequences were annotated successfully. A total of 23,539 potential EST-SSRs were identified from 16,057 sequences. Excluding mononucleotides, the most abundant motifs were trinucleotide SSRs (47.80%), followed by di- (46.80%), tetra- (2.98%), hexa- (1.58%) and pentanucleotide SSRs (0.84%). Among the 100 designed EST-SSRs, 18 were polymorphic with high PIC values (0.721 and 0.683) and could be used for analyses of the genetic diversity and population structure of P. wulianensis. These full-length transcriptome sequencing data will facilitate gene discovery and functional genomics research in P. wulianensis, and the novel EST-SSRs developed in our study will promote molecular-assisted breeding, genetic diversity and conservation biology research in this species.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Wu</LastName><ForeName>Qichao</ForeName><Initials>Q</Initials><AffiliationInfo><Affiliation>College of Forestry, Key Laboratory of State Forestry Administration for Silviculture of the Lower Yellow River, Shandong Agricultural University, Tai'an, 271018, People's Republic of China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zang</LastName><ForeName>Fengqi</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, People's Republic of China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Xie</LastName><ForeName>Xiaoman</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>Center for Forest Genetic Resources of Shandong Province, Jinan, 250014, People's Republic of China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ma</LastName><ForeName>Yan</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>College of Forestry, Key Laboratory of State Forestry Administration for Silviculture of the Lower Yellow River, Shandong Agricultural University, Tai'an, 271018, People's Republic of China. myiris@sina.com.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zheng</LastName><ForeName>Yongqi</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, People's Republic of China.</Affiliation></AffiliationInfo></Author><Author 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sortKey="Zang, Fengqi" sort="Zang, Fengqi" uniqKey="Zang F" first="Fengqi" last="Zang">Fengqi Zang</name><name sortKey="Zheng, Yongqi" sort="Zheng, Yongqi" uniqKey="Zheng Y" first="Yongqi" last="Zheng">Yongqi Zheng</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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