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EST-SSR marker development based on transcriptome sequencing and genetic analyses of Phoebe bournei (Lauraceae)
High-throughput sequencing of the Phoebe bournei transcriptome was performed, and novel SSR markers were identified. A total of 73,518 nonredundant unigenes were assembled and annotated by sequence similarity searching in diverse public databases. A total of 40,853 SSRs were identified from 73,518 u...
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| Published in: | Molecular biology reports 2021-03, Vol.48 (3), p.2201-2208 |
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| creator | Zhou, Qi Zhou, Peng-Yan Zou, Wen-Tao Li, Yin-Gang |
| description | High-throughput sequencing of the
Phoebe bournei
transcriptome was performed, and novel SSR markers were identified. A total of 73,518 nonredundant unigenes were assembled and annotated by sequence similarity searching in diverse public databases. A total of 40,853 SSRs were identified from 73,518 unigenes. Twenty-three pairs of polymorphic EST-SSR markers were selected from 98 markers and used for genetic analyses in 75 individuals from three
P. bournei
populations. The 23 pairs of markers could detect abundant genetic information from the samples (PIC = 0.769), and cross-species amplification was successfully performed in other related species. Three populations had high level of genetic diversity (He = 0.658 in average), of which the population YS from Jiangxi province had the most abundant genetic diversity (He = 0.722). The results of genetic structure analyses showed that the population YS from Jiangxi province had obvious genetic differences from the other two populations, and the genetic information of the population SX from Fujian province was related to that of the population LC from Guangdong province and the population YS. The transcriptomic resources and EST-SSR markers are valuable tools not only for the ecological conservation of
P. bournei
but also for phylogenetic studies. |
| doi_str_mv | 10.1007/s11033-021-06228-w |
| format | article |
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Phoebe bournei
transcriptome was performed, and novel SSR markers were identified. A total of 73,518 nonredundant unigenes were assembled and annotated by sequence similarity searching in diverse public databases. A total of 40,853 SSRs were identified from 73,518 unigenes. Twenty-three pairs of polymorphic EST-SSR markers were selected from 98 markers and used for genetic analyses in 75 individuals from three
P. bournei
populations. The 23 pairs of markers could detect abundant genetic information from the samples (PIC = 0.769), and cross-species amplification was successfully performed in other related species. Three populations had high level of genetic diversity (He = 0.658 in average), of which the population YS from Jiangxi province had the most abundant genetic diversity (He = 0.722). The results of genetic structure analyses showed that the population YS from Jiangxi province had obvious genetic differences from the other two populations, and the genetic information of the population SX from Fujian province was related to that of the population LC from Guangdong province and the population YS. The transcriptomic resources and EST-SSR markers are valuable tools not only for the ecological conservation of
P. bournei
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Phoebe bournei
transcriptome was performed, and novel SSR markers were identified. A total of 73,518 nonredundant unigenes were assembled and annotated by sequence similarity searching in diverse public databases. A total of 40,853 SSRs were identified from 73,518 unigenes. Twenty-three pairs of polymorphic EST-SSR markers were selected from 98 markers and used for genetic analyses in 75 individuals from three
P. bournei
populations. The 23 pairs of markers could detect abundant genetic information from the samples (PIC = 0.769), and cross-species amplification was successfully performed in other related species. Three populations had high level of genetic diversity (He = 0.658 in average), of which the population YS from Jiangxi province had the most abundant genetic diversity (He = 0.722). The results of genetic structure analyses showed that the population YS from Jiangxi province had obvious genetic differences from the other two populations, and the genetic information of the population SX from Fujian province was related to that of the population LC from Guangdong province and the population YS. The transcriptomic resources and EST-SSR markers are valuable tools not only for the ecological conservation of
P. bournei
but also for phylogenetic studies.</description><subject>Animal Anatomy</subject><subject>Animal Biochemistry</subject><subject>Biomedical and Life Sciences</subject><subject>Expressed sequence tags</subject><subject>Expressed Sequence Tags - metabolism</subject><subject>Genetic analysis</subject><subject>Genetic diversity</subject><subject>Genetic Markers</subject><subject>Genetic structure</subject><subject>Histology</subject><subject>Lauraceae - genetics</subject><subject>Life Sciences</subject><subject>Microsatellite Repeats - genetics</subject><subject>Morphology</subject><subject>Next-generation sequencing</subject><subject>Original Article</subject><subject>Phoebe bournei</subject><subject>Phylogeny</subject><subject>Polymorphism, Genetic</subject><subject>Population</subject><subject>Population genetics</subject><subject>RNA, Messenger - genetics</subject><subject>RNA, Messenger - metabolism</subject><subject>Sequence Analysis, RNA</subject><subject>Transcriptome - genetics</subject><subject>Transcriptomes</subject><issn>0301-4851</issn><issn>1573-4978</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><recordid>eNp9kctuFDEQRa0IRCYDP5AFssQmWRj86vZ4iaK8pJFATFhbflQPHbrtwe5OlL_HYUKQsmBVJdWpW1d1ETpm9COjVH0qjFEhCOWM0JbzFbk_QAvWKEGkVqtXaEEFZUSuGnaIjkq5pZRKppo36FCIlmtO2QKl880N2Wy-4dHmn5BxgDsY0m6EOGFnCwScIp6yjcXnfjelEXCBXzNE38cttjHgLUSYel97OzwUKDh1-OuPBA6wS3OO0OOTtZ2z9WDh9C163dmhwLunukTfL85vzq7I-svl9dnnNfFCNRNptQangmBhpaXTUlPtAm-DcsK5VkLX6saC1wpUI1UAJYTnHkLjg-00t2KJTva6u5yq3TKZsS8ehsFGSHMxXGohpW5rWaIPL9DbR9_VneGNUkoqzVil-J7yOZWSoTO73NenPRhGzWMcZh-HqXGYP3GY-7r0_kl6diOE55W__6-A2AOljuIW8r_b_5H9DSqDlrU</recordid><startdate>20210301</startdate><enddate>20210301</enddate><creator>Zhou, Qi</creator><creator>Zhou, Peng-Yan</creator><creator>Zou, Wen-Tao</creator><creator>Li, Yin-Gang</creator><general>Springer Netherlands</general><general>Springer Nature B.V</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7TK</scope><scope>7TM</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>88I</scope><scope>8AO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M2P</scope><scope>M7P</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>Q9U</scope><scope>RC3</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0002-3680-281X</orcidid></search><sort><creationdate>20210301</creationdate><title>EST-SSR marker development based on transcriptome sequencing and genetic analyses of Phoebe bournei (Lauraceae)</title><author>Zhou, Qi ; Zhou, Peng-Yan ; Zou, Wen-Tao ; Li, Yin-Gang</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c375t-699eb7d31d894b94909bd26d7b3bb64ef695aec97e7547de733c2ced5cdaf92a3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Animal Anatomy</topic><topic>Animal Biochemistry</topic><topic>Biomedical and Life Sciences</topic><topic>Expressed sequence tags</topic><topic>Expressed Sequence Tags - metabolism</topic><topic>Genetic analysis</topic><topic>Genetic diversity</topic><topic>Genetic Markers</topic><topic>Genetic structure</topic><topic>Histology</topic><topic>Lauraceae - genetics</topic><topic>Life Sciences</topic><topic>Microsatellite Repeats - genetics</topic><topic>Morphology</topic><topic>Next-generation sequencing</topic><topic>Original Article</topic><topic>Phoebe bournei</topic><topic>Phylogeny</topic><topic>Polymorphism, Genetic</topic><topic>Population</topic><topic>Population genetics</topic><topic>RNA, Messenger - genetics</topic><topic>RNA, Messenger - metabolism</topic><topic>Sequence Analysis, RNA</topic><topic>Transcriptome - genetics</topic><topic>Transcriptomes</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Zhou, Qi</creatorcontrib><creatorcontrib>Zhou, Peng-Yan</creatorcontrib><creatorcontrib>Zou, Wen-Tao</creatorcontrib><creatorcontrib>Li, Yin-Gang</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Science Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni)</collection><collection>ProQuest Central</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>ProQuest Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Biological Sciences</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>ProQuest Science Journals</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>ProQuest Central Basic</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Molecular biology reports</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Zhou, Qi</au><au>Zhou, Peng-Yan</au><au>Zou, Wen-Tao</au><au>Li, Yin-Gang</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>EST-SSR marker development based on transcriptome sequencing and genetic analyses of Phoebe bournei (Lauraceae)</atitle><jtitle>Molecular biology reports</jtitle><stitle>Mol Biol Rep</stitle><addtitle>Mol Biol Rep</addtitle><date>2021-03-01</date><risdate>2021</risdate><volume>48</volume><issue>3</issue><spage>2201</spage><epage>2208</epage><pages>2201-2208</pages><issn>0301-4851</issn><eissn>1573-4978</eissn><abstract>High-throughput sequencing of the
Phoebe bournei
transcriptome was performed, and novel SSR markers were identified. A total of 73,518 nonredundant unigenes were assembled and annotated by sequence similarity searching in diverse public databases. A total of 40,853 SSRs were identified from 73,518 unigenes. Twenty-three pairs of polymorphic EST-SSR markers were selected from 98 markers and used for genetic analyses in 75 individuals from three
P. bournei
populations. The 23 pairs of markers could detect abundant genetic information from the samples (PIC = 0.769), and cross-species amplification was successfully performed in other related species. Three populations had high level of genetic diversity (He = 0.658 in average), of which the population YS from Jiangxi province had the most abundant genetic diversity (He = 0.722). The results of genetic structure analyses showed that the population YS from Jiangxi province had obvious genetic differences from the other two populations, and the genetic information of the population SX from Fujian province was related to that of the population LC from Guangdong province and the population YS. The transcriptomic resources and EST-SSR markers are valuable tools not only for the ecological conservation of
P. bournei
but also for phylogenetic studies.</abstract><cop>Dordrecht</cop><pub>Springer Netherlands</pub><pmid>33629201</pmid><doi>10.1007/s11033-021-06228-w</doi><tpages>8</tpages><orcidid>https://orcid.org/0000-0002-3680-281X</orcidid></addata></record> |
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| subjects | Animal Anatomy Animal Biochemistry Biomedical and Life Sciences Expressed sequence tags Expressed Sequence Tags - metabolism Genetic analysis Genetic diversity Genetic Markers Genetic structure Histology Lauraceae - genetics Life Sciences Microsatellite Repeats - genetics Morphology Next-generation sequencing Original Article Phoebe bournei Phylogeny Polymorphism, Genetic Population Population genetics RNA, Messenger - genetics RNA, Messenger - metabolism Sequence Analysis, RNA Transcriptome - genetics Transcriptomes |
| title | EST-SSR marker development based on transcriptome sequencing and genetic analyses of Phoebe bournei (Lauraceae) |
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