Plastid markers from whole plastome sequencing for gene-flow studies in the endangered endemic bellflowers of St Helena, Wahlenbergia angustifolia and Wahlenbergia linifolia (Campanulaceae)
St Helena is an endemic rich but ecologically devastated island in the South Atlantic Ocean. Many of the endemic plants are extinct or critically endangered. The genus Wahlenbergia is an example. Two species are extinct, one species critically endangered (population
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| Veröffentlicht in: | Conservation genetics resources 2017-03, Vol.9 (1), p.131-137 |
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| creator | Yang, Ji Y. Lambdon, Phil Williams, Vanessa Cronk, Quentin C. |
| description | St Helena is an endemic rich but ecologically devastated island in the South Atlantic Ocean. Many of the endemic plants are extinct or critically endangered. The genus
Wahlenbergia
is an example. Two species are extinct, one species critically endangered (population |
| doi_str_mv | 10.1007/s12686-016-0612-1 |
| format | Article |
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Wahlenbergia
is an example. Two species are extinct, one species critically endangered (population <50:
Wahlenbergia linifolia
) and one species vulnerable (population c. 8800:
Wahlenbergia angustifolia
). Gene flow between these two remaining species has been suspected. To aid parental analysis of these ultra-rare endemics we used whole genome sequencing to generate large plastome contigs from two individuals of
W. angustifolia
. These were then used to develop sufficient plastid markers (indels, snps and microsatellites) to enable discrimination of plastotypes within and between species. Ten polymorphic plastid indels ranging between 7 and 19 bp along with three microsatellites and one SNP were selected using this next generation sequencing approach. Nine
W. angustifolia
and 35
W. linifolia
plants were scored for these markers. Seven species-specific markers were found of which five were indels. We identified eight plastotypes within
W. angustifolia
and one plastotype in
W. linifolia
. Preliminary results indicate that gene flow has occurred between the two species. The results show the ease with which highly variable plastid markers can be found using next generation sequencing. The indel markers are particularly valuable as these can be scored using cheap and safe agarose gels. The markers will help generate breeding system data that is of direct relevance for the conservation of these species.</description><identifier>ISSN: 1877-7252</identifier><identifier>EISSN: 1877-7260</identifier><identifier>DOI: 10.1007/s12686-016-0612-1</identifier><language>eng</language><publisher>Dordrecht: Springer Netherlands</publisher><subject>Animal Genetics and Genomics ; Biodiversity ; Biomedical and Life Sciences ; Conservation Biology/Ecology ; Ecology ; Endangered & extinct species ; Endangered species ; Evolutionary Biology ; Gels ; Gene flow ; Genomes ; Life Sciences ; Methods and Resources Article ; Microsatellites ; Next-generation sequencing ; Plant Genetics and Genomics ; Single-nucleotide polymorphism ; Wahlenbergia ; Whole genome sequencing</subject><ispartof>Conservation genetics resources, 2017-03, Vol.9 (1), p.131-137</ispartof><rights>Springer Science+Business Media Dordrecht 2016</rights><rights>Springer Science+Business Media Dordrecht 2016.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c2311-5a258d4b5e6601986e4c3417af01d0a22203e33008367e3208f5ba641bfdfb253</citedby><cites>FETCH-LOGICAL-c2311-5a258d4b5e6601986e4c3417af01d0a22203e33008367e3208f5ba641bfdfb253</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s12686-016-0612-1$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s12686-016-0612-1$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,776,780,27901,27902,41464,42533,51294</link.rule.ids></links><search><creatorcontrib>Yang, Ji Y.</creatorcontrib><creatorcontrib>Lambdon, Phil</creatorcontrib><creatorcontrib>Williams, Vanessa</creatorcontrib><creatorcontrib>Cronk, Quentin C.</creatorcontrib><title>Plastid markers from whole plastome sequencing for gene-flow studies in the endangered endemic bellflowers of St Helena, Wahlenbergia angustifolia and Wahlenbergia linifolia (Campanulaceae)</title><title>Conservation genetics resources</title><addtitle>Conservation Genet Resour</addtitle><description>St Helena is an endemic rich but ecologically devastated island in the South Atlantic Ocean. Many of the endemic plants are extinct or critically endangered. The genus
Wahlenbergia
is an example. Two species are extinct, one species critically endangered (population <50:
Wahlenbergia linifolia
) and one species vulnerable (population c. 8800:
Wahlenbergia angustifolia
). Gene flow between these two remaining species has been suspected. To aid parental analysis of these ultra-rare endemics we used whole genome sequencing to generate large plastome contigs from two individuals of
W. angustifolia
. These were then used to develop sufficient plastid markers (indels, snps and microsatellites) to enable discrimination of plastotypes within and between species. Ten polymorphic plastid indels ranging between 7 and 19 bp along with three microsatellites and one SNP were selected using this next generation sequencing approach. Nine
W. angustifolia
and 35
W. linifolia
plants were scored for these markers. Seven species-specific markers were found of which five were indels. We identified eight plastotypes within
W. angustifolia
and one plastotype in
W. linifolia
. Preliminary results indicate that gene flow has occurred between the two species. The results show the ease with which highly variable plastid markers can be found using next generation sequencing. The indel markers are particularly valuable as these can be scored using cheap and safe agarose gels. The markers will help generate breeding system data that is of direct relevance for the conservation of these species.</description><subject>Animal Genetics and Genomics</subject><subject>Biodiversity</subject><subject>Biomedical and Life Sciences</subject><subject>Conservation Biology/Ecology</subject><subject>Ecology</subject><subject>Endangered & extinct species</subject><subject>Endangered species</subject><subject>Evolutionary Biology</subject><subject>Gels</subject><subject>Gene flow</subject><subject>Genomes</subject><subject>Life Sciences</subject><subject>Methods and Resources Article</subject><subject>Microsatellites</subject><subject>Next-generation sequencing</subject><subject>Plant Genetics and Genomics</subject><subject>Single-nucleotide polymorphism</subject><subject>Wahlenbergia</subject><subject>Whole genome sequencing</subject><issn>1877-7252</issn><issn>1877-7260</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2017</creationdate><recordtype>article</recordtype><sourceid>BENPR</sourceid><recordid>eNp1UctKxDAULaLg-PgAdwE3ClZvkjatSxnUEQQFFZchbW9mOqbJmLSIH-e_mTqiuHARcsN53HBOkhxQOKUAxVmgTJQiBRqPoCylG8mElkWRFkzA5s-cs-1kJ4QlgCg5Y5Pk496o0LcN6ZR_QR-I9q4jbwtnkKxGyHVIAr4OaOvWzol2nszRYqqNeyOhH5oWA2kt6RdI0DbKztFjM47YtTWp0JiROlo7TR56MkODVp2QZ7WIQ4V-3ioSZUP8hnbm69H8RU1rv6GjqepWyg5G1ajweC_Z0soE3P--d5Onq8vH6Sy9vbu-mV7cpjXjlKa5YnnZZFWOQgA9LwVmNc9ooTTQBhRjDDhyDlByUSBnUOq8UiKjlW50xXK-mxyufVfexShCL5du8DaulCwDcV5AmY0sumbV3oXgUcuVb2Ou75KCHFuS65ZkbEmOLUkaNWytCZE7Zvfr_L_oE3oUmAQ</recordid><startdate>20170301</startdate><enddate>20170301</enddate><creator>Yang, Ji Y.</creator><creator>Lambdon, Phil</creator><creator>Williams, Vanessa</creator><creator>Cronk, Quentin C.</creator><general>Springer Netherlands</general><general>Springer Nature B.V</general><scope>AAYXX</scope><scope>CITATION</scope><scope>8FE</scope><scope>8FH</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>LK8</scope><scope>M7P</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope></search><sort><creationdate>20170301</creationdate><title>Plastid markers from whole plastome sequencing for gene-flow studies in the endangered endemic bellflowers of St Helena, Wahlenbergia angustifolia and Wahlenbergia linifolia (Campanulaceae)</title><author>Yang, Ji Y. ; Lambdon, Phil ; Williams, Vanessa ; Cronk, Quentin C.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c2311-5a258d4b5e6601986e4c3417af01d0a22203e33008367e3208f5ba641bfdfb253</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2017</creationdate><topic>Animal Genetics and Genomics</topic><topic>Biodiversity</topic><topic>Biomedical and Life Sciences</topic><topic>Conservation Biology/Ecology</topic><topic>Ecology</topic><topic>Endangered & extinct species</topic><topic>Endangered species</topic><topic>Evolutionary Biology</topic><topic>Gels</topic><topic>Gene flow</topic><topic>Genomes</topic><topic>Life Sciences</topic><topic>Methods and Resources Article</topic><topic>Microsatellites</topic><topic>Next-generation sequencing</topic><topic>Plant Genetics and Genomics</topic><topic>Single-nucleotide polymorphism</topic><topic>Wahlenbergia</topic><topic>Whole genome sequencing</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Yang, Ji Y.</creatorcontrib><creatorcontrib>Lambdon, Phil</creatorcontrib><creatorcontrib>Williams, Vanessa</creatorcontrib><creatorcontrib>Cronk, Quentin C.</creatorcontrib><collection>CrossRef</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>ProQuest Central UK/Ireland</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>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>Biological Sciences</collection><collection>Biological Science Database</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><jtitle>Conservation genetics resources</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Yang, Ji Y.</au><au>Lambdon, Phil</au><au>Williams, Vanessa</au><au>Cronk, Quentin C.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Plastid markers from whole plastome sequencing for gene-flow studies in the endangered endemic bellflowers of St Helena, Wahlenbergia angustifolia and Wahlenbergia linifolia (Campanulaceae)</atitle><jtitle>Conservation genetics resources</jtitle><stitle>Conservation Genet Resour</stitle><date>2017-03-01</date><risdate>2017</risdate><volume>9</volume><issue>1</issue><spage>131</spage><epage>137</epage><pages>131-137</pages><issn>1877-7252</issn><eissn>1877-7260</eissn><abstract>St Helena is an endemic rich but ecologically devastated island in the South Atlantic Ocean. Many of the endemic plants are extinct or critically endangered. The genus
Wahlenbergia
is an example. Two species are extinct, one species critically endangered (population <50:
Wahlenbergia linifolia
) and one species vulnerable (population c. 8800:
Wahlenbergia angustifolia
). Gene flow between these two remaining species has been suspected. To aid parental analysis of these ultra-rare endemics we used whole genome sequencing to generate large plastome contigs from two individuals of
W. angustifolia
. These were then used to develop sufficient plastid markers (indels, snps and microsatellites) to enable discrimination of plastotypes within and between species. Ten polymorphic plastid indels ranging between 7 and 19 bp along with three microsatellites and one SNP were selected using this next generation sequencing approach. Nine
W. angustifolia
and 35
W. linifolia
plants were scored for these markers. Seven species-specific markers were found of which five were indels. We identified eight plastotypes within
W. angustifolia
and one plastotype in
W. linifolia
. Preliminary results indicate that gene flow has occurred between the two species. The results show the ease with which highly variable plastid markers can be found using next generation sequencing. The indel markers are particularly valuable as these can be scored using cheap and safe agarose gels. The markers will help generate breeding system data that is of direct relevance for the conservation of these species.</abstract><cop>Dordrecht</cop><pub>Springer Netherlands</pub><doi>10.1007/s12686-016-0612-1</doi><tpages>7</tpages></addata></record> |
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| subjects | Animal Genetics and Genomics Biodiversity Biomedical and Life Sciences Conservation Biology/Ecology Ecology Endangered & extinct species Endangered species Evolutionary Biology Gels Gene flow Genomes Life Sciences Methods and Resources Article Microsatellites Next-generation sequencing Plant Genetics and Genomics Single-nucleotide polymorphism Wahlenbergia Whole genome sequencing |
| title | Plastid markers from whole plastome sequencing for gene-flow studies in the endangered endemic bellflowers of St Helena, Wahlenbergia angustifolia and Wahlenbergia linifolia (Campanulaceae) |
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