Next-generation genomic shotgun sequencing indicates greater genetic variability in the mitochondria of Hypophthalmichthys molitrix relative to H. nobilis from the Mississippi River, USA and provides tools for research and detection
We characterized variation within the mitochondrial genomes of the invasive silver carp (Hypophthalmichthys molitrix) and bighead carp (H. nobilis) from the Mississippi River drainage by mapping our Next-Generation sequences to their publicly available genomes. Variant detection resulted in 338 sing...
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| Veröffentlicht in: | Conservation genetics resources 2015-03, Vol.7 (1), p.9-11 |
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| creator | Miller, John J Eackles, Michael S Stauffer, Jay R King, Tim L |
| description | We characterized variation within the mitochondrial genomes of the invasive silver carp (Hypophthalmichthys molitrix) and bighead carp (H. nobilis) from the Mississippi River drainage by mapping our Next-Generation sequences to their publicly available genomes. Variant detection resulted in 338 single-nucleotide polymorphisms for H. molitrix and 39 for H. nobilis. The much greater genetic variation in H. molitrix mitochondria relative to H. nobilis may be indicative of a greater North American female effective population size of the former. When variation was quantified by gene, many tRNA loci appear to have little or no variability based on our results whereas protein-coding regions were more frequently polymorphic. These results provide biologists with additional regions of DNA to be used as markers to study the invasion dynamics of these species. |
| doi_str_mv | 10.1007/s12686-014-0296-3 |
| format | Article |
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Variant detection resulted in 338 single-nucleotide polymorphisms for H. molitrix and 39 for H. nobilis. The much greater genetic variation in H. molitrix mitochondria relative to H. nobilis may be indicative of a greater North American female effective population size of the former. When variation was quantified by gene, many tRNA loci appear to have little or no variability based on our results whereas protein-coding regions were more frequently polymorphic. These results provide biologists with additional regions of DNA to be used as markers to study the invasion dynamics of these species.</description><identifier>ISSN: 1877-7252</identifier><identifier>EISSN: 1877-7260</identifier><identifier>DOI: 10.1007/s12686-014-0296-3</identifier><language>eng</language><publisher>Dordrecht: Springer-Verlag</publisher><subject>Animal Genetics and Genomics ; Aristichthys nobilis ; Biodiversity ; biologists ; Biomedical and Life Sciences ; Conservation Biology/Ecology ; drainage ; Ecology ; Evolutionary Biology ; Gene mapping ; genes ; Genetic variability ; genetic variation ; Genomes ; Hypophthalmichthys molitrix ; Invasive species ; Life Sciences ; loci ; Mitochondria ; mitochondrial DNA ; Next-generation sequencing ; Plant Genetics and Genomics ; population size ; Rivers ; sequence analysis ; Single-nucleotide polymorphism ; Technical Note ; transfer RNA ; tRNA</subject><ispartof>Conservation genetics resources, 2015-03, Vol.7 (1), p.9-11</ispartof><rights>Springer Science+Business Media Dordrecht (outside the USA) 2014</rights><rights>Springer Science+Business Media Dordrecht (outside the USA) 2014.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c340t-8253fb7e548cb52d4a4de13f462183a24beb6889a86a195fbd4e9025076d3aba3</citedby><cites>FETCH-LOGICAL-c340t-8253fb7e548cb52d4a4de13f462183a24beb6889a86a195fbd4e9025076d3aba3</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/s12686-014-0296-3$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s12686-014-0296-3$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,780,784,27924,27925,41488,42557,51319</link.rule.ids></links><search><creatorcontrib>Miller, John J</creatorcontrib><creatorcontrib>Eackles, Michael S</creatorcontrib><creatorcontrib>Stauffer, Jay R</creatorcontrib><creatorcontrib>King, Tim L</creatorcontrib><title>Next-generation genomic shotgun sequencing indicates greater genetic variability in the mitochondria of Hypophthalmichthys molitrix relative to H. nobilis from the Mississippi River, USA and provides tools for research and detection</title><title>Conservation genetics resources</title><addtitle>Conservation Genet Resour</addtitle><description>We characterized variation within the mitochondrial genomes of the invasive silver carp (Hypophthalmichthys molitrix) and bighead carp (H. nobilis) from the Mississippi River drainage by mapping our Next-Generation sequences to their publicly available genomes. Variant detection resulted in 338 single-nucleotide polymorphisms for H. molitrix and 39 for H. nobilis. The much greater genetic variation in H. molitrix mitochondria relative to H. nobilis may be indicative of a greater North American female effective population size of the former. When variation was quantified by gene, many tRNA loci appear to have little or no variability based on our results whereas protein-coding regions were more frequently polymorphic. These results provide biologists with additional regions of DNA to be used as markers to study the invasion dynamics of these species.</description><subject>Animal Genetics and Genomics</subject><subject>Aristichthys nobilis</subject><subject>Biodiversity</subject><subject>biologists</subject><subject>Biomedical and Life Sciences</subject><subject>Conservation Biology/Ecology</subject><subject>drainage</subject><subject>Ecology</subject><subject>Evolutionary Biology</subject><subject>Gene mapping</subject><subject>genes</subject><subject>Genetic variability</subject><subject>genetic variation</subject><subject>Genomes</subject><subject>Hypophthalmichthys molitrix</subject><subject>Invasive species</subject><subject>Life Sciences</subject><subject>loci</subject><subject>Mitochondria</subject><subject>mitochondrial DNA</subject><subject>Next-generation sequencing</subject><subject>Plant Genetics and Genomics</subject><subject>population size</subject><subject>Rivers</subject><subject>sequence analysis</subject><subject>Single-nucleotide polymorphism</subject><subject>Technical Note</subject><subject>transfer RNA</subject><subject>tRNA</subject><issn>1877-7252</issn><issn>1877-7260</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</creationdate><recordtype>article</recordtype><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNp9kc1u1TAQhSMEEqX0AVhhiS0p_ouTLKsKuEgFJNq7tpxkkrhK7GD7XvW-cR-jkwbBDsnSWJrvnBn7ZNk7Ri8ZpeWnyLiqVE6ZzCmvVS5eZGesKsu85Iq-_Hsv-OvsTYz3lKpKcH6WPf6Ah5QP4CCYZL0jePWzbUkcfRoOjkT4fQDXWjcQ6zrbmgSRDAGwhhWGhPDRBGsaO9l0QoqkEchsk29H7zrsEN-T3Wnxy5hGM6E71lMks0dBsA8kwITDj0CSJ7tL4vxqFUkf_Pzs9d3GuJ5lseQXcuEj2d9eEeM6sgR_tB2ulLyfUOIDukUwoR2f-x0kaNeHvc1e9WaKcPGnnmf7L5_vrnf5zc-v366vbvJWSJryiheib0ooZNU2Be-kkR0w0UvFWSUMlw00qqpqUynD6qJvOgk15QUtVSdMY8R59mHzxc3w52LS9_4QHI7UXFJVl5IxgRTbqDb4GAP0egl2NuGkGdVroHoLVGOgeg1Urxq-aSKyboDwz_l_ovebqDdemyHYqPe3nLKCUqaYVEo8AXIys3Q</recordid><startdate>20150301</startdate><enddate>20150301</enddate><creator>Miller, John J</creator><creator>Eackles, Michael S</creator><creator>Stauffer, Jay R</creator><creator>King, Tim L</creator><general>Springer-Verlag</general><general>Springer Netherlands</general><general>Springer Nature B.V</general><scope>FBQ</scope><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>20150301</creationdate><title>Next-generation genomic shotgun sequencing indicates greater genetic variability in the mitochondria of Hypophthalmichthys molitrix relative to H. nobilis from the Mississippi River, USA and provides tools for research and detection</title><author>Miller, John J ; Eackles, Michael S ; Stauffer, Jay R ; King, Tim L</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c340t-8253fb7e548cb52d4a4de13f462183a24beb6889a86a195fbd4e9025076d3aba3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>Animal Genetics and Genomics</topic><topic>Aristichthys nobilis</topic><topic>Biodiversity</topic><topic>biologists</topic><topic>Biomedical and Life Sciences</topic><topic>Conservation Biology/Ecology</topic><topic>drainage</topic><topic>Ecology</topic><topic>Evolutionary Biology</topic><topic>Gene mapping</topic><topic>genes</topic><topic>Genetic variability</topic><topic>genetic variation</topic><topic>Genomes</topic><topic>Hypophthalmichthys molitrix</topic><topic>Invasive species</topic><topic>Life Sciences</topic><topic>loci</topic><topic>Mitochondria</topic><topic>mitochondrial DNA</topic><topic>Next-generation sequencing</topic><topic>Plant Genetics and Genomics</topic><topic>population size</topic><topic>Rivers</topic><topic>sequence analysis</topic><topic>Single-nucleotide polymorphism</topic><topic>Technical Note</topic><topic>transfer RNA</topic><topic>tRNA</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Miller, John J</creatorcontrib><creatorcontrib>Eackles, Michael S</creatorcontrib><creatorcontrib>Stauffer, Jay R</creatorcontrib><creatorcontrib>King, Tim L</creatorcontrib><collection>AGRIS</collection><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>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Biological Science Collection</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>Miller, John J</au><au>Eackles, Michael S</au><au>Stauffer, Jay R</au><au>King, Tim L</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Next-generation genomic shotgun sequencing indicates greater genetic variability in the mitochondria of Hypophthalmichthys molitrix relative to H. nobilis from the Mississippi River, USA and provides tools for research and detection</atitle><jtitle>Conservation genetics resources</jtitle><stitle>Conservation Genet Resour</stitle><date>2015-03-01</date><risdate>2015</risdate><volume>7</volume><issue>1</issue><spage>9</spage><epage>11</epage><pages>9-11</pages><issn>1877-7252</issn><eissn>1877-7260</eissn><abstract>We characterized variation within the mitochondrial genomes of the invasive silver carp (Hypophthalmichthys molitrix) and bighead carp (H. nobilis) from the Mississippi River drainage by mapping our Next-Generation sequences to their publicly available genomes. Variant detection resulted in 338 single-nucleotide polymorphisms for H. molitrix and 39 for H. nobilis. The much greater genetic variation in H. molitrix mitochondria relative to H. nobilis may be indicative of a greater North American female effective population size of the former. When variation was quantified by gene, many tRNA loci appear to have little or no variability based on our results whereas protein-coding regions were more frequently polymorphic. These results provide biologists with additional regions of DNA to be used as markers to study the invasion dynamics of these species.</abstract><cop>Dordrecht</cop><pub>Springer-Verlag</pub><doi>10.1007/s12686-014-0296-3</doi><tpages>3</tpages></addata></record> |
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| subjects | Animal Genetics and Genomics Aristichthys nobilis Biodiversity biologists Biomedical and Life Sciences Conservation Biology/Ecology drainage Ecology Evolutionary Biology Gene mapping genes Genetic variability genetic variation Genomes Hypophthalmichthys molitrix Invasive species Life Sciences loci Mitochondria mitochondrial DNA Next-generation sequencing Plant Genetics and Genomics population size Rivers sequence analysis Single-nucleotide polymorphism Technical Note transfer RNA tRNA |
| title | Next-generation genomic shotgun sequencing indicates greater genetic variability in the mitochondria of Hypophthalmichthys molitrix relative to H. nobilis from the Mississippi River, USA and provides tools for research and detection |
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