Development and characterization of thirty two microsatellite markers for the anchovy, Engraulis ringens Jenyns, 1842 (Clupeiformes, Engraulidae) via 454 pyrosequencing
The anchovy, Engraulis ringens, is an economically valuable fish, and the most heavily exploited resource in the Humboldt Current System. To analyze its genetic structure and diversity, microsatellite markers were developed using 454 pyrosequencing. A total of 27,352 reads containing di-, tri-, tetr...
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| Veröffentlicht in: | Latin american journal of aquatic research 2018-05, Vol.46 (2), p.452-456 |
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| description | The anchovy, Engraulis ringens, is an economically valuable fish, and the most heavily exploited resource in the Humboldt Current System. To analyze its genetic structure and diversity, microsatellite markers were developed using 454 pyrosequencing. A total of 27,352 reads containing di-, tri-, tetra-, penta-, and hexanucleotide microsatellite repeat units were identified from 136,537 reads. Among 80 loci containing more than six repeat motifs, 32 primer sets (40%) produced reproducible PCR products, and all of these loci were polymorphic. Some loci showed deviations from HWE and possible null allele's presence, results of an excess of homozygotes. In an analysis of 45 individuals from one E. ringens population, the number of alleles per locus ranged from 2 to 33, observed heterozygosity ranged from 0.171 to 0.976, and the probability of identity values ranged from 0.006 to 0.513. These microsatellites will be useful for numerous ecological studies focused on this important pelagic fish; including the examination of population genetic structure, estimating effective population size and providing information for fisheries management. |
| doi_str_mv | 10.3856/vol46-issue2-fulltext-19 |
| format | Article |
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To analyze its genetic structure and diversity, microsatellite markers were developed using 454 pyrosequencing. A total of 27,352 reads containing di-, tri-, tetra-, penta-, and hexanucleotide microsatellite repeat units were identified from 136,537 reads. Among 80 loci containing more than six repeat motifs, 32 primer sets (40%) produced reproducible PCR products, and all of these loci were polymorphic. Some loci showed deviations from HWE and possible null allele's presence, results of an excess of homozygotes. In an analysis of 45 individuals from one E. ringens population, the number of alleles per locus ranged from 2 to 33, observed heterozygosity ranged from 0.171 to 0.976, and the probability of identity values ranged from 0.006 to 0.513. These microsatellites will be useful for numerous ecological studies focused on this important pelagic fish; including the examination of population genetic structure, estimating effective population size and providing information for fisheries management.</description><identifier>ISSN: 0718-560X</identifier><identifier>EISSN: 0718-560X</identifier><identifier>DOI: 10.3856/vol46-issue2-fulltext-19</identifier><language>eng</language><publisher>Valparaiso: Pontificia Universidad Catolica de Valparaiso, Escuela de Ciencias del Mar</publisher><subject>Alleles ; Clupeiformes ; Clupeoid fisheries ; DNA ; Ecological monitoring ; Ecological studies ; Engraulidae ; Engraulis ringens ; Fish ; FISHERIES ; Fisheries management ; Fishery management ; Genetic diversity ; Genetic markers ; Genetic structure ; Heterozygosity ; Homozygotes ; Information management ; Loci ; MARINE & FRESHWATER BIOLOGY ; Markers ; Microsatellites ; Nucleotide sequence ; OCEANOGRAPHY ; PCR ; Pelagic fish ; Pelagic fisheries ; Population genetics ; Population number ; Probability theory ; Trachurus murphyi</subject><ispartof>Latin american journal of aquatic research, 2018-05, Vol.46 (2), p.452-456</ispartof><rights>COPYRIGHT 2018 Pontificia Universidad Catolica de Valparaiso, Escuela de Ciencias del Mar</rights><rights>Copyright Pontificia Universidad Catolica de Valparaiso May 2018</rights><rights>This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c430t-36a1a5030fbe3342682c3192b9f99578ce316acf802d6db97a39e363f1a772493</citedby></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>230,314,777,781,882,27905,27906</link.rule.ids></links><search><creatorcontrib>Ferrada-Fuentes, Sandra</creatorcontrib><creatorcontrib>Galleguillos, Ricardo</creatorcontrib><creatorcontrib>Canales-Aguirre, Cristian B</creatorcontrib><creatorcontrib>Herrera-Yanez, Victoria</creatorcontrib><title>Development and characterization of thirty two microsatellite markers for the anchovy, Engraulis ringens Jenyns, 1842 (Clupeiformes, Engraulidae) via 454 pyrosequencing</title><title>Latin american journal of aquatic research</title><addtitle>Lat. Am. J. Aquat. Res</addtitle><description>The anchovy, Engraulis ringens, is an economically valuable fish, and the most heavily exploited resource in the Humboldt Current System. To analyze its genetic structure and diversity, microsatellite markers were developed using 454 pyrosequencing. A total of 27,352 reads containing di-, tri-, tetra-, penta-, and hexanucleotide microsatellite repeat units were identified from 136,537 reads. Among 80 loci containing more than six repeat motifs, 32 primer sets (40%) produced reproducible PCR products, and all of these loci were polymorphic. Some loci showed deviations from HWE and possible null allele's presence, results of an excess of homozygotes. In an analysis of 45 individuals from one E. ringens population, the number of alleles per locus ranged from 2 to 33, observed heterozygosity ranged from 0.171 to 0.976, and the probability of identity values ranged from 0.006 to 0.513. These microsatellites will be useful for numerous ecological studies focused on this important pelagic fish; including the examination of population genetic structure, estimating effective population size and providing information for fisheries management.</description><subject>Alleles</subject><subject>Clupeiformes</subject><subject>Clupeoid fisheries</subject><subject>DNA</subject><subject>Ecological monitoring</subject><subject>Ecological studies</subject><subject>Engraulidae</subject><subject>Engraulis ringens</subject><subject>Fish</subject><subject>FISHERIES</subject><subject>Fisheries management</subject><subject>Fishery management</subject><subject>Genetic diversity</subject><subject>Genetic markers</subject><subject>Genetic structure</subject><subject>Heterozygosity</subject><subject>Homozygotes</subject><subject>Information management</subject><subject>Loci</subject><subject>MARINE & FRESHWATER BIOLOGY</subject><subject>Markers</subject><subject>Microsatellites</subject><subject>Nucleotide sequence</subject><subject>OCEANOGRAPHY</subject><subject>PCR</subject><subject>Pelagic fish</subject><subject>Pelagic fisheries</subject><subject>Population genetics</subject><subject>Population number</subject><subject>Probability theory</subject><subject>Trachurus murphyi</subject><issn>0718-560X</issn><issn>0718-560X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2018</creationdate><recordtype>article</recordtype><sourceid>N95</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNpVUtuKFDEUbETBZd1_CPiiML3m0rc8LuN6Y8EHFXwLmfRJT9bupM1Jj45f5GeacZTZSSAJoapOUqeKgjB6Lbq6ebULY9WUDnEBXtplHBP8TCWTj4oL2rKurBv69fGD89PiCvGe5lEL1vD6ovj9GnYwhnkCn4j2PTFbHbVJEN0vnVzwJFiSti6mPUk_ApmciQF1gnF0Ccik4zeISGyIGQVZwWzDbr8it36Iehkdkuj8AB7JB_B7jyvCuoqTF-txmcFl2gR4QvcaXpKd06SqKzLvcyX4voA3WeJZ8cTqEeHq335ZfHlz-3n9rrz7-Pb9-uauNJWgqRSNZrqmgtoNCFHxpuNGMMk30kpZt52B_HFtbEd53_Qb2WohQTTCMt22vJLisrg-6qJx2Rh1H5boc0H16eCiOrjIKeuyhZzSquaZ8PxImGPIj8V0onDacFnzqqMn1KBHUM7bkLLNk0OjbupKNIxJ1p2Kn6Hy7CEbHzxYl-_PCKsHhM2CzgPmBd2wTTjoBfEc3h3hhyZiBKvm6HIP94pRdUiU-psodUyU-p8oxaT4A10BwzE</recordid><startdate>20180501</startdate><enddate>20180501</enddate><creator>Ferrada-Fuentes, Sandra</creator><creator>Galleguillos, Ricardo</creator><creator>Canales-Aguirre, Cristian B</creator><creator>Herrera-Yanez, Victoria</creator><general>Pontificia Universidad Catolica de Valparaiso, Escuela de Ciencias del Mar</general><general>Pontificia Universidad Catolica de Valparaiso</general><general>Pontificia Universidad Católica de Valparaíso. 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Galleguillos, Ricardo ; Canales-Aguirre, Cristian B ; Herrera-Yanez, Victoria</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c430t-36a1a5030fbe3342682c3192b9f99578ce316acf802d6db97a39e363f1a772493</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2018</creationdate><topic>Alleles</topic><topic>Clupeiformes</topic><topic>Clupeoid fisheries</topic><topic>DNA</topic><topic>Ecological monitoring</topic><topic>Ecological studies</topic><topic>Engraulidae</topic><topic>Engraulis ringens</topic><topic>Fish</topic><topic>FISHERIES</topic><topic>Fisheries management</topic><topic>Fishery management</topic><topic>Genetic diversity</topic><topic>Genetic markers</topic><topic>Genetic structure</topic><topic>Heterozygosity</topic><topic>Homozygotes</topic><topic>Information management</topic><topic>Loci</topic><topic>MARINE & FRESHWATER BIOLOGY</topic><topic>Markers</topic><topic>Microsatellites</topic><topic>Nucleotide sequence</topic><topic>OCEANOGRAPHY</topic><topic>PCR</topic><topic>Pelagic fish</topic><topic>Pelagic fisheries</topic><topic>Population genetics</topic><topic>Population number</topic><topic>Probability theory</topic><topic>Trachurus murphyi</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Ferrada-Fuentes, Sandra</creatorcontrib><creatorcontrib>Galleguillos, Ricardo</creatorcontrib><creatorcontrib>Canales-Aguirre, Cristian B</creatorcontrib><creatorcontrib>Herrera-Yanez, Victoria</creatorcontrib><collection>CrossRef</collection><collection>Gale Business: Insights</collection><collection>Business Insights: Essentials</collection><collection>Gale OneFile: Informe Academico</collection><collection>ProQuest Central (Corporate)</collection><collection>Aqualine</collection><collection>Water Resources Abstracts</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Science Database (Alumni Edition)</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest One Sustainability</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>Earth, Atmospheric & Aquatic Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>Latin America & Iberia Database</collection><collection>ProQuest Central Korea</collection><collection>ASFA: Aquatic Sciences and Fisheries Abstracts</collection><collection>ProQuest Central Student</collection><collection>Aquatic Science & Fisheries Abstracts (ASFA) 1: Biological Sciences & Living Resources</collection><collection>SciTech Premium Collection</collection><collection>Aquatic Science & Fisheries Abstracts (ASFA) Professional</collection><collection>ProQuest Biological Science Collection</collection><collection>Science Database</collection><collection>Biological Science Database</collection><collection>Earth, Atmospheric & Aquatic Science Database</collection><collection>Publicly Available Content 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><collection>ProQuest Central Basic</collection><collection>SciELO</collection><jtitle>Latin american journal of aquatic research</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Ferrada-Fuentes, Sandra</au><au>Galleguillos, Ricardo</au><au>Canales-Aguirre, Cristian B</au><au>Herrera-Yanez, Victoria</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Development and characterization of thirty two microsatellite markers for the anchovy, Engraulis ringens Jenyns, 1842 (Clupeiformes, Engraulidae) via 454 pyrosequencing</atitle><jtitle>Latin american journal of aquatic research</jtitle><addtitle>Lat. Am. J. Aquat. Res</addtitle><date>2018-05-01</date><risdate>2018</risdate><volume>46</volume><issue>2</issue><spage>452</spage><epage>456</epage><pages>452-456</pages><issn>0718-560X</issn><eissn>0718-560X</eissn><abstract>The anchovy, Engraulis ringens, is an economically valuable fish, and the most heavily exploited resource in the Humboldt Current System. To analyze its genetic structure and diversity, microsatellite markers were developed using 454 pyrosequencing. A total of 27,352 reads containing di-, tri-, tetra-, penta-, and hexanucleotide microsatellite repeat units were identified from 136,537 reads. Among 80 loci containing more than six repeat motifs, 32 primer sets (40%) produced reproducible PCR products, and all of these loci were polymorphic. Some loci showed deviations from HWE and possible null allele's presence, results of an excess of homozygotes. In an analysis of 45 individuals from one E. ringens population, the number of alleles per locus ranged from 2 to 33, observed heterozygosity ranged from 0.171 to 0.976, and the probability of identity values ranged from 0.006 to 0.513. These microsatellites will be useful for numerous ecological studies focused on this important pelagic fish; including the examination of population genetic structure, estimating effective population size and providing information for fisheries management.</abstract><cop>Valparaiso</cop><pub>Pontificia Universidad Catolica de Valparaiso, Escuela de Ciencias del Mar</pub><doi>10.3856/vol46-issue2-fulltext-19</doi><tpages>5</tpages><oa>free_for_read</oa></addata></record> |
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| source | Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals |
| subjects | Alleles Clupeiformes Clupeoid fisheries DNA Ecological monitoring Ecological studies Engraulidae Engraulis ringens Fish FISHERIES Fisheries management Fishery management Genetic diversity Genetic markers Genetic structure Heterozygosity Homozygotes Information management Loci MARINE & FRESHWATER BIOLOGY Markers Microsatellites Nucleotide sequence OCEANOGRAPHY PCR Pelagic fish Pelagic fisheries Population genetics Population number Probability theory Trachurus murphyi |
| title | Development and characterization of thirty two microsatellite markers for the anchovy, Engraulis ringens Jenyns, 1842 (Clupeiformes, Engraulidae) via 454 pyrosequencing |
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