Genome survey and microsatellite motif identification of Pogonophryne albipinna
The genus Pogonophryne is a speciose group that includes 28 species inhabiting the coastal or deep waters of the Antarctic Southern Ocean. The genus has been divided into five species groups, among which the P. albipinna group is the most deep-living group and is characterized by a lack of spots on...
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| Veröffentlicht in: | Bioscience reports 2021-07, Vol.41 (7) |
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| creator | Jo, Euna Cho, Yll Hwan Lee, Seung Jae Choi, Eunkyung Kim, Jinmu Kim, Jeong-Hoon Chi, Young Min Park, Hyun |
| description | The genus Pogonophryne is a speciose group that includes 28 species inhabiting the coastal or deep waters of the Antarctic Southern Ocean. The genus has been divided into five species groups, among which the P. albipinna group is the most deep-living group and is characterized by a lack of spots on the top of the head. Here, we carried out genome survey sequencing of P. albipinna using the Illumina HiSeq platform to estimate the genomic characteristics and identify genome-wide microsatellite motifs. The genome size was predicted to be ∼883.8 Mb by K-mer analysis (K = 25), and the heterozygosity and repeat ratio were 0.289 and 39.03%, respectively. The genome sequences were assembled into 571624 contigs, covering a total length of ∼819.3 Mb with an N50 of 2867 bp. A total of 2217422 simple sequence repeat (SSR) motifs were identified from the assembly data, and the number of repeats decreased as the length and number of repeats increased. These data will provide a useful foundation for the development of new molecular markers for the P. albipinna group as well as for further whole-genome sequencing of P. albipinna. |
| doi_str_mv | 10.1042/BSR20210824 |
| format | Article |
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The genus has been divided into five species groups, among which the P. albipinna group is the most deep-living group and is characterized by a lack of spots on the top of the head. Here, we carried out genome survey sequencing of P. albipinna using the Illumina HiSeq platform to estimate the genomic characteristics and identify genome-wide microsatellite motifs. The genome size was predicted to be ∼883.8 Mb by K-mer analysis (K = 25), and the heterozygosity and repeat ratio were 0.289 and 39.03%, respectively. The genome sequences were assembled into 571624 contigs, covering a total length of ∼819.3 Mb with an N50 of 2867 bp. A total of 2217422 simple sequence repeat (SSR) motifs were identified from the assembly data, and the number of repeats decreased as the length and number of repeats increased. These data will provide a useful foundation for the development of new molecular markers for the P. albipinna group as well as for further whole-genome sequencing of P. albipinna.</description><identifier>ISSN: 0144-8463</identifier><identifier>EISSN: 1573-4935</identifier><identifier>DOI: 10.1042/BSR20210824</identifier><identifier>PMID: 34223611</identifier><language>eng</language><publisher>England: Portland Press Ltd The Biochemical Society</publisher><subject>Animals ; Coastal waters ; Evolutionary Biology ; Fish Proteins - genetics ; Gene sequencing ; Genetic Markers ; Genome ; Genome Size ; Genomes ; Genomics ; Heterozygosity ; High-Throughput Nucleotide Sequencing ; Microsatellite Repeats ; Morphology ; Nucleotide Motifs ; Perciformes - genetics ; Surveys ; Whole genome sequencing</subject><ispartof>Bioscience reports, 2021-07, Vol.41 (7)</ispartof><rights>2021 The Author(s).</rights><rights>2021. 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The genus has been divided into five species groups, among which the P. albipinna group is the most deep-living group and is characterized by a lack of spots on the top of the head. Here, we carried out genome survey sequencing of P. albipinna using the Illumina HiSeq platform to estimate the genomic characteristics and identify genome-wide microsatellite motifs. The genome size was predicted to be ∼883.8 Mb by K-mer analysis (K = 25), and the heterozygosity and repeat ratio were 0.289 and 39.03%, respectively. The genome sequences were assembled into 571624 contigs, covering a total length of ∼819.3 Mb with an N50 of 2867 bp. A total of 2217422 simple sequence repeat (SSR) motifs were identified from the assembly data, and the number of repeats decreased as the length and number of repeats increased. These data will provide a useful foundation for the development of new molecular markers for the P. albipinna group as well as for further whole-genome sequencing of P. albipinna.</description><subject>Animals</subject><subject>Coastal waters</subject><subject>Evolutionary Biology</subject><subject>Fish Proteins - genetics</subject><subject>Gene sequencing</subject><subject>Genetic Markers</subject><subject>Genome</subject><subject>Genome Size</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Heterozygosity</subject><subject>High-Throughput Nucleotide Sequencing</subject><subject>Microsatellite Repeats</subject><subject>Morphology</subject><subject>Nucleotide Motifs</subject><subject>Perciformes - genetics</subject><subject>Surveys</subject><subject>Whole genome sequencing</subject><issn>0144-8463</issn><issn>1573-4935</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>8G5</sourceid><sourceid>BENPR</sourceid><sourceid>GUQSH</sourceid><sourceid>M2O</sourceid><recordid>eNpdkctLxDAQh4Mouj5O3qXgRZBqHrNtehF08QWC4uMc0naikTZZk1bY_94sPlBPc5iPH9_Mj5BdRo8YBX589nDPKWdUclghEzYtRQ6VmK6SCWUAuYRCbJDNGF8ppWkB62RDAOeiYGxCbi_R-R6zOIZ3XGTatVlvm-CjHrDr7IBZ7wdrMtuiS9M2erDeZd5kd_7ZOz9_CQuHme5qO7fO6W2yZnQXcedrbpGni_PH2VV-c3t5PTu9yRtgMOQIRgIFWciaNtJUpWFatwBcGNFCk_RkDSDQYFLGttSMi7ZuJLSF4bpCsUVOPnPnY91j2yS7oDs1D7bXYaG8turvxtkX9ezfleQVLwuaAg6-AoJ_GzEOqrexSTdrh36Mik-THZOsgITu_0Nf_RhcOk_xSpQViKJcBh5-UsvvxYDmR4ZRtSxK_Soq0Xu__X_Y72bEB1k9j00</recordid><startdate>20210730</startdate><enddate>20210730</enddate><creator>Jo, Euna</creator><creator>Cho, Yll Hwan</creator><creator>Lee, Seung Jae</creator><creator>Choi, Eunkyung</creator><creator>Kim, Jinmu</creator><creator>Kim, Jeong-Hoon</creator><creator>Chi, Young Min</creator><creator>Park, Hyun</creator><general>Portland Press Ltd The Biochemical Society</general><general>Portland Press Ltd</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>7QL</scope><scope>7QO</scope><scope>7T7</scope><scope>7TK</scope><scope>7TM</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>88I</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>8G5</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>GUQSH</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M2O</scope><scope>M2P</scope><scope>M7N</scope><scope>M7P</scope><scope>MBDVC</scope><scope>P64</scope><scope>PATMY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>PYCSY</scope><scope>Q9U</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0002-8055-2010</orcidid><orcidid>https://orcid.org/0000-0001-7484-6111</orcidid></search><sort><creationdate>20210730</creationdate><title>Genome survey and microsatellite motif identification of Pogonophryne albipinna</title><author>Jo, Euna ; Cho, Yll Hwan ; Lee, Seung Jae ; Choi, Eunkyung ; Kim, Jinmu ; Kim, Jeong-Hoon ; Chi, Young Min ; Park, Hyun</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c414t-e4f8404868b0c8f97f1aad4423f3d4c4228b443efe049ed7a123dbc84d6f2a9e3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Animals</topic><topic>Coastal waters</topic><topic>Evolutionary Biology</topic><topic>Fish Proteins - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Bioscience reports</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Jo, Euna</au><au>Cho, Yll Hwan</au><au>Lee, Seung Jae</au><au>Choi, Eunkyung</au><au>Kim, Jinmu</au><au>Kim, Jeong-Hoon</au><au>Chi, Young Min</au><au>Park, Hyun</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genome survey and microsatellite motif identification of Pogonophryne albipinna</atitle><jtitle>Bioscience reports</jtitle><addtitle>Biosci Rep</addtitle><date>2021-07-30</date><risdate>2021</risdate><volume>41</volume><issue>7</issue><issn>0144-8463</issn><eissn>1573-4935</eissn><abstract>The genus Pogonophryne is a speciose group that includes 28 species inhabiting the coastal or deep waters of the Antarctic Southern Ocean. The genus has been divided into five species groups, among which the P. albipinna group is the most deep-living group and is characterized by a lack of spots on the top of the head. Here, we carried out genome survey sequencing of P. albipinna using the Illumina HiSeq platform to estimate the genomic characteristics and identify genome-wide microsatellite motifs. The genome size was predicted to be ∼883.8 Mb by K-mer analysis (K = 25), and the heterozygosity and repeat ratio were 0.289 and 39.03%, respectively. The genome sequences were assembled into 571624 contigs, covering a total length of ∼819.3 Mb with an N50 of 2867 bp. A total of 2217422 simple sequence repeat (SSR) motifs were identified from the assembly data, and the number of repeats decreased as the length and number of repeats increased. These data will provide a useful foundation for the development of new molecular markers for the P. albipinna group as well as for further whole-genome sequencing of P. albipinna.</abstract><cop>England</cop><pub>Portland Press Ltd The Biochemical Society</pub><pmid>34223611</pmid><doi>10.1042/BSR20210824</doi><orcidid>https://orcid.org/0000-0002-8055-2010</orcidid><orcidid>https://orcid.org/0000-0001-7484-6111</orcidid><oa>free_for_read</oa></addata></record> |
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| source | Research Library; MEDLINE; Research Library (Alumni Edition); Research Library Prep; EZB-FREE-00999 freely available EZB journals; PubMed Central; ProQuest Central |
| subjects | Animals Coastal waters Evolutionary Biology Fish Proteins - genetics Gene sequencing Genetic Markers Genome Genome Size Genomes Genomics Heterozygosity High-Throughput Nucleotide Sequencing Microsatellite Repeats Morphology Nucleotide Motifs Perciformes - genetics Surveys Whole genome sequencing |
| title | Genome survey and microsatellite motif identification of Pogonophryne albipinna |
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