Genome survey and microsatellite motif identification of Pogonophryne albipinna
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...
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crportlandpress:10.1042/bsr20210824 2024-09-15T17:41:48+00:00 Genome survey and microsatellite motif identification of Pogonophryne albipinna Jo, Euna Cho, Yll Hwan Lee, Seung Jae Choi, Eunkyung Kim, Jinmu Kim, Jeong-Hoon Chi, Young Min Park, Hyun 2021 http://dx.doi.org/10.1042/bsr20210824 https://portlandpress.com/bioscirep/article-pdf/doi/10.1042/BSR20210824/917003/bsr-2021-0824.pdf en eng Portland Press Ltd. https://creativecommons.org/licenses/by/4.0/ Bioscience Reports volume 41, issue 7 ISSN 0144-8463 1573-4935 journal-article 2021 crportlandpress https://doi.org/10.1042/bsr20210824 2024-08-01T04:17:39Z 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. Article in Journal/Newspaper Antarc* Antarctic Southern Ocean Portland Press Bioscience Reports 41 7 |
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English |
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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. |
format |
Article in Journal/Newspaper |
author |
Jo, Euna Cho, Yll Hwan Lee, Seung Jae Choi, Eunkyung Kim, Jinmu Kim, Jeong-Hoon Chi, Young Min Park, Hyun |
spellingShingle |
Jo, Euna Cho, Yll Hwan Lee, Seung Jae Choi, Eunkyung Kim, Jinmu Kim, Jeong-Hoon Chi, Young Min Park, Hyun Genome survey and microsatellite motif identification of Pogonophryne albipinna |
author_facet |
Jo, Euna Cho, Yll Hwan Lee, Seung Jae Choi, Eunkyung Kim, Jinmu Kim, Jeong-Hoon Chi, Young Min Park, Hyun |
author_sort |
Jo, Euna |
title |
Genome survey and microsatellite motif identification of Pogonophryne albipinna |
title_short |
Genome survey and microsatellite motif identification of Pogonophryne albipinna |
title_full |
Genome survey and microsatellite motif identification of Pogonophryne albipinna |
title_fullStr |
Genome survey and microsatellite motif identification of Pogonophryne albipinna |
title_full_unstemmed |
Genome survey and microsatellite motif identification of Pogonophryne albipinna |
title_sort |
genome survey and microsatellite motif identification of pogonophryne albipinna |
publisher |
Portland Press Ltd. |
publishDate |
2021 |
url |
http://dx.doi.org/10.1042/bsr20210824 https://portlandpress.com/bioscirep/article-pdf/doi/10.1042/BSR20210824/917003/bsr-2021-0824.pdf |
genre |
Antarc* Antarctic Southern Ocean |
genre_facet |
Antarc* Antarctic Southern Ocean |
op_source |
Bioscience Reports volume 41, issue 7 ISSN 0144-8463 1573-4935 |
op_rights |
https://creativecommons.org/licenses/by/4.0/ |
op_doi |
https://doi.org/10.1042/bsr20210824 |
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Bioscience Reports |
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41 |
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7 |
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