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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Online Access: | http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8292760/ http://www.ncbi.nlm.nih.gov/pubmed/34223611 https://doi.org/10.1042/BSR20210824 |
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ftpubmed:oai:pubmedcentral.nih.gov:8292760 2023-05-15T13:45:58+02:00 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 2021-07-20 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8292760/ http://www.ncbi.nlm.nih.gov/pubmed/34223611 https://doi.org/10.1042/BSR20210824 en eng Portland Press Ltd. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8292760/ http://www.ncbi.nlm.nih.gov/pubmed/34223611 http://dx.doi.org/10.1042/BSR20210824 © 2021 The Author(s). https://creativecommons.org/licenses/by/4.0/This is an open access article published by Portland Press Limited on behalf of the Biochemical Society and distributed under the Creative Commons Attribution License 4.0 (CC BY) (https://creativecommons.org/licenses/by/4.0/) . CC-BY Biosci Rep Genomics Text 2021 ftpubmed https://doi.org/10.1042/BSR20210824 2021-08-08T00:39:06Z 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. Text Antarc* Antarctic Southern Ocean PubMed Central (PMC) Antarctic Southern Ocean The Antarctic Bioscience Reports 41 7 |
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ftpubmed |
language |
English |
topic |
Genomics |
spellingShingle |
Genomics 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 |
topic_facet |
Genomics |
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. |
format |
Text |
author |
Jo, Euna Cho, Yll Hwan Lee, Seung Jae Choi, Eunkyung Kim, Jinmu Kim, Jeong-Hoon Chi, Young Min Park, Hyun |
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://www.ncbi.nlm.nih.gov/pmc/articles/PMC8292760/ http://www.ncbi.nlm.nih.gov/pubmed/34223611 https://doi.org/10.1042/BSR20210824 |
geographic |
Antarctic Southern Ocean The Antarctic |
geographic_facet |
Antarctic Southern Ocean The Antarctic |
genre |
Antarc* Antarctic Southern Ocean |
genre_facet |
Antarc* Antarctic Southern Ocean |
op_source |
Biosci Rep |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8292760/ http://www.ncbi.nlm.nih.gov/pubmed/34223611 http://dx.doi.org/10.1042/BSR20210824 |
op_rights |
© 2021 The Author(s). https://creativecommons.org/licenses/by/4.0/This is an open access article published by Portland Press Limited on behalf of the Biochemical Society and distributed under the Creative Commons Attribution License 4.0 (CC BY) (https://creativecommons.org/licenses/by/4.0/) . |
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CC-BY |
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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1766233769435463680 |