A First Genome Survey and Genomic SSR Marker Analysis of <i>Trematomus loennbergii</i> Regan, 1913

<i>Trematomus loennbergii</i> Regan, 1913, is an evolutionarily important marine fish species distributed in the Antarctic Ocean. However, its genome has not been studied to date. In the present study, whole genome sequencing was performed using next-generation sequencing (NGS) technolog...

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Autores principales:	Eunkyung Choi, Sun Hee Kim, Seung Jae Lee, Euna Jo, Jinmu Kim, Jeong-Hoon Kim, Steven J. Parker, Young-Min Chi, Hyun Park
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	<i>Trematomus loennbergii</i> scaly rockcod repeat motif SSR microsatellite Illumina Veterinary medicine SF600-1100 Zoology QL1-991
Acceso en línea:	https://doaj.org/article/1c25cda83add43638fe36ce171984f4f
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spelling	oai:doaj.org-article:1c25cda83add43638fe36ce171984f4f2021-11-25T16:18:36ZA First Genome Survey and Genomic SSR Marker Analysis of <i>Trematomus loennbergii</i> Regan, 191310.3390/ani111131862076-2615https://doaj.org/article/1c25cda83add43638fe36ce171984f4f2021-11-01T00:00:00Zhttps://www.mdpi.com/2076-2615/11/11/3186https://doaj.org/toc/2076-2615<i>Trematomus loennbergii</i> Regan, 1913, is an evolutionarily important marine fish species distributed in the Antarctic Ocean. However, its genome has not been studied to date. In the present study, whole genome sequencing was performed using next-generation sequencing (NGS) technology to characterize its genome and develop genomic microsatellite markers. The 25-mer frequency distribution was estimated to be the best, and the genome size was predicted to be 815,042,992 bp. The heterozygosity, average rate of read duplication, and sequencing error rates were 0.536%, 0.724%, and 0.292%, respectively. These data were used to analyze microsatellite markers, and a total of 2,264,647 repeat motifs were identified. The most frequent repeat motif was di-nucleotide with 87.00% frequency, followed by tri-nucleotide (10.45%), tetra-nucleotide (1.94%), penta-nucleotide (0.34%), and hexa-nucleotide (0.27%). The AC repeat motif was the most abundant motif among di-nucleotides and among all repeat motifs. Among microsatellite markers, 181 markers were selected and PCR technology was used to validate several markers. A total of 15 markers produced only one band. In summary, these results provide a good basis for further studies, including evolutionary biology studies and population genetics of Antarctic fish species.Eunkyung ChoiSun Hee KimSeung Jae LeeEuna JoJinmu KimJeong-Hoon KimSteven J. ParkerYoung-Min ChiHyun ParkMDPI AGarticle<i>Trematomus loennbergii</i>scaly rockcodrepeat motifSSRmicrosatelliteIlluminaVeterinary medicineSF600-1100ZoologyQL1-991ENAnimals, Vol 11, Iss 3186, p 3186 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	<i>Trematomus loennbergii</i> scaly rockcod repeat motif SSR microsatellite Illumina Veterinary medicine SF600-1100 Zoology QL1-991
spellingShingle	<i>Trematomus loennbergii</i> scaly rockcod repeat motif SSR microsatellite Illumina Veterinary medicine SF600-1100 Zoology QL1-991 Eunkyung Choi Sun Hee Kim Seung Jae Lee Euna Jo Jinmu Kim Jeong-Hoon Kim Steven J. Parker Young-Min Chi Hyun Park A First Genome Survey and Genomic SSR Marker Analysis of <i>Trematomus loennbergii</i> Regan, 1913
description	<i>Trematomus loennbergii</i> Regan, 1913, is an evolutionarily important marine fish species distributed in the Antarctic Ocean. However, its genome has not been studied to date. In the present study, whole genome sequencing was performed using next-generation sequencing (NGS) technology to characterize its genome and develop genomic microsatellite markers. The 25-mer frequency distribution was estimated to be the best, and the genome size was predicted to be 815,042,992 bp. The heterozygosity, average rate of read duplication, and sequencing error rates were 0.536%, 0.724%, and 0.292%, respectively. These data were used to analyze microsatellite markers, and a total of 2,264,647 repeat motifs were identified. The most frequent repeat motif was di-nucleotide with 87.00% frequency, followed by tri-nucleotide (10.45%), tetra-nucleotide (1.94%), penta-nucleotide (0.34%), and hexa-nucleotide (0.27%). The AC repeat motif was the most abundant motif among di-nucleotides and among all repeat motifs. Among microsatellite markers, 181 markers were selected and PCR technology was used to validate several markers. A total of 15 markers produced only one band. In summary, these results provide a good basis for further studies, including evolutionary biology studies and population genetics of Antarctic fish species.
format	article
author	Eunkyung Choi Sun Hee Kim Seung Jae Lee Euna Jo Jinmu Kim Jeong-Hoon Kim Steven J. Parker Young-Min Chi Hyun Park
author_facet	Eunkyung Choi Sun Hee Kim Seung Jae Lee Euna Jo Jinmu Kim Jeong-Hoon Kim Steven J. Parker Young-Min Chi Hyun Park
author_sort	Eunkyung Choi
title	A First Genome Survey and Genomic SSR Marker Analysis of <i>Trematomus loennbergii</i> Regan, 1913
title_short	A First Genome Survey and Genomic SSR Marker Analysis of <i>Trematomus loennbergii</i> Regan, 1913
title_full	A First Genome Survey and Genomic SSR Marker Analysis of <i>Trematomus loennbergii</i> Regan, 1913
title_fullStr	A First Genome Survey and Genomic SSR Marker Analysis of <i>Trematomus loennbergii</i> Regan, 1913
title_full_unstemmed	A First Genome Survey and Genomic SSR Marker Analysis of <i>Trematomus loennbergii</i> Regan, 1913
title_sort	first genome survey and genomic ssr marker analysis of <i>trematomus loennbergii</i> regan, 1913
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/1c25cda83add43638fe36ce171984f4f
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A First Genome Survey and Genomic SSR Marker Analysis of <i>Trematomus loennbergii</i> Regan, 1913

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