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Genomic Survey and Microsatellite Marker Investigation of Patagonian Moray Cod (Muraenolepis orangiensis)
SIMPLE SUMMARY: Patagonian moray cod is known to inhabit the cold waters near Antarctica, and it belongs to the Muraenolepis genus. This genus has seven species, and five of them are recently reported. The Muraenolepis genus has similar morphological characters, and this is a limitation of taxonomic...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9265078/ https://www.ncbi.nlm.nih.gov/pubmed/35804506 http://dx.doi.org/10.3390/ani12131608 |
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author | Choi, Eunkyung Lee, Seung Jae Jo, Euna Kim, Jinmu Parker, Steven J. Kim, Jeong-Hoon Park, Hyun |
author_facet | Choi, Eunkyung Lee, Seung Jae Jo, Euna Kim, Jinmu Parker, Steven J. Kim, Jeong-Hoon Park, Hyun |
author_sort | Choi, Eunkyung |
collection | PubMed |
description | SIMPLE SUMMARY: Patagonian moray cod is known to inhabit the cold waters near Antarctica, and it belongs to the Muraenolepis genus. This genus has seven species, and five of them are recently reported. The Muraenolepis genus has similar morphological characters, and this is a limitation of taxonomical classification. In this study, a genome survey and microsatellite marker analysis were conducted to characterize the genome profile for classification. As a result, genomic data such as genome size and microsatellite motifs were obtained. ABSTRACT: The Muraenolepididae family of fishes, known as eel cods, inhabits continental slopes and shelves in the Southern Hemisphere. This family belongs to the Gadiformes order, which constitutes one of the most important commercial fish resources worldwide, but the classification of the fish species in this order is ambiguous because it is only based on the morphological and habitat characteristics of the fishes. Here, the genome of Patagonian moray cod was sequenced using the Illumina HiSeq platform, and screened for microsatellite motifs. The genome was predicted to be 748.97 Mb, with a heterozygosity rate of 0.768%, via K-mer analysis (K = 25). The genome assembly showed that the total size of scaffolds was 711.92 Mb and the N50 scaffold length was 1522 bp. Additionally, 4,447,517 microsatellite motifs were identified from the genome survey assembly, and the most abundant motif type was found to be AC/GT. In summary, these data may facilitate the identification of molecular markers in Patagonian moray cod, which would be a good basis for further whole-genome sequencing with long read sequencing technology and chromosome conformation capture technology, as well as population genetics. |
format | Online Article Text |
id | pubmed-9265078 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-92650782022-07-09 Genomic Survey and Microsatellite Marker Investigation of Patagonian Moray Cod (Muraenolepis orangiensis) Choi, Eunkyung Lee, Seung Jae Jo, Euna Kim, Jinmu Parker, Steven J. Kim, Jeong-Hoon Park, Hyun Animals (Basel) Article SIMPLE SUMMARY: Patagonian moray cod is known to inhabit the cold waters near Antarctica, and it belongs to the Muraenolepis genus. This genus has seven species, and five of them are recently reported. The Muraenolepis genus has similar morphological characters, and this is a limitation of taxonomical classification. In this study, a genome survey and microsatellite marker analysis were conducted to characterize the genome profile for classification. As a result, genomic data such as genome size and microsatellite motifs were obtained. ABSTRACT: The Muraenolepididae family of fishes, known as eel cods, inhabits continental slopes and shelves in the Southern Hemisphere. This family belongs to the Gadiformes order, which constitutes one of the most important commercial fish resources worldwide, but the classification of the fish species in this order is ambiguous because it is only based on the morphological and habitat characteristics of the fishes. Here, the genome of Patagonian moray cod was sequenced using the Illumina HiSeq platform, and screened for microsatellite motifs. The genome was predicted to be 748.97 Mb, with a heterozygosity rate of 0.768%, via K-mer analysis (K = 25). The genome assembly showed that the total size of scaffolds was 711.92 Mb and the N50 scaffold length was 1522 bp. Additionally, 4,447,517 microsatellite motifs were identified from the genome survey assembly, and the most abundant motif type was found to be AC/GT. In summary, these data may facilitate the identification of molecular markers in Patagonian moray cod, which would be a good basis for further whole-genome sequencing with long read sequencing technology and chromosome conformation capture technology, as well as population genetics. MDPI 2022-06-22 /pmc/articles/PMC9265078/ /pubmed/35804506 http://dx.doi.org/10.3390/ani12131608 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Choi, Eunkyung Lee, Seung Jae Jo, Euna Kim, Jinmu Parker, Steven J. Kim, Jeong-Hoon Park, Hyun Genomic Survey and Microsatellite Marker Investigation of Patagonian Moray Cod (Muraenolepis orangiensis) |
title | Genomic Survey and Microsatellite Marker Investigation of Patagonian Moray Cod (Muraenolepis orangiensis) |
title_full | Genomic Survey and Microsatellite Marker Investigation of Patagonian Moray Cod (Muraenolepis orangiensis) |
title_fullStr | Genomic Survey and Microsatellite Marker Investigation of Patagonian Moray Cod (Muraenolepis orangiensis) |
title_full_unstemmed | Genomic Survey and Microsatellite Marker Investigation of Patagonian Moray Cod (Muraenolepis orangiensis) |
title_short | Genomic Survey and Microsatellite Marker Investigation of Patagonian Moray Cod (Muraenolepis orangiensis) |
title_sort | genomic survey and microsatellite marker investigation of patagonian moray cod (muraenolepis orangiensis) |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9265078/ https://www.ncbi.nlm.nih.gov/pubmed/35804506 http://dx.doi.org/10.3390/ani12131608 |
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