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Whole Genome Sequencing of the Giant Grouper (Epinephelus lanceolatus) and High-Throughput Screening of Putative Antimicrobial Peptide Genes

Giant groupers, the largest grouper type in the world, are of economic importance in marine aquaculture for their rapid growth. At the same time, bacterial and viral diseases have become the main threats to the grouper industry. Here, we report a high-quality genome of a giant grouper sequenced by a...

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Autores principales: Wang, Dengdong, Chen, Xiyang, Zhang, Xinhui, Li, Jia, Yi, Yunhai, Bian, Chao, Shi, Qiong, Lin, Haoran, Li, Shuisheng, Zhang, Yong, You, Xinxin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6780625/
https://www.ncbi.nlm.nih.gov/pubmed/31466296
http://dx.doi.org/10.3390/md17090503
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author Wang, Dengdong
Chen, Xiyang
Zhang, Xinhui
Li, Jia
Yi, Yunhai
Bian, Chao
Shi, Qiong
Lin, Haoran
Li, Shuisheng
Zhang, Yong
You, Xinxin
author_facet Wang, Dengdong
Chen, Xiyang
Zhang, Xinhui
Li, Jia
Yi, Yunhai
Bian, Chao
Shi, Qiong
Lin, Haoran
Li, Shuisheng
Zhang, Yong
You, Xinxin
author_sort Wang, Dengdong
collection PubMed
description Giant groupers, the largest grouper type in the world, are of economic importance in marine aquaculture for their rapid growth. At the same time, bacterial and viral diseases have become the main threats to the grouper industry. Here, we report a high-quality genome of a giant grouper sequenced by an Illumina HiSeq X-Ten and PacBio Bioscience Sequel platform. A total of 254 putative antimicrobial peptide (AMP) genes were identified, which can be divided into 34 classes according to the annotation of the Antimicrobial Peptides Database (APD3). Their locations in pseudochromosomes were also determined. Thrombin-, lectin-, and scolopendin-derived putative AMPs were the three largest parts. In addition, expressions of putative AMPs were measured by our transcriptome data. Two putative AMP genes (gapdh1 and gapdh2) were involved in glycolysis, which had extremely high expression levels in giant grouper muscle. As it has been reported that AMPs inhibit the growth of a broad spectrum of microbes and participate in regulating innate and adaptive immune responses, genome sequencing of this study provides a comprehensive cataloging of putative AMPs of groupers, supporting antimicrobial research and aquaculture therapy. These genomic resources will be beneficial to further molecular breeding of this economically important fish.
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spelling pubmed-67806252019-10-30 Whole Genome Sequencing of the Giant Grouper (Epinephelus lanceolatus) and High-Throughput Screening of Putative Antimicrobial Peptide Genes Wang, Dengdong Chen, Xiyang Zhang, Xinhui Li, Jia Yi, Yunhai Bian, Chao Shi, Qiong Lin, Haoran Li, Shuisheng Zhang, Yong You, Xinxin Mar Drugs Article Giant groupers, the largest grouper type in the world, are of economic importance in marine aquaculture for their rapid growth. At the same time, bacterial and viral diseases have become the main threats to the grouper industry. Here, we report a high-quality genome of a giant grouper sequenced by an Illumina HiSeq X-Ten and PacBio Bioscience Sequel platform. A total of 254 putative antimicrobial peptide (AMP) genes were identified, which can be divided into 34 classes according to the annotation of the Antimicrobial Peptides Database (APD3). Their locations in pseudochromosomes were also determined. Thrombin-, lectin-, and scolopendin-derived putative AMPs were the three largest parts. In addition, expressions of putative AMPs were measured by our transcriptome data. Two putative AMP genes (gapdh1 and gapdh2) were involved in glycolysis, which had extremely high expression levels in giant grouper muscle. As it has been reported that AMPs inhibit the growth of a broad spectrum of microbes and participate in regulating innate and adaptive immune responses, genome sequencing of this study provides a comprehensive cataloging of putative AMPs of groupers, supporting antimicrobial research and aquaculture therapy. These genomic resources will be beneficial to further molecular breeding of this economically important fish. MDPI 2019-08-28 /pmc/articles/PMC6780625/ /pubmed/31466296 http://dx.doi.org/10.3390/md17090503 Text en © 2019 by the authors. 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 (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Wang, Dengdong
Chen, Xiyang
Zhang, Xinhui
Li, Jia
Yi, Yunhai
Bian, Chao
Shi, Qiong
Lin, Haoran
Li, Shuisheng
Zhang, Yong
You, Xinxin
Whole Genome Sequencing of the Giant Grouper (Epinephelus lanceolatus) and High-Throughput Screening of Putative Antimicrobial Peptide Genes
title Whole Genome Sequencing of the Giant Grouper (Epinephelus lanceolatus) and High-Throughput Screening of Putative Antimicrobial Peptide Genes
title_full Whole Genome Sequencing of the Giant Grouper (Epinephelus lanceolatus) and High-Throughput Screening of Putative Antimicrobial Peptide Genes
title_fullStr Whole Genome Sequencing of the Giant Grouper (Epinephelus lanceolatus) and High-Throughput Screening of Putative Antimicrobial Peptide Genes
title_full_unstemmed Whole Genome Sequencing of the Giant Grouper (Epinephelus lanceolatus) and High-Throughput Screening of Putative Antimicrobial Peptide Genes
title_short Whole Genome Sequencing of the Giant Grouper (Epinephelus lanceolatus) and High-Throughput Screening of Putative Antimicrobial Peptide Genes
title_sort whole genome sequencing of the giant grouper (epinephelus lanceolatus) and high-throughput screening of putative antimicrobial peptide genes
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6780625/
https://www.ncbi.nlm.nih.gov/pubmed/31466296
http://dx.doi.org/10.3390/md17090503
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