Genome-wide mapping and characterization of microsatellites in the swamp eel genome

Abstract We described genome-wide screening and characterization of microsatellites in the swamp eel genome. A total of 99,293 microsatellite loci were identified in the genome with an overall density of 179 microsatellites per megabase of genomic sequences. The dinucleotide microsatellites were the...

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Autores principales:	Zhigang Li, Feng Chen, Chunhua Huang, Weixin Zheng, Chunlai Yu, Hanhua Cheng, Rongjia Zhou
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/b12ae52eb21643ed8df34b14a5743b95
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spelling	oai:doaj.org-article:b12ae52eb21643ed8df34b14a5743b952021-12-02T16:06:39ZGenome-wide mapping and characterization of microsatellites in the swamp eel genome10.1038/s41598-017-03330-72045-2322https://doaj.org/article/b12ae52eb21643ed8df34b14a5743b952017-06-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-03330-7https://doaj.org/toc/2045-2322Abstract We described genome-wide screening and characterization of microsatellites in the swamp eel genome. A total of 99,293 microsatellite loci were identified in the genome with an overall density of 179 microsatellites per megabase of genomic sequences. The dinucleotide microsatellites were the most abundant type representing 71% of the total microsatellite loci and the AC-rich motifs were the most recurrent in all repeat types. Microsatellite frequency decreased as numbers of repeat units increased, which was more obvious in long than short microsatellite motifs. Most of microsatellites were located in non-coding regions, whereas only approximately 1% of the microsatellites were detected in coding regions. Trinucleotide repeats were most abundant microsatellites in the coding regions, which represented amino acid repeats in proteins. There was a chromosome-biased distribution of microsatellites in non-coding regions, with the highest density of 203.95/Mb on chromosome 8 and the least on chromosome 7 (164.06/Mb). The most abundant dinucleotides (AC)n was mainly located on chromosome 8. Notably, genomic mapping showed that there was a chromosome-biased association of genomic distributions between microsatellites and transposon elements. Thus, the novel dataset of microsatellites in swamp eel provides a valuable resource for further studies on QTL-based selection breeding, genetic resource conservation and evolutionary genetics.Zhigang LiFeng ChenChunhua HuangWeixin ZhengChunlai YuHanhua ChengRongjia ZhouNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-9 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Zhigang Li Feng Chen Chunhua Huang Weixin Zheng Chunlai Yu Hanhua Cheng Rongjia Zhou Genome-wide mapping and characterization of microsatellites in the swamp eel genome
description	Abstract We described genome-wide screening and characterization of microsatellites in the swamp eel genome. A total of 99,293 microsatellite loci were identified in the genome with an overall density of 179 microsatellites per megabase of genomic sequences. The dinucleotide microsatellites were the most abundant type representing 71% of the total microsatellite loci and the AC-rich motifs were the most recurrent in all repeat types. Microsatellite frequency decreased as numbers of repeat units increased, which was more obvious in long than short microsatellite motifs. Most of microsatellites were located in non-coding regions, whereas only approximately 1% of the microsatellites were detected in coding regions. Trinucleotide repeats were most abundant microsatellites in the coding regions, which represented amino acid repeats in proteins. There was a chromosome-biased distribution of microsatellites in non-coding regions, with the highest density of 203.95/Mb on chromosome 8 and the least on chromosome 7 (164.06/Mb). The most abundant dinucleotides (AC)n was mainly located on chromosome 8. Notably, genomic mapping showed that there was a chromosome-biased association of genomic distributions between microsatellites and transposon elements. Thus, the novel dataset of microsatellites in swamp eel provides a valuable resource for further studies on QTL-based selection breeding, genetic resource conservation and evolutionary genetics.
format	article
author	Zhigang Li Feng Chen Chunhua Huang Weixin Zheng Chunlai Yu Hanhua Cheng Rongjia Zhou
author_facet	Zhigang Li Feng Chen Chunhua Huang Weixin Zheng Chunlai Yu Hanhua Cheng Rongjia Zhou
author_sort	Zhigang Li
title	Genome-wide mapping and characterization of microsatellites in the swamp eel genome
title_short	Genome-wide mapping and characterization of microsatellites in the swamp eel genome
title_full	Genome-wide mapping and characterization of microsatellites in the swamp eel genome
title_fullStr	Genome-wide mapping and characterization of microsatellites in the swamp eel genome
title_full_unstemmed	Genome-wide mapping and characterization of microsatellites in the swamp eel genome
title_sort	genome-wide mapping and characterization of microsatellites in the swamp eel genome
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/b12ae52eb21643ed8df34b14a5743b95
work_keys_str_mv	AT zhigangli genomewidemappingandcharacterizationofmicrosatellitesintheswampeelgenome AT fengchen genomewidemappingandcharacterizationofmicrosatellitesintheswampeelgenome AT chunhuahuang genomewidemappingandcharacterizationofmicrosatellitesintheswampeelgenome AT weixinzheng genomewidemappingandcharacterizationofmicrosatellitesintheswampeelgenome AT chunlaiyu genomewidemappingandcharacterizationofmicrosatellitesintheswampeelgenome AT hanhuacheng genomewidemappingandcharacterizationofmicrosatellitesintheswampeelgenome AT rongjiazhou genomewidemappingandcharacterizationofmicrosatellitesintheswampeelgenome
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Genome-wide mapping and characterization of microsatellites in the swamp eel genome

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