Genomic Microsatellite Mining and Characteristic Analysis of Gobiidae Fish

IF 0.6 4区生物学 Q4 GENETICS & HEREDITY Russian Journal of Genetics Pub Date : 2024-06-19 DOI:10.1134/s1022795424700224

S. Ma, N. Song

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Abstract

Microsatellites or single sequence repeats (SSRs) are widespread in the genome of eukaryotes and prokaryotes, and are usually used for studying genetic diversity and constructing the genetic map. The distribution characteristics and effective markers of microsatellites in the Gobiidae family were still unclearly. In this study, genomes of 16 Gobiidae fish were downloaded from the National Center for Biotechnology Information (NCBI) and Ensembl Genomes databases which were analyzed by bioinformatics. The content of microsatellites for Gobiidae fish occurred differently and the coverage degree varied from 0.12 to 2.36%. The total number of microsatellites ranged from 288 730 to 846 829 and the total sequence length ranged from 515 577 to 1 561 092. The mononucleotide repeats were the most common types in the microsatellites for 13 Gobiidae fish, but dinucleotide repeats were most common for Acanthogobius ommaturus, Chaenogobius annularis and Eucyclogobius newberryi. Moreover, the frequency of microsatellite motifs varied in Gobiidae fish. Within the dinucleotide repeats, the AC/GT was the most abundant microsatellite of 13 Gobiidae fish, while the most dinucleotide repeat was AG/CT of Lythrypnus dalli, Lesueurigobius sanzi and Rhinogobius similis. Our study suggested that the distribution and characteristics of microsatellites are various in these Gobiidae genomes, which may be related to the genome diversity of Gobiidae. The data could not only provide new insights into the studies of genetic evolution but also provide powerful support for the development of more microsatellites of Gobiidae.

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戈壁鱼基因组微卫星挖掘与特征分析

摘要微卫星或单序列重复序列（SSR）广泛存在于真核生物和原核生物的基因组中，通常用于研究遗传多样性和构建遗传图谱。微卫星在戈壁鱼科中的分布特征和有效标记尚不清楚。本研究从美国国家生物技术信息中心（NCBI）和Ensembl基因组数据库下载了16种戈壁鱼类的基因组，并进行了生物信息学分析。结果表明，戈壁鱼的微卫星含量各不相同，覆盖率从 0.12% 到 2.36% 不等。微卫星总数在 288 730 至 846 829 之间，序列总长度在 515 577 至 1 561 092 之间。13种戈壁鱼的微卫星中最常见的是单核苷酸重复序列，而双核苷酸重复序列在Acanthogobius ommaturus、Chaenogobius annularis和Eucyclogobius newberryi中最为常见。此外，戈壁鱼类中微卫星图案的频率也各不相同。在二核苷酸重复序列中，AC/GT是13种戈壁鱼类中最多的微卫星，而在Lythrypnus dalli、Lesueurigobius sanzi和Rhinogobius similis中最多的二核苷酸重复序列是AG/CT。我们的研究表明，微卫星在戈壁鱼类基因组中的分布和特征各不相同，这可能与戈壁鱼类基因组的多样性有关。这些数据不仅为遗传进化研究提供了新的思路，也为开发更多的戈壁鱼科微卫星提供了有力的支持。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Russian Journal of Genetics 生物-遗传学

CiteScore

1.00

自引率

33.30%

发文量

126

审稿时长

1 months

期刊介绍： Russian Journal of Genetics is a journal intended to make significant contribution to the development of genetics. The journal publishes reviews and experimental papers in the areas of theoretical and applied genetics. It presents fundamental research on genetic processes at molecular, cell, organism, and population levels, including problems of the conservation and rational management of genetic resources and the functional genomics, evolutionary genomics and medical genetics.