Teleost genomic repeat landscapes in light of diversification rates and ecology.

IF 4.7 2区 生物学 Q1 GENETICS & HEREDITY Mobile DNA Pub Date : 2023-10-03 DOI:10.1186/s13100-023-00302-9
William B Reinar, Ole K Tørresen, Alexander J Nederbragt, Michael Matschiner, Sissel Jentoft, Kjetill S Jakobsen
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Abstract

Repetitive DNA make up a considerable fraction of most eukaryotic genomes. In fish, transposable element (TE) activity has coincided with rapid species diversification. Here, we annotated the repetitive content in 100 genome assemblies, covering the major branches of the diverse lineage of teleost fish. We investigated if TE content correlates with family level net diversification rates and found support for a weak negative correlation. Further, we demonstrated that TE proportion correlates with genome size, but not to the proportion of short tandem repeats (STRs), which implies independent evolutionary paths. Marine and freshwater fish had large differences in STR content, with the most extreme propagation detected in the genomes of codfish species and Atlantic herring. Such a high density of STRs is likely to increase the mutational load, which we propose could be counterbalanced by high fecundity as seen in codfishes and herring.

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根据多样化率和生态学,远隔基因组重复景观。
重复DNA在大多数真核生物基因组中占相当大的比例。在鱼类中,转座元件(TE)的活性与物种的快速多样化相吻合。在这里,我们注释了100个基因组组装中的重复内容,涵盖了硬骨鱼不同谱系的主要分支。我们调查了TE含量是否与家庭层面的净多样化率相关,并发现支持弱负相关。此外,我们证明TE比例与基因组大小相关,但与短串联重复序列(STR)的比例无关,这意味着独立的进化路径。海洋鱼类和淡水鱼类的STR含量差异很大,鳕鱼和大西洋鲱鱼的基因组中检测到最极端的繁殖。如此高密度的STR可能会增加突变负荷,我们认为这可能会被鳕鱼和鲱鱼的高繁殖力所抵消。
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来源期刊
Mobile DNA
Mobile DNA GENETICS & HEREDITY-
CiteScore
8.20
自引率
6.10%
发文量
26
审稿时长
11 weeks
期刊介绍: Mobile DNA is an online, peer-reviewed, open access journal that publishes articles providing novel insights into DNA rearrangements in all organisms, ranging from transposition and other types of recombination mechanisms to patterns and processes of mobile element and host genome evolution. In addition, the journal will consider articles on the utility of mobile genetic elements in biotechnological methods and protocols.
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