Transposable element libraries from 101 fish

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 found that TE proportion correlate to genome size, but not to the proportion of short tandem repeats (STRs), which implies independent evolutionary paths. Marine and freshwater fish have large differences in STR content. The most extreme propagation was found 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.

重复DNA（Repetitive DNA）在多数真核生物基因组中占比可观。在鱼类中，转座因子（transposable element, TE）的活性与物种快速分化过程相伴发生。本研究对覆盖物种多样性丰富的硬骨鱼支系主要演化分支的100份基因组组装结果中的重复序列内容进行了注释，并探究了转座因子含量与科水平净分化速率之间的相关性，结果证实二者存在微弱的负相关关系。进一步研究发现，转座因子占比与基因组大小相关，但与短串联重复序列（short tandem repeats, STRs）的占比无显著关联，这表明二者有着独立的演化路径。海洋鱼类与淡水鱼类的短串联重复序列含量差异显著。在鳕鱼类物种与大西洋鲱的基因组中，短串联重复序列的扩增程度最为极端。如此高的短串联重复序列密度大概率会增加突变负荷，我们推测该负荷可通过鳕鱼与大西洋鲱所具备的高繁殖力得到平衡。