Data from: Survey sequencing reveals elevated DNA transposon activity, novel elements, and variation in repetitive landscapes among vesper bats

The repetitive landscapes of mammalian genomes typically display high Class I (retrotransposon) transposable element (TE) content, usually around half of the genome. In contrast, the Class II (DNA transposon) contribution is typically small (<3% in model mammals). Most mammalian genomes also exhibit a precipitous decline in Class II activity beginning roughly 40 million years ago (Ma). The first signs of more recently active mammalian Class II TEs were obtained from the little brown bat, Myotis lucifugus and are reflected by higher genome content (~5%). To aid in determining taxonomic limits and potential impacts of this elevated Class II activity, we performed 454 survey sequencing of a second Myotis species as well as four additional taxa within the family Vespertilionidae and an outgroup species from Phyllostomidae. Graph-based clustering methods were used to reconstruct the major repeat families present in each species and novel elements were identified in several taxa. Retrotransposons remained the dominant group with regard to overall genome mass. Elevated Class II TE composition (3-4%) was observed in all five vesper bats while less than 0.5% of the phyllostomid reads were identified as Class II derived. Differences in satellite DNA and Class I TE content are also described among vespertilionid taxa. These analyses present the first cohesive description of TE evolution across closely related mammals, revealing genome-scale differences in TE content within a single family.

哺乳动物基因组的重复序列区域通常具有较高的第一类（反转录转座子，retrotransposon）转座因子（transposable element, TE）占比，通常可达基因组总量的一半左右。与之相对，第二类（DNA转座子）转座因子的占比通常极低（模式哺乳动物中不足3%）。绝大多数哺乳动物基因组的第二类转座子活性自约4000万年前（Ma，即百万年）起便急剧下降。首个具有近期活性的哺乳动物第二类转座子相关证据来自小棕蝠（Myotis lucifugus），其基因组中第二类转座因子占比约为5%，印证了这一现象。为明确此类升高的第二类转座子活性的分类学边界与潜在影响，我们对第二种鼠耳蝠属（Myotis）物种、蝙蝠科（Vespertilionidae）内的另外4个类群，以及一科来自叶口蝠科（Phyllostomidae）的外类群物种开展了454测序调查。本研究采用基于图的聚类方法重构了各物种中的主要重复序列家族，并在多个类群中鉴定到了新型转座因子。就基因组总质量而言，反转录转座子仍是占主导地位的重复序列类别。我们在全部5种蝙蝠科物种中均观察到了占比升高的第二类转座因子（3%~4%），而叶口蝠科的测序读数中仅有不足0.5%被鉴定为第二类转座因子来源。此外，本研究还描述了蝙蝠科类群间卫星DNA与第一类转座因子占比的差异。本分析首次对近缘哺乳动物的转座因子演化进行了系统性描述，揭示了同一科内不同物种间基因组尺度上的转座因子含量差异。