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包含较高占比的第一类转座因子（反转录转座子，retrotransposon；转座因子，transposable element，TE），其占比通常可达基因组总量的一半左右。与之相对，第二类转座因子（DNA转座子，DNA transposon）的占比通常极低（模式哺乳动物中不足3%）。多数哺乳动物基因组的第二类转座因子活性在约4000万年前（Ma）出现急剧下降。首个被报道的具有近期活性的哺乳动物第二类转座因子来自小棕蝠（Myotis lucifugus），该物种基因组中此类因子的占比约为5%，这一发现印证了前述特征。为明确这类升高的第二类转座因子活性的分类学范围与潜在影响，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，以及叶口蝠科（Phyllostomidae）的1个外群物种开展了454测序筛查（454 survey sequencing）。我们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，反转录转座子仍为占主导地位的重复序列类群。我们在全部5种蝙蝠科蝙蝠中均观测到了升高的第二类转座因子占比（3%~4%），而叶口蝠科的测序读段中被鉴定为第二类转座因子来源的占比不足0.5%。此外，本研究还描述了蝙蝠科类群间卫星DNA（satellite DNA）与第一类转座因子占比的差异。本分析首次针对近缘哺乳动物的转座因子演化进行了连贯全面的描述，揭示了同一科内哺乳动物基因组中转座因子占比的基因组尺度差异。