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富含第一类转座因子（反转录转座子，retrotransposon），其占比通常可达基因组的一半左右。与之相反，第二类转座因子（DNA转座子，DNA transposon）的占比通常极低，在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自约4000万年前（Ma，即百万年）起便呈现急剧下降趋势。首个被发现的近期具有活性的哺乳动物第二类转座因子来自小棕蝠（Myotis lucifugus），其基因组中该类转座因子的占比约为5%。为明确该升高的第二类转座因子活性的分类学范围及其潜在影响，我们对第二种鼠耳蝠属物种、蝙蝠科（Vespertilionidae）的另外四个类群，以及叶口蝠科（Phyllostomidae）的一个外群物种开展了454测序（454 survey sequencing）分析。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。反转录转座子仍是决定基因组总质量的主要组分。五只蝙蝠科蝙蝠均呈现第二类转座因子占比升高的现象（3%~4%），而叶口蝠科样本的测序读段中仅不足0.5%被鉴定为第二类转座因子来源。本研究还阐述了蝙蝠科类群间卫星DNA（satellite DNA）及第一类转座因子含量的差异。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连贯阐述，揭示了同一科内不同类群间转座因子含量的全基因组尺度差异。