The ability to generate multiple RNA transcript isoforms from the same gene is a general phenomenon in eukaryotes. However, the complexity and diversity of alternative isoforms in natural populations remain largely unexplored. Using a newly developed full-length transcript enrichment protocol with 5′ CAP selection, we sequenced full-length RNA transcripts of 48 individuals from outbred populations and subspecies of Mus musculus, and from the closely related sister species Mus spretus and Mus spicilegus as outgroups. The data set represents the most extensive full-length high-quality isoform catalog at the population level to date. In total, we reliably identify 117,728 distinct isoforms, of which only 51% were previously annotated. We show that the population-specific distribution pattern of isoforms is phylogenetically informative and reflects the segregating single nucleotide polymorphism (SNP) diversity between the populations. We find that ancient housekeeping genes are a major source of the overall isoform diversity, and that the generation of alternative first exons plays a major role in generating new isoforms. Given that our data allow us to distinguish between population-specific isoforms and isoforms that are conserved across multiple populations, it is possible to refine the annotation of the reference mouse genome to a set of about 40,000 isoforms that should be most relevant for comparative functional analysis across species.

中文翻译：

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全长 RNA 转录本测序可追踪家鼠自然种群中的脑亚型多样性


从同一基因产生多个 RNA 转录本亚型的能力是真核生物的普遍现象。然而，自然种群中替代亚型的复杂性和多样性在很大程度上仍未得到探索。使用新开发的具有 5' CAP 选择的全长转录本富集方案，我们对来自近交种群和 Mus musculus 亚种以及密切相关的姐妹物种 Mus spretus 和 Mus spicilegus 作为外群的 48 个个体的全长 RNA 转录本进行了测序。该数据集代表了迄今为止种群水平上最广泛的全长高质量亚型目录。我们总共可靠地鉴定了 117,728 种不同的亚型，其中只有 51% 之前有注释。我们表明，亚型的群体特异性分布模式具有系统发育信息，并反映了种群之间分离的单核苷酸多态性 （SNP） 多样性。我们发现，古老的看家基因是整体亚型多样性的主要来源，并且替代第一个外显子的产生在产生新的亚型中起着重要作用。鉴于我们的数据使我们能够区分群体特异性亚型和在多个种群中保守的亚型，因此可以将参考小鼠基因组的注释细化为一组大约 40,000 个亚型，这些亚型应该与跨物种的比较功能分析最相关。