Full-length RNA transcript sequencing traces brain isoform diversity in house mouse natural populations

生物 遗传学 基因亚型 人口 管家基因 外显子 基因 亚种 进化生物学 计算生物学 基因表达 动物 人口学 社会学
作者
Wenyu Zhang,Anja Guenther,Yuanxiao Gao,Kristian K Ullrich,Bruno Hüettel,Aftab Ahmad,Lei Duan,Kaizong Wei,Diethard Tautz
出处
期刊:Genome Research [Cold Spring Harbor Laboratory Press]
卷期号:: gr.279166.124-gr.279166.124 被引量:1
标识
DOI:10.1101/gr.279166.124
摘要

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 transcripts 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 dataset represents the most extensive full-length high-quality isoform catalog at the population level to date. In total, we reliably identified 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 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.
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