Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America.
Department of Biological Sciences, Ft Hays State University, Ft Hays, Kansas, United States of America.
PLoS Genet. 2019 Sep 23;15(9):e1008314. doi: 10.1371/journal.pgen.1008314. eCollection 2019 Sep.
The origins of new genes are among the most fundamental questions in evolutionary biology. Our understanding of the ways that new genetic material appears and how that genetic material shapes population variation remains incomplete. De novo genes and duplicate genes are a key source of new genetic material on which selection acts. To better understand the origins of these new gene sequences, we explored the ways that structural variation might alter expression patterns and form novel transcripts. We provide evidence that chromosomal rearrangements are a source of novel genetic variation that facilitates the formation of de novo exons in Drosophila. We identify 51 cases of de novo exon formation created by chromosomal rearrangements in 14 strains of D. yakuba. These new genes inherit transcription start signals and open reading frames when the 5' end of existing genes are combined with previously untranscribed regions. Such new genes would appear with novel peptide sequences, without the necessity for secondary transitions from non-coding RNA to protein. This mechanism of new peptide formations contrasts with canonical theory of de novo gene progression requiring non-coding intermediaries that must acquire new mutations prior to loss via pseudogenization. Hence, these mutations offer a means to de novo gene creation and protein sequence formation in a single mutational step, answering a long standing open question concerning new gene formation. We further identify gene expression changes to 134 existing genes, indicating that these mutations can alter gene regulation. Population variability for chromosomal rearrangements is considerable, with 2368 rearrangements observed across 14 inbred lines. More rearrangements were identified on the X chromosome than any of the autosomes, suggesting the X is more susceptible to chromosome alterations. Together, these results suggest that chromosomal rearrangements are a source of variation in populations that is likely to be important to explain genetic and therefore phenotypic diversity.
新基因的起源是进化生物学中最基本的问题之一。我们对新遗传物质出现的方式以及遗传物质如何塑造种群变异的理解仍然不完整。从头基因和复制基因是新遗传物质的关键来源，这些新遗传物质受选择作用的影响。为了更好地理解这些新基因序列的起源，我们探索了结构变异可能改变表达模式并形成新转录本的方式。我们提供的证据表明，染色体重排是一种新的遗传变异的来源，这种变异有助于在果蝇中形成新的外显子。我们在 14 个 D. yakuba 品系中发现了 51 个由染色体重排产生的新外显子形成的案例。当现有基因的 5'端与以前未转录的区域结合时，这些新基因会继承转录起始信号和开放阅读框。这种新基因会出现新的肽序列，而无需非编码 RNA 向蛋白质的二次转变。这种新肽形成的机制与从头基因进化的经典理论形成对比，经典理论要求非编码中间产物在通过假基因化丧失之前必须获得新的突变。因此，这些突变提供了一种在单个突变步骤中产生新基因和蛋白质序列的方法，回答了关于新基因形成的一个长期存在的开放性问题。我们进一步鉴定了 134 个现有基因的表达变化，表明这些突变可以改变基因调控。染色体重排的种群变异性很大，在 14 个近交系中观察到 2368 个重排。X 染色体上的重排比任何一条常染色体都多，这表明 X 染色体更容易发生染色体改变。总的来说，这些结果表明，染色体重排是种群变异的一个来源，这很可能对解释遗传和表型多样性很重要。
