Department of Evolution and Ecology, University of California Davis, Davis, CA 95616, USA.
G3 (Bethesda). 2023 Aug 9;13(8). doi: 10.1093/g3journal/jkad122.
Most eukaryotic genes have been vertically transmitted to the present from distant ancestors. However, variable gene number across species indicates that gene gain and loss also occurs. While new genes typically originate as products of duplications and rearrangements of preexisting genes, putative de novo genes-genes born out of ancestrally nongenic sequence-have been identified. Previous studies of de novo genes in Drosophila have provided evidence that expression in male reproductive tissues is common. However, no studies have focused on female reproductive tissues. Here we begin addressing this gap in the literature by analyzing the transcriptomes of 3 female reproductive tract organs (spermatheca, seminal receptacle, and parovaria) in 3 species-our focal species, Drosophila melanogaster-and 2 closely related species, Drosophila simulans and Drosophila yakuba, with the goal of identifying putative D. melanogaster-specific de novo genes expressed in these tissues. We discovered several candidate genes, located in sequence annotated as intergenic. Consistent with the literature, these genes tend to be short, single exon, and lowly expressed. We also find evidence that some of these genes are expressed in other D. melanogaster tissues and both sexes. The relatively small number of intergenic candidate genes discovered here is similar to that observed in the accessory gland, but substantially fewer than that observed in the testis.
大多数真核基因都是从遥远的祖先那里垂直传递到现在的。然而，物种间基因数量的变化表明基因的获得和丢失也在发生。虽然新基因通常起源于现有基因的重复和重排产物，但也已经鉴定出了假定的从头基因——由祖先非基因序列产生的基因。先前对果蝇中从头基因的研究提供了证据，表明在雄性生殖组织中的表达是常见的。然而，没有研究集中在雌性生殖组织上。在这里，我们通过分析 3 个物种（我们的研究焦点——黑腹果蝇，以及 2 个密切相关的物种——拟暗果蝇和粗糙拟暗果蝇）的 3 个雌性生殖道器官（受精囊、精囊和侧体）的转录组，开始填补这一文献空白，目的是鉴定这些组织中表达的假定的黑腹果蝇特异性从头基因。我们发现了几个候选基因，位于注释为基因间的序列中。与文献一致，这些基因往往较短，只有一个外显子，表达水平较低。我们还发现了一些证据表明，这些基因中的一些在其他黑腹果蝇组织和两性中都有表达。这里发现的基因间候选基因数量相对较少，与在附腺中观察到的数量相似，但明显少于在睾丸中观察到的数量。
