Bie Lingzi, Sun Jiahe, Wang Yi, Wang Chunfang
Biological Science Research Center, Southwest University, Chongqing 400715, China.
Southwest University Hospital, Chongqing 400715, China.
Genes (Basel). 2024 Dec 21;15(12):1641. doi: 10.3390/genes15121641.
During the domestication of silkworm, an economic insect, its physiological characteristics have changed greatly. RNA-based gene duplication, known as retrocopy, plays an important role in the formation of new genes and genome evolution, but the retrocopies of lepidopteran insects have not been fully identified and analyzed, which not only severely limits researchers from exploring the effects of retrocopies on lepidopteran insects but also affects the studies on the domestication of silkworm.
We compared the genomes and proteomes of eight lepidopteran insects and used a series of screening criteria for auxiliary screening to obtain the retrocopies in lepidopteran insects and explored their characteristics. In addition, based on the silkworm transcriptome data from the SilkDB3.0 website, we explored the functions of the retrocopies on the domestication of the silkworm.
A total of 1993 retrocopies and 1208 parental genes in lepidopteran insects were obtained. We revealed that the retrocopies in Lepidoptera do not conform to the "out of X" hypothesis but fit the "out of testis" hypothesis. These retrocopies were subject to strong functional constraints and performed important functions in growth and development. Transcriptome analysis revealed that the expression pattern of the retrocopies and their parental genes were irrelevant. Through the analysis of the retrocopies in silkworm generated after domestication and located in the candidate domestication regions, the possible universal connection between the retrocopies and the domestication of silkworm were found.
Our study pioneered the exploration of retrocopies in multiple Lepidoptera species and found the potential association between the retrocopies and the domestication of silkworm.
家蚕作为一种经济昆虫，在驯化过程中其生理特征发生了很大变化。基于RNA的基因复制，即反转录转座，在新基因形成和基因组进化中起着重要作用，但鳞翅目昆虫的反转录转座尚未得到充分鉴定和分析，这不仅严重限制了研究人员探索反转录转座对鳞翅目昆虫的影响，也影响了对家蚕驯化的研究。
我们比较了八种鳞翅目昆虫的基因组和蛋白质组，并使用一系列筛选标准进行辅助筛选，以获得鳞翅目昆虫中的反转录转座，并探索它们的特征。此外，基于SilkDB3.0网站的家蚕转录组数据，我们探索了反转录转座在家蚕驯化中的功能。
共获得了1993个鳞翅目昆虫的反转录转座和1208个亲本基因。我们发现鳞翅目中的反转录转座不符合“X外”假说，而是符合“睾丸外”假说。这些反转录转座受到强烈的功能限制，并在生长发育中发挥重要作用。转录组分析表明，反转录转座及其亲本基因的表达模式无关。通过对驯化后位于候选驯化区域的家蚕反转录转座的分析，发现了反转录转座与家蚕驯化之间可能的普遍联系。
我们的研究率先探索了多种鳞翅目物种中的反转录转座，并发现了反转录转座与家蚕驯化之间的潜在关联。
