Identification of Retrocopies in Lepidoptera and Impact on Domestication of Silkworm

• Published in: Genes Vol. 15; no. 12; p. 1641
• Main Authors: Bie, Lingzi, Sun, Jiahe, Wang, Yi, Wang, Chunfang
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 21.12.2024; MDPI
• Subjects: Amino acids; Animals; Bombyx - genetics; Chromosomes; Comparative analysis; Domestication; Evolution & development; Evolution, Molecular; Evolutionary genetics; Gene Duplication; Gene Expression Profiling; Genes; Genetic engineering; Genome, Insect; Genomes; Genomics; Insect Proteins - genetics; Insects; Lepidoptera; Lepidoptera - genetics; Phylogeny; Proteins; Proteome - genetics; Proteomes; Retroelements - genetics; RNA; Transcriptome - genetics; Transcriptomes; China; Kansas; functional genomics; adaptive evolution; retrocopy; gene duplication; lepidopteran insects
• ISSN: 2073-4425; 2073-4425
• DOI: 10.3390/genes15121641

Background: 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. Methods: 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. Results: 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. Conclusions: Our study pioneered the exploration of retrocopies in multiple Lepidoptera species and found the potential association between the retrocopies and the domestication of silkworm.