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. 2024 Dec 21;15(12):1641.
doi: 10.3390/genes15121641.

Identification of Retrocopies in Lepidoptera and Impact on Domestication of Silkworm

Lingzi Bie  1 , Jiahe Sun  1 , Yi Wang  1 , Chunfang Wang  2
Affiliations

Identification of Retrocopies in Lepidoptera and Impact on Domestication of Silkworm

Lingzi Bie et al. Genes (Basel). .

Abstract

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.

Keywords: adaptive evolution; functional genomics; gene duplication; lepidopteran insects; retrocopy.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

Figure 1
Figure 1
Retrocopies in the eight lepidopteran insect genomes. (A) Number of retrocopies and their parental genes. (B) Percentage of retrotransposable elements of retrocopies. (C) Percentage of types of retrocopies. (D) Distribution of ka/ks values of retrogenes and their parental genes.
Figure 2
Figure 2
Retrocopy evolution within lepidopteran genomes. (A) Distribution of the Ks values. (B) Distribution relationship of the Ks values and Ka/Ks values. (C) Orthologous retrocopies and species-specific retrocopies. The left figure shows the number of orthologous retrocopies. The number in the dark blue semicircle on the branch represents the number of orthologous retrocopies behind the note on the tree, and the number in the light blue semicircle represents the number of orthologous retrocopies of one species behind the note and seven other lepidopteran species. The right figure shows the numbers of specific retrocopies in eight lepidopteran insects.
Figure 3
Figure 3
Expression analysis of retrocopies in silkworm. (A) The number of retrocopies of silkworm expressed in different tissues at different times. The numbers represent the level of retrocopy expression, and 0 meant that there are no transcriptome data in this tissue during this period. (B) Percentage of tissue-specific expression ability of retrocopies of silkworm in different tissues at different stages. (C) Correlation comparison of the expression patterns of the retrocopies and their parental genes in silkworm represented by Ks and Y = log(1 + R)/(1 − R). A positive linear regression of the Ks and Y values for each retrocopy revealed no correlation (the blue line). (D) Expression patterns of the retrocopies and the parental genes. *** indicates p < 0.001.
Figure 4
Figure 4
Relationship between retrocopies and silkworm domestication. (A) Expression values of 25 retrocopies. (B) Expression values of q-PCR of two retrocopies (Retrocopy52 and Retrocopy152). (C) Expression values of retrocopies in domestication candidate domestication regions of silkworm (L5D3).
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