| The generation and subsequent development of new genes has been described as an important origin of genetic information and phenotypic diversity in organisms.Retrocopy,which is mediated by RNA,a nucleotide sequence formed by reinsertion of reverse transcribed m RNA into a new genomic region,is one of the main sources of new gene.In human and higher animal genomes,retrocopies have been annotated by analyzing genome sequences,and a large number of functional retrocopies related to growth,development,and disease have been found.A growing number of experimental studies have shown that retrocopies exhibit novel biological functions that contribute to genome evolution.Therefore,the identification and analysis of retrocopy has a great significance to study the formation of new gene.Retrocopy has been intensively studied in animals and plants such as human,zebrafish and Arabidopsis,but less in insects.Lepidoptera are used as the research objects of various biological processes,and they are rich in genetic resources and fast in evolution,which are valuable resources for the study of retrocopy.In Lepidoptera,retrocopies of individual model insects has been studied,but no in-depth research has been carried out,which severely limits the role of retrocopies in Lepidopteran.Therefore,it is necessary to conduct deeply research on the retrocopies of Lepidopteran,to study the genetic and phenotypic diversity of Lepidopteran,and to provide new ideas for the evolution of Lepidopteran.In this study,firstly,eight species of Lepidopteran were identified,and a large number of retrocopies were identified,and the structure,sequence characteristics,functions and evolutionary relationships of retrocopies of Lepidopteran were comprehensively analyzed.Secondly,based on the transcriptome data of B.mori on Silk DB 3.0 website,the expression patterns of retrocopies and its parental genes were analyzed,and the function of retrocopies in domestication was preliminarily explored.Finally,according to the needs of results analysis,this research uses R language and R package to build a retrocopy results visualization online website RetroExplorer,which is based on data interaction and simplifies data expression with the help of graphic elements,providing users with an extremely friendly visualization interface.This study provides a new data basis for the study of retrocopies in Lepidopteran,helps to understand the characteristics and functions of retrocopies in Lepidopteran,can compare the evolution of retrocopies in Lepidopteran,and is helpful for the study function of retrocopies in B.mori during domestication.The main results are as follows:1.Retrocopies in genomes of LepidopteranIn this study,a large number of retrocopies were found in eight species of Lepidoptera(Bombyx mori,Bombyx mandarina,Spodoptera litura,Spodoptera frugiperda,Trichoplusia ni,Manduca sexta,Plutella xylostella and Bicyclus anynana).Based on these data,this study conducts a systematic analysis of retrocopies in Lepidoptera.First,the formation discipline of retrocopies in Lepidoptera,has no preference in chromosome distribution,which does not conform to the “out of X” hypothesis of retrocopies in animals.Second,the structural characteristics of the retrocopies of Lepidoptera,compared with the parental genes,the retrocopies in the process of evolution by inserting into the new gene,recruiting new regulatory elements,losing enhancers and other functional genes,are likely to evolve into a new protein gene,and promote genetic innovation and adaptive evolution.Third,the selection pressure of retrocopies in Lepidoptera.99% of the retrocopies’ Ka/Ks values less than 1,indicating that they are subject to purification selection;91.7%of the retrocopies’ Ka/Ks values less than 0.5 showing that most of the retrocopies of are strictly functionally restricted.Fourth,functional annotation of retrocopies in Lepidoptera,GO functional classification and KEGG pathway analysis of retrocopies of Lepidoptera insects show that the most significant GO clusters are mainly concentrated in the biological process of growth,immunity and metabolism,which may be in Lepidoptera.It plays an important role in the growth and development of Lepidoptera.Fifth,the evolutionary analysis of retrocopies in Lepidoptera,retrocopies have experienced two bursts,and retrocopies are mainly formed by ancient retrotransposition,with an average of 0.811 retrocopies per million years.There are many retrocopies unique to species of Lepidoptera,which may be formed independently after the species diverges from the ancestral species,which is an important starting point for further exploration of the evolution of Lepidoptera.2.Expression analysis of retrocopies in B.morieThis study comprehensively analyzes the expression patterns of retrocopies and their parental genes in B.mori.First,B.mori has excess retrocopies with testis-specific expression at different times(4.83 times the average of other tissues),and subsequently evolves a broad expression pattern,which indicates that the expression of B.mori retrocopies conforms to the “out of testis” hypothesis.Secondly,in B.mori genome,there are significant differences in the expression of ancient retrocopies,young retrocopies and parental gene,and the expression patterns are not similar,indicating that there is no linear correlation between the expression of retrocopies and the father gene,indicating that retrocopies may be functions have evolved rapidly,and retrocopies are not functionally similar to the parent gene.Finally,8 retrocopies overlaps with genes in the domestication hotspot,and 7 of them are annotated as functional genes in the genome and are restricted by strict selectivity,presumably playing a role in the domestication process.3.Design of retrocopy’s online visualization toolIn this study,RetroExplorer,an online visualization tool for retrocopy,was developed.This tool is not limited by species.Users can identify retro’copy of any species and upload the results to the visualization website for visualization of the results.RetroExplorer is based on simple interaction and simplifies the data presentation of retrocopy with the help of graphic elements.The result mainly includes four parts:Summary,Retrocopy,KaKs and Expression.RetroExplorer helps researchers quickly identify information clues from complex data,provides users with a clear and comprehensive information display of retrocopy and its parental genes,simplifies the analysis of retrocopy results and provides a powerful tool for promoting gene duplication and the origin of new genes. |
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