Intron Loss After The Domestication Of The Silkworm,Bombyx Mori

Numerous instances of intron gain and loss have been documented in eukaryotes.The question of whether intron variation occurs randomly due to neutral evolution,or driven by positive selection has not yet yielded a definitive answer.Herein,we utilize genome resequencing data of Bombyx mori and Bombyx mandarina and the methods of population genomics to systematically analyze the events of intron gain and loss between Bombyx mori and Bombyx mandarina.Key research contents include the number of introns loss and gain,selection pressure of intron region,the relationship between introns and evolution.The main results as follow:1.Intron gain/loss event screening and experimental verification142659 deletions and insertions are obtained by genomic data with a valid base number of 220 GB.Then,108 intron loss and 3519 intron gain events are identified by comparing the reference genome,location and annotation information.These events are located on the genes of each sample and screen for the most characteristic 11 candidate genes which suspected of intron insertion or loss.Experiments verify three genes: BGIBMGA012143₂,BGIBMGA010953₁ and BGIBMGA004952₁0.The identity has been confirmed that three genes are intron loss event happened in Bombyx mori by using outgroup of Japanese Bombyx mandarina genome and Bombyx mandarina RNA.The length of missing intron is 60 bp,128 bp,and 78 bp respectively.2.Analysis of polymorphisms and bottleneck effects of intron loss genesIn polymorphism analysis and coalescent simulation of Bombyx mandarina and Bombyx mori,it is observed that the BGIBMGA012143 and BGIBMGA010953 genes are experienced strong positive selection in the silkworm population,while the selection power in the wild silkworm population is weak.The BGIBMGA004952 gene has been suffered purify selection in Bombyx mandarina,obeying the neutral evolution.3.Expression level comparison and functional exploration of silkworm and wild silkwormBGIBMGA012143 and BGIBMGA004952 in Bombyx mori are significantly up-regulated after loss of introns,while BGIBMGA010953 shows the opposite phenomenon.There are two types of transcripts in wild silkworm with different biases.The antedisplacement of translation initiation site takes place due to intron loss of the BGIBMGA010953 gene,which led to the loss of a ?-sheet on the secondary structure of the protein.And the function of this gene is associated with movement.We find that expression level of BGIBMGA012143 gene changes significantly after infecting by using chip data of bacteria,parasites,and insecticides infesting with silkworms,which indicate that this gene may be related to digestion and detoxification.In addition,it is found that BGIBMGA012143 and BGIBMGA004952 are closely related to the transposon.In summary,we found three intron loss genes that collectively occur in the silkworm population.The polymorphism of these genes are abundant in the process of domestication because of various degrees of selection.Changes in intron sequences not only cause differences in the expression level of RNA,but also cause dramatic influence in amino acid sequence and protein structure.That has developed the physiological function of the silkworm,making the silkworm more adapTable to the artificial breeding environment.