Study Of Fish Genome Duplication Based On New Annotation

Whole-genome duplication(WGD)events have shaped the history of many evolutionary lineages.Additionally to the WGD at the base of teleost evolution,more recent genome duplications have shaped fish evolution.WGD events are well established for both salmonids and cyprinids.Compared to the known evolutionary time of other species,the study speculated that the common carp's evolution occurred later nearly 820mya(Million years ago).Within Cyprinidae,the common carp have been suggested to be tetraploid.To explore the functional differences after gene duplicates and the correlation of homologous gene expression during the evolution process,we reassembled the entire genome of the common carp.The results of the updated whole genome were evaluated by seven indicators,including the assembly genome size of 11 species,as well as the entire genome of the former carp.After comparison,the number of common carp genes decreased,the number of exons per gene and the number of introns were significantly increased.Meanwhile,according to the TreeFam,the number of genes in each family of the carp was compared with that of other species in the same gene family to determine the state of the gene.Therefore,there are 34477 genes are expansion,7250 genes are remain and only 18 genes are contraction.Thus,most of the common carp genes have been duplicated.On this basis,three types of gene GO annotation were found that the enrichment of genes in the exercise and immune pathways was more evident than in other pathways,including : swim bladder development,strialum development,exploration behavior and detection of biotic stimulus.These are all motor related functions.It is speculated that lymphangiogenesis and migration function in enrichment results are related to common carp immunity.This also proves the advantage of common carp as a species of aquaculture.The immune function makes common carp highly adaptable and easy to promote in various breeding environments.The remian genes are mainly the construction of small molecule protein and the function of signal reception,so as to maintain the basic life activity of the common carp.Finally,based on the expansion genes of the common carp,according to the same gene copy number analysis of common carp genetic number in the family is twice that number of zebrafish genes,analyze its expression,found that most of the expansion genes retain high similarity,on the functional differentiation and to show too much of a difference.The ancestor of all extant salmonids underwent a tetraploidization event,according to most recent estimations probably between 80 and 50 mya.From the 1970 ies on,it has been suspected that the salmonid-specific genome duplication event,which preceded the origin of migratory behavior,it also provides a genetic basis for evolutionary change.Besides explored heterologous genome doubling common carp,we also extended to the homologous genome doubling of rainbow trout,and study hypothesizes steelhead the fourth round of replication occurred in 96 mya,occurred late in time compared to other species,rainbow trout can be used as an ideal material of evolution.Similarly,we have reassembled the rainbow trout genome,and set the Atlantic salmon which has the fourth round duplication.According to the method of 13 species like common carp,13 indexes and exon length,exon number per gene,gene length and protein length with accumulation map to establish.Therefore,it can be seen that the whole updated genome of rainbow trout in the exon length is longer than the former rainbow trout.While,in order to explore the expression differences between rainbow trout expansion genes.With the SRA data of 15 tissues,after cleaning and pairing then aligned to the whole updated genome of rainbow trout.Extracted the FPKM value of 15914 expanded genes and the correlation coefficient were calculated.Results showed that when the correlation coefficient reaches 0.6 or so,the number of the expansion genes up to half,then prove ed that high degree of genetic correlation between expansion genes,duplicated genes didn't show clear difference in function,they expressed in the same organization at the same time.To explore the family classification and functional differences of the rainbow trout genes.The files generated by TreeFam compared the number of copies of rainbow trout genes in the family with those of other species.Divided into three types: expansion,contraction and remain with GO annotation and KEGG annotation.We found that the expansion genes of rainbow trout and the expansion genes of common carp had some common functions,and the gene function of rainbow trout mainly was: regulation of actin cytoskeleton,neuroactive ligand-receptor interaction,focal adhesion,tight junction and axon guidance,mainly related to signal pathway and cell activity.However,according to the results of KEGG pathway enrichment,most of the genes retained were related to metabolism.For example,oxidative phosphorylation,hematopoietic cell lineage,complement and coagulation cascades etc.Presumably these functions are to maintain the basic life activities of rainbow trout.Sex-related genes have always been the focus of research,and through the assembly XX chromosome related genes aligned to the rainbow trout whole genome,with the Y-specific genes to identify three part of Y-chromosome region of 158 genes.Based on the homology of the Y and W genes of mammals,we compared the rainbow trout Y genes with the W genes of the tongue sole as well as other seven mammals to infer the homology of evolution.According to the alignment results,the sex-related genes of fish and mammalian sex-related genes are significantly different,and their homology is lower.And the X/Y and the W/Z showed that the sex-related genes in fish were less differentiated in evolution than the sex-related genes in mammals.