Comparative Genomic Analysis Of Larimichthys Polyactis And L.crocea In Growth-related Traits

The small yel ow croaker(Larimichthys polyactis)is an important commercia l marine fish of East China Sea.As the development and popularization of HighThroughput Sequencing technology and the decline in sequencing cost,we employed the Next Generation Sequencing(NGS)technology to screen the preliminary genome of small yel ow croaker.The comparative genomics analysis of two yel ow croakers(L.polyactis and Larimichthys crocea),we extract the positive selection genes related to immunization in the genome of yellow croakers,which provided a new idea to solve the problems arising in large yel ow croaker breeding.The main result are as follows: 1.Small yel ow croaker genome assemblyIn this study,we sequenced a wild small yel ow croaker which captured from the East China Sea,obtained 141 x coverage DNA sequence data.The small yel ow croaker genome has high hybridity or high repetition.At the initial stage of assembly,a variety of genome assembly software were compared to get the best assembly strategy at the same time.Finally,the genome of 649 Mb was obtained by Platanus.We find that a total of 99.28% of short read fragments can be remapped to the small yel ow croaker genome.The N50 values of Contig and Scaffold are 3,761 bp and 40,284 bp,respectively.As the result of the initial assembly,the quality of the small yel ow croaker genome assembly is not good enough,based on the N50 value.And there is a problem of sequence fragmentation.The repetitive elements and gene annotation of small yel ow croaker were carried out with ab initio and database based homologous prediction analysis strategy.The repetitive elements comprise 19.03% of the small yel ow croaker genome,which is close to the repetitive elements in the genome of the large yel ow croaker.Using homologous protein comparison prediction and ab initio prediction method,5,3726 genes were annotated in the genome of small yel ow croaker,and the number of genes was much higher than that of normal diploid fish genome.We think it is because the fragmentation of genome assembly result which leads to the gene sequence was divided into several segments by artificial,multiple signal sites of a gene were detected by the ab initio prediction method,leading to ab initio prediction gene number substantia l increasing.Finaly,the result of the combination of EVM gene sets deviates from the normal number of genes.2.Comparative genomic analysis between two croakers(L.polyactis and L.crocea)The collinear analysis based on whole genome fasta sequence alignment shows that those two croaker genome possesses good linearity.This conclusion was proved by phylogenetic tree constructed by four bony fishes(L.crocea,L.polyactis,O.latipes and X.maculatus),L.crocea and L.polyactis are clustered on one branch.The comparison of the protein coding sequences of two croakers found that they shared 13,575 genes.3.Growth related genesWe studied the genes that were positively selected in the genome of L.crocea and L.polyactis,and compared the Ka/Ks values by introducing an outgroup fish,the Atlantic cod(Gadus morhua).It was found that 784 genes in large yel ow croaker were selected,and 759 genes in small yel ow croaker were selected.There were a large number of fin morphogenesis,bone morphogenesis and growth related genes under positive selection in L.polyactis.We think those genes might cause the disproportionation of growth traits among two yellow croakers,the growth traits of small yel ow croaker is under strong natural selection,the large yel ow croaker shall more closely related to their common ancestor.We found that a large number of conserved immune genes existed in the genome of small yel ow croaker.