The Whole Genome And Growth Related Genes Of Collichthys Lucidus (Richardson 1844) (Actinopterygii,Sciaenidae)

Collichthys lucidus is an economically important fish in China.In recent years,the artificial cultivation of C.lucidus has been on the rise in China.Up to now,most studies on this species are still in the aspect of population genetics,and there is no research on genomics.In our study,we have completed the assembly and annotation of genome of C.lucidus,and conducted evolutionary analysis with other four species of Perciformes.We have extracted genes related to the growth traits of C.lucidus,in order to provide a contribution to the artificial breeding of this species.We addressed the following issues:1.The assembly and annotation of the C.lucidus genomeIn this study,we employed next-generation high-throughput DNA sequencing to characterize whole genome sequences of C.lucidus via de novo assembly.The genome size of C.lucidus is 672 Mb(contig N50 = 12 kb;scaffolds N50 = 663 kb).Assess the quality of the assembly by mapping the reads back to the genome,98.59%of reads can be mapped to the genome.The genomic quality assessed by BUSCO was90.9%.The C.lucidus genome contains approximately 19.02% of repetitive sequences.Gene annotation was performed on C.lucidus genome based on de novo prediction and homology prediction,and 28,601 genes were obtained,average CDS length of1371,and BUSCO evaluation was 85.3%.The high degree of heterozygosity in the wild C.lucidus genome affects the quality of genome assembly,which in turn affects the quality of annotations.2.Evolutionary analysisWe did an evolutionary relationship analysis among C.lucidus,Larimichthys crocea,Larimichthys polyactis,Miichthys miiuy and Dicentrarchus labrax.We clustered gene families for five species,and got a total of 19,471 gene families.Analysis of the expansion and contraction of the gene family of C.lucidus showed that 88 gene families expanded significantly and 219 gene families contractedsignificantly.7,403 single-copy homologous gene families were identified from result of gene family analysis,and used for phylogenetic analysis and divergence time calculation of five species.Phylogenetic tree is consistent with taxonomy.The results of the divergence time analysis showed that the common ancestors of the Collichthys and Larimichthys differentiated from the ancestors of the Collichthys and the ancestor of the Larimichthys from about 67 million years to 43 million years ago.3.Growth-related genesIdentify 243 genes related to growth in single-copy homologous genes based on the functional annotation of C.lucidus,and conduct a clustering relationship study by constructing a clustering tree.Identify 6 genes that can distinguish large fish group from small fish group,which is considered to be related to the body size.This will help us to further study the genes related to the growth traits of C.lucidus.This study completed the assembly and annotation of C.lucidus genome,which can provide a reference for the follow-up study of C.lucidus.We have studied the evolutionary relationship of C.lucidus in the family of Sciaenidae,especially between C.lucidus and Larimichthys.We have searched for growth-related genes that can be used as candidate genes for genetic engineering breeding of C.lucidus.