Analysis Of Sox Gene Family Structure And Expression Pattern Of Yellow River Carp

Sox(Sry-related HMG-box)gene family is a family of transcription factors with high sequence similarity to the conservative region of mammalian testicular determinant gene--Sry,which plays a key role in biological processes such as sex determination and differentiation.In teleost fishes,many species have experienced one or more genome doubling,resulting in a large number of Sox genes in fish,which is a good material for studying the origin and functional differentiation of gene families.As a famous and high-quality aquatic economic breed in Henan Province,the Yellow River carp has great economic value.It is recognized that its genome has been doubled many times and is a diploid tetraploid.A comprehensive analysis of the structure and function of its Sox gene is helpful to understand the evolution and functional variation of gene families in polyploid fish.In this study,using carp genome data and multiple tissue transcripts data as materials,the number,gene structure,chromosome location,evolution and function of CcSox gene family members were systematically identified and analyzed by bioinformatics methods.At the same time,the expression pattern of CcSox gene in different tissues and the molecular mechanism of nano silver stress were studied.The main results are as follows:1.A total of 39 Sox genes were identified in the carp genome,distributed on different chromosomes or sequence skeletons.According to the conserved motifs of their amino acid sequence and phylogenetic relationship,39 members of the CcSox family were subdivided into 7 subfamilies.Members of different CcSox subfamilies showed different gene structures,but the exon-intron structures between the same subfamilies were conservative.Protein characteristic analysis showed that the amino acid sequence length of CcSox proteins were 238-733 aa,and the range of isoelectric point were 4.98-9.82,all of which were hydrophilic nucleoproteins.2.The results of gene replication analysis showed that six pairs of replication genes were found in the CcSox gene family,namely Sox1b-1/Sox1b-2,Sox4a-1/Sox4a-3,Sox12-1/Sox12-2,Sox14-1/Sox14-2,Sox19a-1/Sox19a-2 and Sox32-1/Sox32-2.Combined with their position on the chromosome,it was inferred that they were all repetitive genes caused by genome polyploidy or chromosome fragment replication.The results of environmental stress analysis showed that 6 pairs of repetitive genes' Ka/Ks < 1,these genes experienced purification and selection after replication,and their functions did not undergo serious differentiation.3.Tissue expression pattern analysis showed that the expression level of CcSox gene varied greatly in different tissues,but all of them were significantly expressed in the brain,except CcSox19 b and CcSox30,which were mainly expressed in ovary and testis,respectively.4.Because the growth rate of females is much faster than that of males,much attention has been paid to the mechanism of sex determination and differentiation of Yellow River carp.Because of the close relationship between B1 subfamily genes and sex differentiation,we analyzed the CcSoxB1 subfamily genes in detail according to the transcriptome sequence data of our laboratory.The six genes of this subfamily in carp are CcSox1a/b,CcSox2,CcSox3 and CcSox19a/b,respectively.The first four genes have no intron,and the last two genes have one intron.The construction of an unrooted phylogenetic tree showed that these six genes were highly homologous to the genes of Sox B1 in other species.Chromosome synteny analysis indicated that the gene arrangement around CcSox3 and CcSox19 a were highly conserved in fish.However,immense change in genomic sequences around the other CcSoxB1 genes had taken place.Numerous essential transcription factor binding sites(TFs)were predicted within the 3000 bp upstream of these genes.These TFs include FOXD3,FOXJ2,Oct1 and so on,which have been shown to involved in the regulation of the nervous system,inhibition of tumor and melanogenesis in vertebrates.Analysis of tissue expression pattern showed that Sox B1 genes were abundant in the brain and with sexual dimorphism.These results indicated that CcSoxB1 plays an important role in the development of the nervous system and may be involved in sexual development.These results provide new information for further studies on the potential functions of Sox B1 genes in carp.5.Due to its unique small size effect,nano silver can easily enter the body and become a potential endocrine regulator.While causing tissue damage,it will also affect the expression and regulation of related genes.Different concentrations of nano silver were used to treat juvenile fish aged 3 to 4 months,and we detected the expression changes of CcSoxB1 genes in different tissues.The results showed that as the treatment concentration increased,the expression levels of CcSoxB1 subfamily genes changed in different tissues,in which CcSox2 decreased significantly in the brain,and the expression levels of other genes in the brain increased at first and then decreased.These results indirectly prove that Sox B1 subfamily genes play an important role in the process of gonadal differentiation and nervous system development.6.The high-throughput sequencing was used to analyze the transcriptome of brain,testis and ovary of juvenile Yellow River carp under nano silver stress in order to reveal the possible molecular mechanism.The clean data of 64.12 Gb was obtained by sequencing,Q30 > 93.5%,and the average GC content was48.07%.The comprehensive analysis of GO function and KEGG pathway enrichment showed that DEGs in different comparison groups was the most involved in molecular function,followed by biological processes,and the least in cellular components.At the same time,they were involved in hormone secretion,signal transduction,immune response,and amino acid metabolism pathways.Significant enrichment indicates that the Yellow River carp under AgNP stress can regulate the relevant physiological and biochemical metabolic pathways by changing the signal transmission process.In this paper,the identification,structure and evolution of Sox gene in the genome of Yellow River carp were analyzed systematically for the first time.The results enriched people's understanding of carp Sox genes,and provided a useful attempt to comprehensively study a gene family in the joint analysis of genome data and transcriptome data in the omics era.The research provided some reference for the study of the mechanism of AgNP on nerve and sex determination in bony fish.