Transcriptome sequencing and screening of genes related to muscle growth and development in Litopenaeus vannamei

【Objective】 To screen out the functional genes and metabolic regulation network of growth and development in Litopenaeus vannamei,reveal the molecular mechanism of its growth and development,and provide a valuable source of genetic data for the subsequent molecular biology research of L. vannamei.【Method】 The muscle tissue of the fast-growing group and the slow-growing group of L. vannamei was used as the research material,high-throughput sequencing analysis was performed on the cDNA library through the Illumina HiSeq^TM2500 platform,and the DESeq2 was used to screen differentially expressed genes after assembly using StringTie,and the functional annotation of differentially expressed genes was performed based on KOG,GO,nr,COG,Swiss-Pro,KEGG and Pfam databases.【Result】 A total of 53458844 Clean reads with Q30 more than 93.00% were obtained after splicing assembly. The comparison efficiency of Clean reads obtained by Illumina sequencing and the reference genome was 87.75% to 87.80%,indicating that the transcriptome sequencing data were true and reliable. SNPEff was used to annotate SNP and InDel variation,results showed that the number of 4 types of SNP loci,A>G,G>A,C>T,and T>C,was large(14950-21562),and the number of synonymous_coding points of InDel loci was the largest(33630). Using StringTie software to splice Mapped Read(Reads that were aligned to the reference genome),a total of 4607 new genes were discovered. The genes were input into COG,GO,KEGG,KOG,Pfam,Swiss-Prot,eggNOG and nr databases for sequence alignment. Finally,it was found that a total of 1098 new genes were annotated,with the largest number of new genes annotated by the nr database(1077),and the smallest number of new genes annotated by the COG database(416). Based on the screening conditions of Q-value<0.05 and Fold Change>2,a total of 1408 differential expression genes were detected,in which 661 genes were significantly upregulated and 747 genes were significantly down-regulated. A total of 1408 differentially expressed genes were annotated to 53 GO function items,in which 22 items were annotated to biological process,16 items were annotated to cellular component,15 items were annotated to molecular function. KEGG signal pathway enrichment analysis revealed three important signal pathways,namely lysosome pathway,amino sugar and nucleotide sugar metabolism pathway and sphingolipid metabolism pathway. In the lysosomal pathway,CTSL gene,Nramp gene,MyoG gene and Myf5 gene were up-regulated in the muscle tissue of fast-growing L. vannamei,while Trypsin gene was down-regulated.【Conclusion】 Through transcriptome sequencing analysis,1408 differentially expressed genes(661 are significantly up-regulated genes and 747 are significantly down-regulated genes)were screened from the muscle tissues of fast-growing and slow-growing L. vannamei,which are mainly enriched in lysosomes,sphingolipid metabolism,amino sugar and nucleotide sugar metabolism pathways. They play an important role in the growth and development of L. vannamei muscle.