Transcriptome Analysis of juvenile Pacific White Shrimp (Litopenaeus vannamei) with symptom of stunted growth

In search for viruses associated with Litopenaeus vannamei with symptom of stunted growth, we have undertaken a comparative transcriptome analysis of total RNA sequences using Illumina based high-throughput sequencing (HTS). We obtain 89000242 and 95126160 high-quality clean reads from cDNA libraries of L.vannamei with stunted growth symptom (sick group) and health shrimp (health group control), respectively. Totally, 108221 unigenes with an average length of 716 bp were obtained from RNA-seq data. The unigenes were annotated against NR, NT, KO, KOG, SwissProt, PFAM and GO databases. 3975 (3.67%) showed significant matches in all the above databases and 39812 (36.78%) unigenes were annotated in at least one database. Comparative transcriptomic analysis revealed that 807 significantly differentially expressed unigenes were identified, including 282 down-regulated genes and 525 up-regulated genes. Thirteen up-regulated virus-related genes were only discovered in the sick shrimp groups, but not in health ones. Five of them were closely related to virus family Picornaviridae. From phylogenetic tree, we could find five viral genes were closely related to genus Ampvirus, Falcovirus, Aquamavirus (Seal picornavirus). Some up-regulated genes in the Sick groups mainly included genes involved in virus infecting processes concerning antigen processing and presenting, apoptosis, lysosome, phagosome and inflammation. While, many down-regulated genes in the Sick groups mainly involved in the process of starch and sucrose metabolism, and protein digestion and absorption. Our research provided some useful information about pathogenic factor and mechanism on the stunted growth symptom of L.vannamei, and was significant for the control and prevention of this disease.