DataSheet_1_Comparative transcriptomic analysis of gill reveals genes belonging to mTORC1 signaling pathway associated with the resistance trait of shrimp to VPAHPND.docx

Selective breeding for acute hepatopancreatic necrosis disease (AHPND) resistant shrimp is an effective way to deal with heavy losses to shrimp aquaculture caused by AHPND. However, knowledge about the molecular mechanism of susceptibility or resistance to AHPND is very limited. We herein performed a comparative transcriptomic analysis of gill tissue between AHPND susceptible and resistant families of the white Pacific shrimp Litopenaeus vannamei during Vibrio parahaemolyticus (VPAHPND) infection. A total of 5,013 genes that were differentially expressed between the two families at 0 and 6 h post-infection, and 1,124 DEGs were shared for both two time points. Both GO and KEGG analyses in each or two time point’s comparisons showed DEGs involved in endocytosis, protein synthesis and cell inflammation were significantly enriched. Several immune DEGs including PRRs, antioxidants and AMPs were also identified. The susceptible shrimp showed enhanced endocytosis, higher aminoacyl-tRNA ligase activity and occurrence of inflammatory response, while the resistant shrimp had much more strong ability in ribosome biogenesis, antioxidant activity and pathogen recognition and clearance. These genes and processes were mostly associated with mTORC1 signaling pathway, which could reflect differences in cell growth, metabolism and immune response between the two families. Our findings indicate a close link between mTORC1 signaling-related genes and Vibrio-resistance phenotype of shrimp, and provide new clues for further research on resistance strategy of shrimp to AHPND.</p

Top 25 differentially expressed pathways between LI and AI shrimp.

<p>Top 25 differentially expressed pathways between LI and AI shrimp.</p

GO annotations of unigenes from the merged database of transcriptome from shrimp at LI and AI stages.

<p>Most non-redundant sequences can be divided into three major categories, including biological process (A), cellular component (B), and molecular function (C).</p

Transcriptome Analysis on Chinese Shrimp <em>Fenneropenaeus chinensis</em> during WSSV Acute Infection

<div><p>Previous studies have discovered a lot of immune-related genes responding to white spot syndrome virus (WSSV) infection in crustacean. However, little information is available in relation to underlying mechanisms of host responses during the WSSV acute infection stage in naturally infected shrimp. In this study, we employed next-generation sequencing and bioinformatic techniques to observe the transcriptome differences of the shrimp between latent infection stage and acute infection stage. A total of 64,188,426 Illumina reads, including 31,685,758 reads from the latent infection group and 32,502,668 reads from the acute infection group, were generated and assembled into 46,676 unigenes (mean length: 676 bp; range: 200–15,094 bp). Approximately 24,000 peptides were predicted and classified based on homology searches, gene ontology, clusters of orthologous groups of proteins, and biological pathway mapping. Among which, 805 differentially expressed genes were identified and categorized into 11 groups based on their possible function. Genes in the Toll and IMD pathways, the Ras-activated endocytosis process, the RNA interference pathway, anti-lipopolysaccharide factors and many other genes, were found to be activated in shrimp from latent infection stage to acute infection stage. The anti-bacterially proPO-activating cascade was firstly uncovered to be probably participated in antiviral process. These genes contain not only members playing function in host defense against WSSV, but also genes utilized by WSSV for its rapid proliferation. In addition, the transcriptome data provides detail information for identifying novel genes in absence of the genome database of shrimp.</p> </div

Multiple alignments of FcALF isoforms with ALF from other species.

<p>Sequence information were summarized in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058627#pone.0058627.s002" target="_blank">Table S2</a>. Identical amino acid residues were highlighted in dark and similar amino acids were highlighted in gray. Inserts (–) were been added to maximize sequence identity. The putative LPS-binding domain was marked in a frame.</p

DataSheet_2_Comparative transcriptomic analysis of gill reveals genes belonging to mTORC1 signaling pathway associated with the resistance trait of shrimp to VPAHPND.xlsx

Selective breeding for acute hepatopancreatic necrosis disease (AHPND) resistant shrimp is an effective way to deal with heavy losses to shrimp aquaculture caused by AHPND. However, knowledge about the molecular mechanism of susceptibility or resistance to AHPND is very limited. We herein performed a comparative transcriptomic analysis of gill tissue between AHPND susceptible and resistant families of the white Pacific shrimp Litopenaeus vannamei during Vibrio parahaemolyticus (VPAHPND) infection. A total of 5,013 genes that were differentially expressed between the two families at 0 and 6 h post-infection, and 1,124 DEGs were shared for both two time points. Both GO and KEGG analyses in each or two time point’s comparisons showed DEGs involved in endocytosis, protein synthesis and cell inflammation were significantly enriched. Several immune DEGs including PRRs, antioxidants and AMPs were also identified. The susceptible shrimp showed enhanced endocytosis, higher aminoacyl-tRNA ligase activity and occurrence of inflammatory response, while the resistant shrimp had much more strong ability in ribosome biogenesis, antioxidant activity and pathogen recognition and clearance. These genes and processes were mostly associated with mTORC1 signaling pathway, which could reflect differences in cell growth, metabolism and immune response between the two families. Our findings indicate a close link between mTORC1 signaling-related genes and Vibrio-resistance phenotype of shrimp, and provide new clues for further research on resistance strategy of shrimp to AHPND.</p

Expression patterns of FcALF isoforms in latent infection (LI) and acute infection (AI) shrimp.

<p>Data were expressed as the mean fold change (means±S.E., n  =  10). Statistical significance was calculated by Tukey multiple comparison tests and the Student’s <i>t-test</i>. Bars with different letters indicate statistical differences (<i>P</i><0.05).</p

Classification of immune-modulation differentially expressed genes (DEGs).

<p>These genes were selected from all DEGs in the transcriptome of latent infection (LI) and acute infection (AI) shrimp.</p

The neighbor-joining phylogenetic tree of FcALF isoforms and ALF homologues from other species.

<p>Sequence information were summarized in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058627#pone.0058627.s002" target="_blank">Table S2</a>. Signal peptide of each ALF was deleted when analyzed. Bootstrap analysis of 1000 replicates was carried out to determine the confidence of tree branch positions. And the numbers marked on the tree branches represent the bootstrap values.</p

Comparison of relative gene expression fold in transcriptome data and qPCR results.

<p>Comparison of relative gene expression fold in transcriptome data and qPCR results.</p