Trascriptome analysis of the Paciﬁc white shrimp Litopenaeus vannamei exposed to nitrite by RNA-seq

Sep 24, 2013Fish & shellfish immunology

Gene activity changes in Pacific white shrimp exposed to nitrite

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Abstract

A total of 42,336 unigenes were generated from the transcriptome of nitrite-exposed Litopenaeus vannamei.

The average length of the unigenes was 561 bp, with a unigene N50 of 736 bp.
Out of the unigenes, 23,532 had clear alignments with reference databases.
Candidate genes linked to immune response, detoxification, and apoptosis pathways were identified.
Expressions of ten selected genes related to immune responses and apoptosis were up-regulated after nitrite exposure.
The findings suggest that these selected genes may play a role in the response to nitrite stress.

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In the present study, transcriptome of nitrite-exposed Litopenaeus vannamei was performed using a newly developed high-throughput sequencing technology (Illumina RNA-seq). As many as 42,336 unigenes were generated with 561 bp of average length and 736 bp of unigene N50 after filtering and assembly. These unigenes from the de novo assembly were further annotated using BLAST and BLAST2GO softwares. A total of 23,532 unigenes were unambiguous alignments to the reference when BLAST against non-redundant protein sequence (Nr), non-redundant nucleotide (Nt), Swiss-Prot, Gene Ontology database (GO), Clusters of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases available at NCBI. Numerous candidate genes associated with immune response, detoxification, apoptosis pathway were identified. Ten candidate genes related to immune responses and apoptosis were selected for validating the results of assembly and annotation by real-time quantitative PCR. Results revealed that the expressions of all these ten genes were up-regulated after nitrite exposure. Combining to our previous study, we speculate that all these selected genes may be involved in the response to nitrite stress. The study shows a systematic overview of the transcriptome analysis in L. vannamei, and provides valuable gene information for studying molecular mechanisms under nitrite exposure.

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Trascriptome analysis of the Paciﬁc white shrimp Litopenaeus vannamei exposed to nitrite by RNA-seq

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