De novo transcriptomic analysis of peripheral blood lymphocytes from the Chinese goose: gene discovery and immune system pathway description.

Mansoor Tariq,Yanjie Liu,Rong Chen,Hongyu Yuan,Chun Xia,Junya Wang,Yanan Wu,Xiao Su

doi:10.1371/journal.pone.0121015

Mansoor Tariq, Yanjie Liu + Show 6 more

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https://doi.org/10.1371/journal.pone.0121015

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Abstract

BackgroundThe Chinese goose is one of the most economically important poultry birds and is a natural reservoir for many avian viruses. However, the nature and regulation of the innate and adaptive immune systems of this waterfowl species are not completely understood due to limited information on the goose genome. Recently, transcriptome sequencing technology was applied in the genomic studies focused on novel gene discovery. Thus, this study described the transcriptome of the goose peripheral blood lymphocytes to identify immunity relevant genes.Principal Findings De novo transcriptome assembly of the goose peripheral blood lymphocytes was sequenced by Illumina-Solexa technology. In total, 211,198 unigenes were assembled from the 69.36 million cleaned reads. The average length, N50 size and the maximum length of the assembled unigenes were 687 bp, 1,298 bp and 18,992 bp, respectively. A total of 36,854 unigenes showed similarity by BLAST search against the NCBI non-redundant (Nr) protein database. For functional classification, 163,161 unigenes were comprised of three Gene Ontology (Go) categories and 67 subcategories. A total of 15,334 unigenes were annotated into 25 eukaryotic orthologous groups (KOGs) categories. Kyoto Encyclopedia of Genes and Genomes (KEGG) database annotated 39,585 unigenes into six biological functional groups and 308 pathways. Among the 2,757 unigenes that participated in the 15 immune system KEGG pathways, 125 of the most important immune relevant genes were summarized and analyzed by STRING analysis to identify gene interactions and relationships. Moreover, 10 genes were confirmed by PCR and analyzed. Of these 125 unigenes, 109 unigenes, approximately 87%, were not previously identified in the goose.ConclusionThis de novo transcriptome analysis could provide important Chinese goose sequence information and highlights the value of new gene discovery, pathways investigation and immune system gene identification, and comparison with other avian species as useful tools to understand the goose immune system.

Highlights

Genomic evaluations are the source of important evidence for determining the immune system characteristics that differ between the goose, chicken, duck, and other birds
Through the functional annotation of the assembled sequences and identification of the sequenced unigenes, our study identified important novel immune genes related to antigen processing and presentation, toll like receptor signaling pathways, complement cascades, natural killer cell-mediated cytotoxicity response, and inflammatory response by chemokines and cytokine-mediated signaling pathways in the goose
A cDNA library of goose peripheral blood lymphocytes was sequenced using Illumina-Solexa sequencing technology

Summary

Introduction

Genomic evaluations are the source of important evidence for determining the immune system characteristics that differ between the goose, chicken, duck, and other birds. Only a few research studies have examined the goose species and their relevant genes; some of the genes, including, CD8α [6], CD4 [4], interleukin(IL)-17A [7], IL-6 [8], Toll like receptor (TLR) 5 [9], MHCI/II [5,10], interferon(IFN)-γ [11], IFN-α [12] and IL-2 [13] were cloned. Despite these studies, many genes related to the goose immune system remain unknown. This study described the transcriptome of the goose peripheral blood lymphocytes to identify immunity relevant genes

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Conclusion