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

Tariq M, Chen R, Yuan H, Liu Y, Wu Y, Wang J, Xia C - PLoS ONE (2015)

Bottom Line: Moreover, 10 genes were confirmed by PCR and analyzed.Of these 125 unigenes, 109 unigenes, approximately 87%, were not previously identified in the goose.This 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, The People's Republic of China; Department of Veterinary Pathology, Faculty of Animal Husbandry and Veterinary Sciences, Sindh Agriculture University, Tando Jam, Sindh, Pakistan.

ABSTRACT

Background: The 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.

Conclusion: This 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.

No MeSH data available.


Related in: MedlinePlus

Histogram presentation of eukaryotic cluster of orthologous groups (KOG) classification.A total of 15,334 sequences were annotated into 25 KOG categories.
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pone.0121015.g002: Histogram presentation of eukaryotic cluster of orthologous groups (KOG) classification.A total of 15,334 sequences were annotated into 25 KOG categories.

Mentions: The rapid assembly of genome sequences is a major challenge to researchers attempting to extract the maximum functional and evolutionary information from the genome data. The NCBI eukaryotic orthologous groups (KOGs) include sequences from 7 eukaryotic genomes [24]. To further evaluate the transcriptome library, the accuracy of our annotation sequences in the KOG functional classification was examined. All unigenes were aligned to the KOG database for prediction and classification into different functional categories. There were 15,334 unigenes annotated into 25 KOG categories (Fig. 2). The largest group was signal transduction mechanism at 5787 (2.74%) followed by the general function prediction only at 2792 (1.32%), posttranslational modification, protein turnover, chaperones at 2168 (1.02%), and cytoskeleton at 1876 (0.88%). Nuclear structure 75 (0.03%) and cell motility 45 (0.02%) were the KOG categories with the least represented unigenes.


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

Tariq M, Chen R, Yuan H, Liu Y, Wu Y, Wang J, Xia C - PLoS ONE (2015)

Histogram presentation of eukaryotic cluster of orthologous groups (KOG) classification.A total of 15,334 sequences were annotated into 25 KOG categories.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4376690&req=5

pone.0121015.g002: Histogram presentation of eukaryotic cluster of orthologous groups (KOG) classification.A total of 15,334 sequences were annotated into 25 KOG categories.
Mentions: The rapid assembly of genome sequences is a major challenge to researchers attempting to extract the maximum functional and evolutionary information from the genome data. The NCBI eukaryotic orthologous groups (KOGs) include sequences from 7 eukaryotic genomes [24]. To further evaluate the transcriptome library, the accuracy of our annotation sequences in the KOG functional classification was examined. All unigenes were aligned to the KOG database for prediction and classification into different functional categories. There were 15,334 unigenes annotated into 25 KOG categories (Fig. 2). The largest group was signal transduction mechanism at 5787 (2.74%) followed by the general function prediction only at 2792 (1.32%), posttranslational modification, protein turnover, chaperones at 2168 (1.02%), and cytoskeleton at 1876 (0.88%). Nuclear structure 75 (0.03%) and cell motility 45 (0.02%) were the KOG categories with the least represented unigenes.

Bottom Line: Moreover, 10 genes were confirmed by PCR and analyzed.Of these 125 unigenes, 109 unigenes, approximately 87%, were not previously identified in the goose.This 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, The People's Republic of China; Department of Veterinary Pathology, Faculty of Animal Husbandry and Veterinary Sciences, Sindh Agriculture University, Tando Jam, Sindh, Pakistan.

ABSTRACT

Background: The 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.

Conclusion: This 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.

No MeSH data available.


Related in: MedlinePlus