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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

Distribution of unigenes involved in the immune system pathways.A total of 2757 unigenes were involved in the immune system.
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pone.0121015.g004: Distribution of unigenes involved in the immune system pathways.A total of 2757 unigenes were involved in the immune system.

Mentions: To evaluate the biological system of the geese, we aligned the annotated sequences to the corresponding KEGG pathways and analyzed the relationship between unigene and pathways to further understand the biological functions and gene interactions [20]. Out of 211,198 unigenes, 39,585 (18.74% of total unigenes) KEGG pathways and annotated unigenes were categorized into six biological functional groups (Table 3). A total of 39,585 unigenes had significant matches in the database and were assigned to 308 KEGG pathways. Some of unigenes were mapped to more than one pathway. Among unigenes mapped into pathways, the highest numbers of unigenes were involved in the human disease category (approximately 28.45%). Other unigenes were assigned into pathways of organismal processes (24.77%), metabolism (14.54%), cellular processes (13.35%), environmental information processing (11.7%) and genetic information processing (7.16%). The lymphocytes have pivotal functions in cell-mediate immunity: the innate (by NK cells) and adaptive (by T-cells) immune systems, as well as the antibody derived humoral (by B cells) immune response, are the main functions of lymphocyte [25]. Our present analysis show that large numbers of the unigenes lye in the immune relevant pathways. Out of the six groups listed above, human diseases and organismal systems contained the most unigenes. Within organismal systems, it is noteworthy that the immune systems group, comprised 2757 (6.96%) out of 39,585 unigenes were involved in 17 KEGG pathways (Table 3). The immune system pathways were further categorized into 15 subcategories as shown in Fig. 4. Among subcategories, the chemokine signaling pathways comprised of highest number of unigenes at 348 followed by leukocyte transendothelial migration at 244 unigenes, T-cell receptor signaling pathway at 204 unigenes, Fc gamma R-mediate phagocytosis at 202 unigenes, Toll-like receptor signaling pathway at 179 unigenes, complement and coagulation cascades at 164 unigenes, natural killer cell mediated cytotoxicity at 137 unigenes, B-cell receptor signaling pathway at 134 unigenes, Fc epsilon RI signaling pathway at 115 unigenes, hematopoietic cell lineage at 114 unigenes, RIG-I-like receptor signaling pathway at 103 unigenes, NOD-like receptor signaling pathway at 89 unigenes, cytosolic DNA-sensing pathway at 78 unigenes, antigen processing and presentation at 74 unigenes, and intestinal immune network for IgA production at 48 unigenes. Out of 2757 unigenes, 125 of the most important immunity relevant genes were identified from the goose transcriptome and are summarized in Table 4.


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)

Distribution of unigenes involved in the immune system pathways.A total of 2757 unigenes were involved in the immune system.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0121015.g004: Distribution of unigenes involved in the immune system pathways.A total of 2757 unigenes were involved in the immune system.
Mentions: To evaluate the biological system of the geese, we aligned the annotated sequences to the corresponding KEGG pathways and analyzed the relationship between unigene and pathways to further understand the biological functions and gene interactions [20]. Out of 211,198 unigenes, 39,585 (18.74% of total unigenes) KEGG pathways and annotated unigenes were categorized into six biological functional groups (Table 3). A total of 39,585 unigenes had significant matches in the database and were assigned to 308 KEGG pathways. Some of unigenes were mapped to more than one pathway. Among unigenes mapped into pathways, the highest numbers of unigenes were involved in the human disease category (approximately 28.45%). Other unigenes were assigned into pathways of organismal processes (24.77%), metabolism (14.54%), cellular processes (13.35%), environmental information processing (11.7%) and genetic information processing (7.16%). The lymphocytes have pivotal functions in cell-mediate immunity: the innate (by NK cells) and adaptive (by T-cells) immune systems, as well as the antibody derived humoral (by B cells) immune response, are the main functions of lymphocyte [25]. Our present analysis show that large numbers of the unigenes lye in the immune relevant pathways. Out of the six groups listed above, human diseases and organismal systems contained the most unigenes. Within organismal systems, it is noteworthy that the immune systems group, comprised 2757 (6.96%) out of 39,585 unigenes were involved in 17 KEGG pathways (Table 3). The immune system pathways were further categorized into 15 subcategories as shown in Fig. 4. Among subcategories, the chemokine signaling pathways comprised of highest number of unigenes at 348 followed by leukocyte transendothelial migration at 244 unigenes, T-cell receptor signaling pathway at 204 unigenes, Fc gamma R-mediate phagocytosis at 202 unigenes, Toll-like receptor signaling pathway at 179 unigenes, complement and coagulation cascades at 164 unigenes, natural killer cell mediated cytotoxicity at 137 unigenes, B-cell receptor signaling pathway at 134 unigenes, Fc epsilon RI signaling pathway at 115 unigenes, hematopoietic cell lineage at 114 unigenes, RIG-I-like receptor signaling pathway at 103 unigenes, NOD-like receptor signaling pathway at 89 unigenes, cytosolic DNA-sensing pathway at 78 unigenes, antigen processing and presentation at 74 unigenes, and intestinal immune network for IgA production at 48 unigenes. Out of 2757 unigenes, 125 of the most important immunity relevant genes were identified from the goose transcriptome and are summarized in Table 4.

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