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De novo RNA-Seq analysis of the venus clam, Cyclina sinensis, and the identification of immune-related genes.

Pan B, Ren Y, Gao J, Gao H - PLoS ONE (2015)

Bottom Line: In recent years, increasing expansive morbidity has occurred in breeding areas, imposing significant losses on the national economy.After trimming, more than 12 M PE reads with an average length greater than 410 bp were assembled into 70,079 transcripts with a mean length of 980 bp.Using a homology analysis, 102 (135 transcripts) potentially immune-related genes were identified, and most of them exhibited a similar pattern in both samples.

View Article: PubMed Central - PubMed

Affiliation: College of Life Sciences, Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin, P. R. China 300387.

ABSTRACT
The Venus clam, Cyclina sinensis, is one of the most important bivalves in China. In recent years, increasing expansive morbidity has occurred in breeding areas, imposing significant losses on the national economy. To understand the molecular mechanisms of immune-related genes, we analyzed and sequenced hemolymph samples that were injected with two pathogenic microorganisms using the Illumina Miseq system. After trimming, more than 12 M PE reads with an average length greater than 410 bp were assembled into 70,079 transcripts with a mean length of 980 bp. Using a homology analysis, 102 (135 transcripts) potentially immune-related genes were identified, and most of them exhibited a similar pattern in both samples. These data indicated that the response of the clam to both types of bacterial infection might follow a similar molecular mechanism. Using the TreeFam method, 9,904 gene families and 1,031 unique families of the clam were preliminarily classified in comparison to five related species. A significant number of SSRs were identified, which could facilitate the identification of polymorphisms in Venus clam populations. These datasets will improve our knowledge of the molecular mechanisms driving the immune response to bacterial infection in clam populations and will provide basic data about clam breeding and disease control.

No MeSH data available.


Related in: MedlinePlus

The expression patterns of immune-related genes in sample M and sample T of the Venus clam, Cyclina sinensis.The selected immune-related genes include alpha-2-macroglobulin(A2M), bactericidal permeability-increasing protein (BPI), cathepsin, leukocyte differentiation antigen (CD36), FAS-associated death domain protein (FADD), galectin, GNBP, interleukin-1 receptor-associated kinase (IRAK), Myd88, peptidoglycan recognition protein (PGRP), scavenger receptor cysteine-rich protein (SRCR), perforin-related protein, toll-like receptor (TLR) and tumor necrosis factor (TNF).
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pone.0123296.g002: The expression patterns of immune-related genes in sample M and sample T of the Venus clam, Cyclina sinensis.The selected immune-related genes include alpha-2-macroglobulin(A2M), bactericidal permeability-increasing protein (BPI), cathepsin, leukocyte differentiation antigen (CD36), FAS-associated death domain protein (FADD), galectin, GNBP, interleukin-1 receptor-associated kinase (IRAK), Myd88, peptidoglycan recognition protein (PGRP), scavenger receptor cysteine-rich protein (SRCR), perforin-related protein, toll-like receptor (TLR) and tumor necrosis factor (TNF).

Mentions: To understand the immune system, 102 (135 transcripts) immune-related genes were identified, including 5 (8) alpha-2-macroglobulin (A2M), 5 (6) bactericidal/permeability-increasing protein (BPI), 4 cathepsin, 2 CD36 antigens, 2 FAS-associated death domain proteins (FADD), 6 (17) galectin, 2 GNBPs, 1 interleukin-1 receptor-associated kinase (IRAK), 4 (7) Myd88, 7 (8) peptidoglycan recognition proteins (PGRP), 6 (12) scavenger receptor cysteine-rich proteins (SRCR), 26 (32) tumor necrosis factors (TNF), and 32 (34) toll-like receptors (TLR) (Fig 2 and S2 Table). In these genes, the average expression levels in M and T were 17.2 and 14.2, respectively, or approximately 1.7 and 1.4 times the average expression of the whole transcripts (the average expression of all of the transcripts in samples M and T: 9.9 and 10.0 FPKM). Most of these genes have a high expression level, with at least one gene or transcript in the gene family highly expressed (over the average expression), such as A2M, BPI, caprin, galectin, GNBP, Myd88, PGRP, SRCR, TNF, and TLR. The highest expression level (569FPKM) belonged to galectin (Unigene9462_sinensis). This finding suggests that this gene may be actively expressed in vivo, which is consistent with previous studies[8,17]. Most of the sequences have a considerable expression level in both M and T, except for 11 transcripts that are differentially expressed between M and T (Fig 2). This result suggests that the clam response to both gram-negative bacteria and gram-positive bacteria follows a similar molecular mechanism.


De novo RNA-Seq analysis of the venus clam, Cyclina sinensis, and the identification of immune-related genes.

Pan B, Ren Y, Gao J, Gao H - PLoS ONE (2015)

The expression patterns of immune-related genes in sample M and sample T of the Venus clam, Cyclina sinensis.The selected immune-related genes include alpha-2-macroglobulin(A2M), bactericidal permeability-increasing protein (BPI), cathepsin, leukocyte differentiation antigen (CD36), FAS-associated death domain protein (FADD), galectin, GNBP, interleukin-1 receptor-associated kinase (IRAK), Myd88, peptidoglycan recognition protein (PGRP), scavenger receptor cysteine-rich protein (SRCR), perforin-related protein, toll-like receptor (TLR) and tumor necrosis factor (TNF).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4390376&req=5

pone.0123296.g002: The expression patterns of immune-related genes in sample M and sample T of the Venus clam, Cyclina sinensis.The selected immune-related genes include alpha-2-macroglobulin(A2M), bactericidal permeability-increasing protein (BPI), cathepsin, leukocyte differentiation antigen (CD36), FAS-associated death domain protein (FADD), galectin, GNBP, interleukin-1 receptor-associated kinase (IRAK), Myd88, peptidoglycan recognition protein (PGRP), scavenger receptor cysteine-rich protein (SRCR), perforin-related protein, toll-like receptor (TLR) and tumor necrosis factor (TNF).
Mentions: To understand the immune system, 102 (135 transcripts) immune-related genes were identified, including 5 (8) alpha-2-macroglobulin (A2M), 5 (6) bactericidal/permeability-increasing protein (BPI), 4 cathepsin, 2 CD36 antigens, 2 FAS-associated death domain proteins (FADD), 6 (17) galectin, 2 GNBPs, 1 interleukin-1 receptor-associated kinase (IRAK), 4 (7) Myd88, 7 (8) peptidoglycan recognition proteins (PGRP), 6 (12) scavenger receptor cysteine-rich proteins (SRCR), 26 (32) tumor necrosis factors (TNF), and 32 (34) toll-like receptors (TLR) (Fig 2 and S2 Table). In these genes, the average expression levels in M and T were 17.2 and 14.2, respectively, or approximately 1.7 and 1.4 times the average expression of the whole transcripts (the average expression of all of the transcripts in samples M and T: 9.9 and 10.0 FPKM). Most of these genes have a high expression level, with at least one gene or transcript in the gene family highly expressed (over the average expression), such as A2M, BPI, caprin, galectin, GNBP, Myd88, PGRP, SRCR, TNF, and TLR. The highest expression level (569FPKM) belonged to galectin (Unigene9462_sinensis). This finding suggests that this gene may be actively expressed in vivo, which is consistent with previous studies[8,17]. Most of the sequences have a considerable expression level in both M and T, except for 11 transcripts that are differentially expressed between M and T (Fig 2). This result suggests that the clam response to both gram-negative bacteria and gram-positive bacteria follows a similar molecular mechanism.

Bottom Line: In recent years, increasing expansive morbidity has occurred in breeding areas, imposing significant losses on the national economy.After trimming, more than 12 M PE reads with an average length greater than 410 bp were assembled into 70,079 transcripts with a mean length of 980 bp.Using a homology analysis, 102 (135 transcripts) potentially immune-related genes were identified, and most of them exhibited a similar pattern in both samples.

View Article: PubMed Central - PubMed

Affiliation: College of Life Sciences, Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin, P. R. China 300387.

ABSTRACT
The Venus clam, Cyclina sinensis, is one of the most important bivalves in China. In recent years, increasing expansive morbidity has occurred in breeding areas, imposing significant losses on the national economy. To understand the molecular mechanisms of immune-related genes, we analyzed and sequenced hemolymph samples that were injected with two pathogenic microorganisms using the Illumina Miseq system. After trimming, more than 12 M PE reads with an average length greater than 410 bp were assembled into 70,079 transcripts with a mean length of 980 bp. Using a homology analysis, 102 (135 transcripts) potentially immune-related genes were identified, and most of them exhibited a similar pattern in both samples. These data indicated that the response of the clam to both types of bacterial infection might follow a similar molecular mechanism. Using the TreeFam method, 9,904 gene families and 1,031 unique families of the clam were preliminarily classified in comparison to five related species. A significant number of SSRs were identified, which could facilitate the identification of polymorphisms in Venus clam populations. These datasets will improve our knowledge of the molecular mechanisms driving the immune response to bacterial infection in clam populations and will provide basic data about clam breeding and disease control.

No MeSH data available.


Related in: MedlinePlus