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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

Summary of the gene family classification of four related species, Cyclina sinensis, Crassostrea gigas, Lottia gigantea and Capitella teleta.Only putative peptides were used in Cyclina sinensis, while whole peptides were used in the other species.
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pone.0123296.g003: Summary of the gene family classification of four related species, Cyclina sinensis, Crassostrea gigas, Lottia gigantea and Capitella teleta.Only putative peptides were used in Cyclina sinensis, while whole peptides were used in the other species.

Mentions: Using TreeFam and the pipeline described in the methods, we obtained 9,904 gene families and 1,031 unique families from C. sinensis and the five reference genomes. The common and unique gene families among C.sinensis, Crassostrea gigas, Lottia gigantea and Capitella teleta are summarized in Fig 3. The results revealed that, compared with other species, C. gigas shared the most gene families (6,643/67.07%) with C. sinensis. Based on the gene family analysis, a significant percentage of transcripts (56.21% / 14,173) in the clam were found to not be from a conserved lineage, which might be due to the presence of novel families. Alternatively, the assembled transcripts may be from non-conserved protein areas where homology or assembly errors are not detected, which is in agreement with several other papers [31,33–34]. The result of the KEGG enrichment is summarized in S4 Table. Interestingly, two signaling molecules and interactions (ECM-receptor interaction, neuroactive ligand-receptor interaction) and three translation pathways (RNA transport, mRNA surveillance pathway, and ribosome biogenesis in eukaryotes) were enriched, which suggests that a large amount of antibody proteins were biosynthesized after macro-organism infection. Additionally, two carbohydrate metabolism pathways (starch and sucrose metabolism, galactose metabolism) may provide a large amount of energy at this stage, which is supported by previous research.


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)

Summary of the gene family classification of four related species, Cyclina sinensis, Crassostrea gigas, Lottia gigantea and Capitella teleta.Only putative peptides were used in Cyclina sinensis, while whole peptides were used in the other species.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0123296.g003: Summary of the gene family classification of four related species, Cyclina sinensis, Crassostrea gigas, Lottia gigantea and Capitella teleta.Only putative peptides were used in Cyclina sinensis, while whole peptides were used in the other species.
Mentions: Using TreeFam and the pipeline described in the methods, we obtained 9,904 gene families and 1,031 unique families from C. sinensis and the five reference genomes. The common and unique gene families among C.sinensis, Crassostrea gigas, Lottia gigantea and Capitella teleta are summarized in Fig 3. The results revealed that, compared with other species, C. gigas shared the most gene families (6,643/67.07%) with C. sinensis. Based on the gene family analysis, a significant percentage of transcripts (56.21% / 14,173) in the clam were found to not be from a conserved lineage, which might be due to the presence of novel families. Alternatively, the assembled transcripts may be from non-conserved protein areas where homology or assembly errors are not detected, which is in agreement with several other papers [31,33–34]. The result of the KEGG enrichment is summarized in S4 Table. Interestingly, two signaling molecules and interactions (ECM-receptor interaction, neuroactive ligand-receptor interaction) and three translation pathways (RNA transport, mRNA surveillance pathway, and ribosome biogenesis in eukaryotes) were enriched, which suggests that a large amount of antibody proteins were biosynthesized after macro-organism infection. Additionally, two carbohydrate metabolism pathways (starch and sucrose metabolism, galactose metabolism) may provide a large amount of energy at this stage, which is supported by previous research.

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