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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

Phylogenetic tree showing the evolutionary relationship of the Venus clam, Cyclina sinensis, to four closely related species (C. gigas, C. teleta, L. gigantea, H. robusta), based on RNA-seq data.The out group was S. purpuratus. Single copy gene families (1,343 genes comprising 873,976 peptide sites) were concatenated and used in the program PhyML with default parameters.
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pone.0123296.g004: Phylogenetic tree showing the evolutionary relationship of the Venus clam, Cyclina sinensis, to four closely related species (C. gigas, C. teleta, L. gigantea, H. robusta), based on RNA-seq data.The out group was S. purpuratus. Single copy gene families (1,343 genes comprising 873,976 peptide sites) were concatenated and used in the program PhyML with default parameters.

Mentions: To understand the evolutionary relationship between C. sinensis and other marine animals, a set of 1,343 single copy gene families were obtained by the TreeFam method and were concatenated into a super-peptide (873,976 peptide sites) for constructing a phylogenetic tree using PhyML; S. purpuratus was used as the out group (Fig 4). C. sinensis and C. gigas belong to Bivalvia, and L. gigantea are from Mollusca. C. teleta and H. robusta are Annelida, and all five belong to Lophotrochozoa. Our tree is consistent with current classification. Molecular evidence is considered more effective for taxonomic classification in comparison with other existing methods. The transcriptome data and mitochondrial genome for phylogeny and orthology analysis have become increasingly popular[35–37]. In particular, certain taxons, such as arthropods, echinoderms, tetrapods and snakes, possess radical transformations, both morphologically and physiologically [38].


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)

Phylogenetic tree showing the evolutionary relationship of the Venus clam, Cyclina sinensis, to four closely related species (C. gigas, C. teleta, L. gigantea, H. robusta), based on RNA-seq data.The out group was S. purpuratus. Single copy gene families (1,343 genes comprising 873,976 peptide sites) were concatenated and used in the program PhyML with default parameters.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0123296.g004: Phylogenetic tree showing the evolutionary relationship of the Venus clam, Cyclina sinensis, to four closely related species (C. gigas, C. teleta, L. gigantea, H. robusta), based on RNA-seq data.The out group was S. purpuratus. Single copy gene families (1,343 genes comprising 873,976 peptide sites) were concatenated and used in the program PhyML with default parameters.
Mentions: To understand the evolutionary relationship between C. sinensis and other marine animals, a set of 1,343 single copy gene families were obtained by the TreeFam method and were concatenated into a super-peptide (873,976 peptide sites) for constructing a phylogenetic tree using PhyML; S. purpuratus was used as the out group (Fig 4). C. sinensis and C. gigas belong to Bivalvia, and L. gigantea are from Mollusca. C. teleta and H. robusta are Annelida, and all five belong to Lophotrochozoa. Our tree is consistent with current classification. Molecular evidence is considered more effective for taxonomic classification in comparison with other existing methods. The transcriptome data and mitochondrial genome for phylogeny and orthology analysis have become increasingly popular[35–37]. In particular, certain taxons, such as arthropods, echinoderms, tetrapods and snakes, possess radical transformations, both morphologically and physiologically [38].

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