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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

Size distribution of the transcripts and CDSs of the Venus clam, Cyclina sinensis.The blue and red bars indicate transcripts and CDS, respectively.
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pone.0123296.g001: Size distribution of the transcripts and CDSs of the Venus clam, Cyclina sinensis.The blue and red bars indicate transcripts and CDS, respectively.

Mentions: The clean reads from samples T and M were pooled for de novo assembly using Trinity [17]. Finally, a total of 70,079 transcripts longer than 250 bp were generated with a mean length of 980 bp and an N50 of 1,670 bp (Table 1). This assembly produced a substantial number of large transcripts: 36,355 transcripts (51.88%) longer than 500 bp, 19,496 transcripts (27.82%) longer than 1,000 bp and 8,455 transcripts (12.65%) longer than 2,000 bp (Fig 1). Using the BWA aligner, 87.49% (in M) and 86.79% (in T) of the reads were realigned to the transcripts, and the transcript coverage was positively related to the length of the given transcripts. The average coverage of all of the transcripts was 75-fold.


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)

Size distribution of the transcripts and CDSs of the Venus clam, Cyclina sinensis.The blue and red bars indicate transcripts and CDS, respectively.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0123296.g001: Size distribution of the transcripts and CDSs of the Venus clam, Cyclina sinensis.The blue and red bars indicate transcripts and CDS, respectively.
Mentions: The clean reads from samples T and M were pooled for de novo assembly using Trinity [17]. Finally, a total of 70,079 transcripts longer than 250 bp were generated with a mean length of 980 bp and an N50 of 1,670 bp (Table 1). This assembly produced a substantial number of large transcripts: 36,355 transcripts (51.88%) longer than 500 bp, 19,496 transcripts (27.82%) longer than 1,000 bp and 8,455 transcripts (12.65%) longer than 2,000 bp (Fig 1). Using the BWA aligner, 87.49% (in M) and 86.79% (in T) of the reads were realigned to the transcripts, and the transcript coverage was positively related to the length of the given transcripts. The average coverage of all of the transcripts was 75-fold.

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