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Transcriptome Analysis Revealed Changes of Multiple Genes Involved in Haliotis discus hannai Innate Immunity during Vibrio parahemolyticus Infection.

Nam BH, Jung M, Subramaniyam S, Yoo SI, Markkandan K, Moon JY, Kim YO, Kim DG, An CM, Shin Y, Jung HJ, Park JH - PLoS ONE (2016)

Bottom Line: A total of 10,575 transcripts exhibiting the differentially expression at least one pair of comparison and the functional annotations highlight genes related to immune response, cell adhesion, immune regulators, redox molecules and mitochondrial coding genes.Mostly, these groups of genes were dominated in hemocytes compared to other tissues.This work is a prerequisite for the identification of those physiological traits controlling H. discus hannai ability to survive against Vibrio infection.

View Article: PubMed Central - PubMed

Affiliation: Biotechnology Research Division, Aquaculture Industry Department, National Fisheries Research and Development Institute, Busan 619-902, Republic of Korea.

ABSTRACT
Abalone (Haliotis discus hannai) is one of the most valuable marine aquatic species in Korea, Japan and China. Tremendous exposure to bacterial infection is common in aquaculture environment, especially by Vibrio sp. infections. It's therefore necessary and urgent to understand the mechanism of H. discus hannai host defense against Vibrio parahemolyticus infection. However studies on its immune system are hindered by the lack of genomic resources. In the present study, we sequenced the transcriptome of control and bacterial challenged H. discus hannai tissues. Totally, 138 MB of reference transcriptome were obtained from de novo assembly of 34 GB clean bases from ten different libraries and annotated with the biological terms (GO and KEGG). A total of 10,575 transcripts exhibiting the differentially expression at least one pair of comparison and the functional annotations highlight genes related to immune response, cell adhesion, immune regulators, redox molecules and mitochondrial coding genes. Mostly, these groups of genes were dominated in hemocytes compared to other tissues. This work is a prerequisite for the identification of those physiological traits controlling H. discus hannai ability to survive against Vibrio infection.

No MeSH data available.


Related in: MedlinePlus

Assembly and annotation summary of H. discus hannai transcriptome.(A) Comparison of transcript length before and after annotation (B) Species distribution of transcript BLASTX results against the nr protein database. Different colors represent different species. Species with proportions of more than 1% are shown.
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pone.0153474.g001: Assembly and annotation summary of H. discus hannai transcriptome.(A) Comparison of transcript length before and after annotation (B) Species distribution of transcript BLASTX results against the nr protein database. Different colors represent different species. Species with proportions of more than 1% are shown.

Mentions: To obtain more detailed information of H. discus hannai transcriptome, adult abalones (6-8cm shell length) were collected and cDNA was transcribed from total RNA followed by cDNA library sequencing with Illumina HiSeq™ 2000 system to obtain as many transcripts as possible. Sequencing of cDNA libraries generated a total of 361,633,550 transcriptomic reads with a length of 36,524,988,550 nucleotides (nt), corresponding to 96% of clean reads. Files containing these data were deposited in the Sequence Read Archive of the National Center for Biotechnology Information (NCBI) with the accession number of SRP059307. Because there is no assembled and annotated Haliotis genomic sequences, Trinity de novo assembler (Grabherr et al. 2011) was used to assemble all the trimmed reads with optimized Kmer length of 25. The high-quality clean reads were assembled into 97,828 non-redundant unigenes ranging from 500bp to 29,122 bp with an average length of approximately 1,416 bp with a threshold level of ≥500 bp were obtained. The number of unigenes longer than 500 bp is another measure used to compare transcriptome assembly. Among these unigenes, 25,674 unigenes (26.2%) were no more than 700 bp in length, 11,275 unigenes (11.5%) were in the length range of 900 to 1,100bp, and 13,857 unigenes (17.1%) were longer than 2,000 bp. The detailed length distribution of the transcripts is shown in Fig 1A, and a summary of sequencing and assembly results are presented in Table 1.


Transcriptome Analysis Revealed Changes of Multiple Genes Involved in Haliotis discus hannai Innate Immunity during Vibrio parahemolyticus Infection.

Nam BH, Jung M, Subramaniyam S, Yoo SI, Markkandan K, Moon JY, Kim YO, Kim DG, An CM, Shin Y, Jung HJ, Park JH - PLoS ONE (2016)

Assembly and annotation summary of H. discus hannai transcriptome.(A) Comparison of transcript length before and after annotation (B) Species distribution of transcript BLASTX results against the nr protein database. Different colors represent different species. Species with proportions of more than 1% are shown.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4835058&req=5

pone.0153474.g001: Assembly and annotation summary of H. discus hannai transcriptome.(A) Comparison of transcript length before and after annotation (B) Species distribution of transcript BLASTX results against the nr protein database. Different colors represent different species. Species with proportions of more than 1% are shown.
Mentions: To obtain more detailed information of H. discus hannai transcriptome, adult abalones (6-8cm shell length) were collected and cDNA was transcribed from total RNA followed by cDNA library sequencing with Illumina HiSeq™ 2000 system to obtain as many transcripts as possible. Sequencing of cDNA libraries generated a total of 361,633,550 transcriptomic reads with a length of 36,524,988,550 nucleotides (nt), corresponding to 96% of clean reads. Files containing these data were deposited in the Sequence Read Archive of the National Center for Biotechnology Information (NCBI) with the accession number of SRP059307. Because there is no assembled and annotated Haliotis genomic sequences, Trinity de novo assembler (Grabherr et al. 2011) was used to assemble all the trimmed reads with optimized Kmer length of 25. The high-quality clean reads were assembled into 97,828 non-redundant unigenes ranging from 500bp to 29,122 bp with an average length of approximately 1,416 bp with a threshold level of ≥500 bp were obtained. The number of unigenes longer than 500 bp is another measure used to compare transcriptome assembly. Among these unigenes, 25,674 unigenes (26.2%) were no more than 700 bp in length, 11,275 unigenes (11.5%) were in the length range of 900 to 1,100bp, and 13,857 unigenes (17.1%) were longer than 2,000 bp. The detailed length distribution of the transcripts is shown in Fig 1A, and a summary of sequencing and assembly results are presented in Table 1.

Bottom Line: A total of 10,575 transcripts exhibiting the differentially expression at least one pair of comparison and the functional annotations highlight genes related to immune response, cell adhesion, immune regulators, redox molecules and mitochondrial coding genes.Mostly, these groups of genes were dominated in hemocytes compared to other tissues.This work is a prerequisite for the identification of those physiological traits controlling H. discus hannai ability to survive against Vibrio infection.

View Article: PubMed Central - PubMed

Affiliation: Biotechnology Research Division, Aquaculture Industry Department, National Fisheries Research and Development Institute, Busan 619-902, Republic of Korea.

ABSTRACT
Abalone (Haliotis discus hannai) is one of the most valuable marine aquatic species in Korea, Japan and China. Tremendous exposure to bacterial infection is common in aquaculture environment, especially by Vibrio sp. infections. It's therefore necessary and urgent to understand the mechanism of H. discus hannai host defense against Vibrio parahemolyticus infection. However studies on its immune system are hindered by the lack of genomic resources. In the present study, we sequenced the transcriptome of control and bacterial challenged H. discus hannai tissues. Totally, 138 MB of reference transcriptome were obtained from de novo assembly of 34 GB clean bases from ten different libraries and annotated with the biological terms (GO and KEGG). A total of 10,575 transcripts exhibiting the differentially expression at least one pair of comparison and the functional annotations highlight genes related to immune response, cell adhesion, immune regulators, redox molecules and mitochondrial coding genes. Mostly, these groups of genes were dominated in hemocytes compared to other tissues. This work is a prerequisite for the identification of those physiological traits controlling H. discus hannai ability to survive against Vibrio infection.

No MeSH data available.


Related in: MedlinePlus