Limits...
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

GO categories and 2 fold expressed transcripts.(A) Histogram presentation of GO classification showed transcripts in numbers after annotated in three categories: cellular components, molecular functions, biological processes. (B) Venn diagram shows 2-fold expression of transcripts in H. discus hannai transcriptome in tissue specific manner. The numbers shown in brackets represent the nucleotide sequences available in GenBank.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4835058&req=5

pone.0153474.g002: GO categories and 2 fold expressed transcripts.(A) Histogram presentation of GO classification showed transcripts in numbers after annotated in three categories: cellular components, molecular functions, biological processes. (B) Venn diagram shows 2-fold expression of transcripts in H. discus hannai transcriptome in tissue specific manner. The numbers shown in brackets represent the nucleotide sequences available in GenBank.

Mentions: To provide putative annotations for the reference transcripts, sequence was annotated using Blast2GO as explained in the method section. A total of 43,843 (45%) unigenes were identified from 97,828 consensus sequences of H. discus hannai. Among these, 23,560 (24%) unigenes belong to three categories of Gene Ontology (GO), and 3,337 (3%) to 7 categories of KEGG (Table 1). In annotations, the lengthy transcripts were contributed more rather than the short transcripts (Fig 1A) and mostly genes/sequences from Lottia gigantea (43%) and Crassostrea gigas (24%) were mapped to H. discus hannai transcripts (Fig 1B). Other bivalve species in the BLASTX top-hit were Capitella teleta (3%), Branchiostoma floridae (3%) and Stronglylocentrotus purpuratus (3%). H. discus hannai (<1%) itself fell in the least position of the top-hit species distribution. This may be explained by the limited number of H. discus hannai proteins that currently available at NCBI database. The rest of the low number of matches indicates a lack of bivalve data in public databases. GO analysis of our dataset showed that among 97,828 assembled unigenes, 22,971 of them were successfully annotated by GO assignments to one or more of the three categories: biological process, cellular component and molecular function (Fig 2A), which fell further into 23, 13 and 12 subcategories with the largest ones being the ‘‘cellular process”, ‘‘cell” and ‘‘binding”, respectively.


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)

GO categories and 2 fold expressed transcripts.(A) Histogram presentation of GO classification showed transcripts in numbers after annotated in three categories: cellular components, molecular functions, biological processes. (B) Venn diagram shows 2-fold expression of transcripts in H. discus hannai transcriptome in tissue specific manner. The numbers shown in brackets represent the nucleotide sequences available in GenBank.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0153474.g002: GO categories and 2 fold expressed transcripts.(A) Histogram presentation of GO classification showed transcripts in numbers after annotated in three categories: cellular components, molecular functions, biological processes. (B) Venn diagram shows 2-fold expression of transcripts in H. discus hannai transcriptome in tissue specific manner. The numbers shown in brackets represent the nucleotide sequences available in GenBank.
Mentions: To provide putative annotations for the reference transcripts, sequence was annotated using Blast2GO as explained in the method section. A total of 43,843 (45%) unigenes were identified from 97,828 consensus sequences of H. discus hannai. Among these, 23,560 (24%) unigenes belong to three categories of Gene Ontology (GO), and 3,337 (3%) to 7 categories of KEGG (Table 1). In annotations, the lengthy transcripts were contributed more rather than the short transcripts (Fig 1A) and mostly genes/sequences from Lottia gigantea (43%) and Crassostrea gigas (24%) were mapped to H. discus hannai transcripts (Fig 1B). Other bivalve species in the BLASTX top-hit were Capitella teleta (3%), Branchiostoma floridae (3%) and Stronglylocentrotus purpuratus (3%). H. discus hannai (<1%) itself fell in the least position of the top-hit species distribution. This may be explained by the limited number of H. discus hannai proteins that currently available at NCBI database. The rest of the low number of matches indicates a lack of bivalve data in public databases. GO analysis of our dataset showed that among 97,828 assembled unigenes, 22,971 of them were successfully annotated by GO assignments to one or more of the three categories: biological process, cellular component and molecular function (Fig 2A), which fell further into 23, 13 and 12 subcategories with the largest ones being the ‘‘cellular process”, ‘‘cell” and ‘‘binding”, respectively.

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