Transcriptome analysis of immune response against Vibrio harveyi infection in orange-spotted grouper (Epinephelus coioides)

Shun Maekawa, Omkar Byadgi, Yao Chung Chen, Takashi Aoki, Haruko Takeyama, Terutoyo Yoshida, Jun Ichi Hikima, Masahiro Sakai, Pei Chi Wang, Shih Chu Chen

    Research output: Contribution to journalArticle

    7 Citations (Scopus)

    Abstract

    Vibrio harveyi is a gram-negative bacterium reported as found in many aquaculture species. To increase knowledge of the immune response against V. harveyi, in this study we performed transcriptome analysis of head kidney and spleen in orange-spotted grouper (Epinephelus coioides) at 1 and 2 days post-infection (dpi), using the Illumina sequencing platform. After de novo assembly, a total of 79,128 unigenes was detected with an N50 of 2511 bp. After alignments with sequences recorded in the major databases (NT, NR, Swiss-Prot COG, KEGG, Interpro and GO), based on sequence similarity, 61,208 (77.4%) of the unigene total could be annotated using at least one database. Comparison of gene expression levels between V. harveyi and a control group at each time point revealed differentially expressed genes (DEGs) (P < 0.05): a total of 7918 (5536 upregulated and 2282 downregulated genes) from head kidney at 1 day post infection (dpi), 4260 (1444 upregulated and 2816 downregulated genes) from head kidney at 2 dpi, 7887 (4892 upregulated and 2995 downregulated genes) from spleen at 1 dpi, and 8952 (7388 upregulated and 1564 downregulated genes) from spleen at 2 dpi. The DEGs were mainly annotated into signal transduction and immune system categories, based on the KEGG database. The DEGs were enriched in immune-related pathway functions, NOD-like receptor signaling pathways, Toll-like receptor signaling pathways, NF-κB signaling pathways, and Jak-STAT signaling pathways. Additionally, we selected several DEGs and validated their expression level by RT-qPCR. The data generated in this study may provide a valuable resource for further immune response research and offer improved strategies against V. harveyi infection in teleost fishes.

    Original languageEnglish
    Pages (from-to)628-637
    Number of pages10
    JournalFish and Shellfish Immunology
    Volume70
    DOIs
    Publication statusPublished - 2017 Nov 1

    Fingerprint

    Epinephelus coioides
    Vibrio harveyi
    immune response
    transcriptomics
    Genes
    gene
    infection
    genes
    unigenes
    spleen
    kidneys
    Aquaculture
    Signal transduction
    analysis
    Immune system
    Toll-Like Receptors
    immune system
    teleost
    Gram-negative bacteria
    Gene expression

    Keywords

    • Illumina paired-end sequencing
    • Immune response
    • Orange-spotted grouper (Epinephelus coioides)
    • Transcriptome
    • Vibrio harveyi

    ASJC Scopus subject areas

    • Environmental Chemistry
    • Aquatic Science

    Cite this

    Transcriptome analysis of immune response against Vibrio harveyi infection in orange-spotted grouper (Epinephelus coioides). / Maekawa, Shun; Byadgi, Omkar; Chen, Yao Chung; Aoki, Takashi; Takeyama, Haruko; Yoshida, Terutoyo; Hikima, Jun Ichi; Sakai, Masahiro; Wang, Pei Chi; Chen, Shih Chu.

    In: Fish and Shellfish Immunology, Vol. 70, 01.11.2017, p. 628-637.

    Research output: Contribution to journalArticle

    Maekawa, Shun ; Byadgi, Omkar ; Chen, Yao Chung ; Aoki, Takashi ; Takeyama, Haruko ; Yoshida, Terutoyo ; Hikima, Jun Ichi ; Sakai, Masahiro ; Wang, Pei Chi ; Chen, Shih Chu. / Transcriptome analysis of immune response against Vibrio harveyi infection in orange-spotted grouper (Epinephelus coioides). In: Fish and Shellfish Immunology. 2017 ; Vol. 70. pp. 628-637.
    @article{6549c2bee2f148b9a81165c9097a902d,
    title = "Transcriptome analysis of immune response against Vibrio harveyi infection in orange-spotted grouper (Epinephelus coioides)",
    abstract = "Vibrio harveyi is a gram-negative bacterium reported as found in many aquaculture species. To increase knowledge of the immune response against V. harveyi, in this study we performed transcriptome analysis of head kidney and spleen in orange-spotted grouper (Epinephelus coioides) at 1 and 2 days post-infection (dpi), using the Illumina sequencing platform. After de novo assembly, a total of 79,128 unigenes was detected with an N50 of 2511 bp. After alignments with sequences recorded in the major databases (NT, NR, Swiss-Prot COG, KEGG, Interpro and GO), based on sequence similarity, 61,208 (77.4{\%}) of the unigene total could be annotated using at least one database. Comparison of gene expression levels between V. harveyi and a control group at each time point revealed differentially expressed genes (DEGs) (P < 0.05): a total of 7918 (5536 upregulated and 2282 downregulated genes) from head kidney at 1 day post infection (dpi), 4260 (1444 upregulated and 2816 downregulated genes) from head kidney at 2 dpi, 7887 (4892 upregulated and 2995 downregulated genes) from spleen at 1 dpi, and 8952 (7388 upregulated and 1564 downregulated genes) from spleen at 2 dpi. The DEGs were mainly annotated into signal transduction and immune system categories, based on the KEGG database. The DEGs were enriched in immune-related pathway functions, NOD-like receptor signaling pathways, Toll-like receptor signaling pathways, NF-κB signaling pathways, and Jak-STAT signaling pathways. Additionally, we selected several DEGs and validated their expression level by RT-qPCR. The data generated in this study may provide a valuable resource for further immune response research and offer improved strategies against V. harveyi infection in teleost fishes.",
    keywords = "Illumina paired-end sequencing, Immune response, Orange-spotted grouper (Epinephelus coioides), Transcriptome, Vibrio harveyi",
    author = "Shun Maekawa and Omkar Byadgi and Chen, {Yao Chung} and Takashi Aoki and Haruko Takeyama and Terutoyo Yoshida and Hikima, {Jun Ichi} and Masahiro Sakai and Wang, {Pei Chi} and Chen, {Shih Chu}",
    year = "2017",
    month = "11",
    day = "1",
    doi = "10.1016/j.fsi.2017.09.052",
    language = "English",
    volume = "70",
    pages = "628--637",
    journal = "Fish and Shellfish Immunology",
    issn = "1050-4648",
    publisher = "Academic Press Inc.",

    }

    TY - JOUR

    T1 - Transcriptome analysis of immune response against Vibrio harveyi infection in orange-spotted grouper (Epinephelus coioides)

    AU - Maekawa, Shun

    AU - Byadgi, Omkar

    AU - Chen, Yao Chung

    AU - Aoki, Takashi

    AU - Takeyama, Haruko

    AU - Yoshida, Terutoyo

    AU - Hikima, Jun Ichi

    AU - Sakai, Masahiro

    AU - Wang, Pei Chi

    AU - Chen, Shih Chu

    PY - 2017/11/1

    Y1 - 2017/11/1

    N2 - Vibrio harveyi is a gram-negative bacterium reported as found in many aquaculture species. To increase knowledge of the immune response against V. harveyi, in this study we performed transcriptome analysis of head kidney and spleen in orange-spotted grouper (Epinephelus coioides) at 1 and 2 days post-infection (dpi), using the Illumina sequencing platform. After de novo assembly, a total of 79,128 unigenes was detected with an N50 of 2511 bp. After alignments with sequences recorded in the major databases (NT, NR, Swiss-Prot COG, KEGG, Interpro and GO), based on sequence similarity, 61,208 (77.4%) of the unigene total could be annotated using at least one database. Comparison of gene expression levels between V. harveyi and a control group at each time point revealed differentially expressed genes (DEGs) (P < 0.05): a total of 7918 (5536 upregulated and 2282 downregulated genes) from head kidney at 1 day post infection (dpi), 4260 (1444 upregulated and 2816 downregulated genes) from head kidney at 2 dpi, 7887 (4892 upregulated and 2995 downregulated genes) from spleen at 1 dpi, and 8952 (7388 upregulated and 1564 downregulated genes) from spleen at 2 dpi. The DEGs were mainly annotated into signal transduction and immune system categories, based on the KEGG database. The DEGs were enriched in immune-related pathway functions, NOD-like receptor signaling pathways, Toll-like receptor signaling pathways, NF-κB signaling pathways, and Jak-STAT signaling pathways. Additionally, we selected several DEGs and validated their expression level by RT-qPCR. The data generated in this study may provide a valuable resource for further immune response research and offer improved strategies against V. harveyi infection in teleost fishes.

    AB - Vibrio harveyi is a gram-negative bacterium reported as found in many aquaculture species. To increase knowledge of the immune response against V. harveyi, in this study we performed transcriptome analysis of head kidney and spleen in orange-spotted grouper (Epinephelus coioides) at 1 and 2 days post-infection (dpi), using the Illumina sequencing platform. After de novo assembly, a total of 79,128 unigenes was detected with an N50 of 2511 bp. After alignments with sequences recorded in the major databases (NT, NR, Swiss-Prot COG, KEGG, Interpro and GO), based on sequence similarity, 61,208 (77.4%) of the unigene total could be annotated using at least one database. Comparison of gene expression levels between V. harveyi and a control group at each time point revealed differentially expressed genes (DEGs) (P < 0.05): a total of 7918 (5536 upregulated and 2282 downregulated genes) from head kidney at 1 day post infection (dpi), 4260 (1444 upregulated and 2816 downregulated genes) from head kidney at 2 dpi, 7887 (4892 upregulated and 2995 downregulated genes) from spleen at 1 dpi, and 8952 (7388 upregulated and 1564 downregulated genes) from spleen at 2 dpi. The DEGs were mainly annotated into signal transduction and immune system categories, based on the KEGG database. The DEGs were enriched in immune-related pathway functions, NOD-like receptor signaling pathways, Toll-like receptor signaling pathways, NF-κB signaling pathways, and Jak-STAT signaling pathways. Additionally, we selected several DEGs and validated their expression level by RT-qPCR. The data generated in this study may provide a valuable resource for further immune response research and offer improved strategies against V. harveyi infection in teleost fishes.

    KW - Illumina paired-end sequencing

    KW - Immune response

    KW - Orange-spotted grouper (Epinephelus coioides)

    KW - Transcriptome

    KW - Vibrio harveyi

    UR - http://www.scopus.com/inward/record.url?scp=85029700755&partnerID=8YFLogxK

    UR - http://www.scopus.com/inward/citedby.url?scp=85029700755&partnerID=8YFLogxK

    U2 - 10.1016/j.fsi.2017.09.052

    DO - 10.1016/j.fsi.2017.09.052

    M3 - Article

    C2 - 28939531

    AN - SCOPUS:85029700755

    VL - 70

    SP - 628

    EP - 637

    JO - Fish and Shellfish Immunology

    JF - Fish and Shellfish Immunology

    SN - 1050-4648

    ER -