A draft genome of the striped catfish, Pangasianodon hypophthalmus, for comparative analysis of genes relevant to development and a resource for aquaculture improvement
العنوان: | A draft genome of the striped catfish, Pangasianodon hypophthalmus, for comparative analysis of genes relevant to development and a resource for aquaculture improvement |
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المؤلفون: | Koki Nishitsuji, Hai V. Nong, Jun G. Inoue, Oanh T. P. Kim, Binh Thanh Le, Noriyuki Satoh, Kanako Hisata, Eiichi Shoguchi, Thuy Thi Bich Vo, Phuong T.M. Nguyen, Vu Dang Hoang Nguyen, Miyuki Kanda, Chuya Shinzato |
المصدر: | BMC Genomics BMC Genomics, Vol 19, Iss 1, Pp 1-16 (2018) |
بيانات النشر: | BMC, 2018. |
سنة النشر: | 2018 |
مصطلحات موضوعية: | 0301 basic medicine, cPLA2, Nuclear gene, animal structures, lcsh:QH426-470, lcsh:Biotechnology, Aquaculture, Genome, Sex-determination genes, 03 medical and health sciences, lcsh:TP248.13-248.65, Genetics, Animals, IGF, Hypothetical chromosome, Zebrafish, Hypophthalmus, Ictaluridae, Catfishes, Whole genome sequencing, biology, fungi, Molecular Sequence Annotation, Vitamin D-binding protein, Genomics, Sex Determination Processes, biology.organism_classification, Striped catfish, lcsh:Genetics, 030104 developmental biology, Draft nuclear genome, Ictalurus, Gadusol biosynthetic genes, Hox cluster, MHCI, Biotechnology, Catfish, Research Article |
الوصف: | Background The striped catfish, Pangasianodon hypophthalmus, is a freshwater and benthopelagic fish common in the Mekong River delta. Catfish constitute a valuable source of dietary protein. Therefore, they are cultured worldwide, and P. hypophthalmus is a food staple in the Mekong area. However, genetic information about the culture stock, is unavailable for breeding improvement, although genetics of the channel catfish, Ictalurus punctatus, has been reported. To acquire genome sequence data as a useful resource for marker-assisted breeding, we decoded a draft genome of P. hypophthalmus and performed comparative analyses. Results Using the Illumina platform, we obtained both nuclear and mitochondrial DNA sequences. Molecular phylogeny using the mitochondrial genome confirmed that P. hypophthalmus is a member of the family Pangasiidae and is nested within a clade including the families Cranoglanididae and Ictaluridae. The nuclear genome was estimated at approximately 700 Mb, assembled into 568 scaffolds with an N50 of 14.29 Mbp, and was estimated to contain ~ 28,600 protein-coding genes, comparable to those of channel catfish and zebrafish. Interestingly, zebrafish produce gadusol, but genes for biosynthesis of this sunscreen compound have been lost from catfish genomes. The differences in gene contents between these two catfishes were found in genes for vitamin D-binding protein and cytosolic phospholipase A2, which have lost only in channel catfish. The Hox cluster in catfish genomes comprised seven paralogous groups, similar to that of zebrafish, and comparative analysis clarified catfish lineage-specific losses of A5a, B10a, and A11a. Genes for insulin-like growth factor (IGF) signaling were conserved between the two catfish genomes. In addition to identification of MHC class I and sex determination-related gene loci, the hypothetical chromosomes by comparison with the channel catfish demonstrated the usefulness of the striped catfish genome as a marker resource. Conclusions We developed genomic resources for the striped catfish. Possible conservation of genes for development and marker candidates were confirmed by comparing the assembled genome to that of a model fish, Danio rerio, and to channel catfish. Since the catfish genomic constituent resembles that of zebrafish, it is likely that zebrafish data for gene functions is applicable to striped catfish as well. Electronic supplementary material The online version of this article (10.1186/s12864-018-5079-x) contains supplementary material, which is available to authorized users. |
اللغة: | English |
تدمد: | 1471-2164 |
URL الوصول: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::b76a2e9b9331d6f25b0d0b3c9991e933 http://id.nii.ac.jp/1394/00000838/ |
حقوق: | OPEN |
رقم الأكسشن: | edsair.doi.dedup.....b76a2e9b9331d6f25b0d0b3c9991e933 |
قاعدة البيانات: | OpenAIRE |
تدمد: | 14712164 |
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