Characterization of the global transcriptome and microsatellite marker information for spotted halibut Verasper variegatus

Jianlong Ge; Siqing Chen; Changlin Liu; Li Bian; Huiling Sun; Jie Tan

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자료유형: 학술저널

저자정보: Jianlong Ge (Chinese Academy of Fishery Sciences) Siqing Chen (Chinese Academy of Fishery Sciences) Changlin Liu (Chinese Academy of Fishery Sciences) Li Bian (Chinese Academy of Fishery Sciences) Huiling Sun (Chinese Academy of Fishery Sciences) Jie Tan (Chinese Academy of Fishery Sciences)

저널정보: 한국유전학회 Genes & Genomics Genes & Genomics Vol.39 No.3

발행연도: 2017.1

수록면: 307 - 316 (10page)

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The spotted halibut Verasper variegatus is an economically important flatfish species distributed in Japan, Korea and China. However, the genomic resources regarding this species were scarcity, which hindered our understanding of the genetics and biological mechanisms in spotted halibut. In this study, we examined the global transcriptome from six major tissues of spotted halibut. Approximately 40 million of high quality reads were generated using Illumina paired-end sequencing technology. More than 9 Gbp data were generated, and de novo assembled into 59,235 unigenes, with an N50 of 938 bp. Based on sequence similarity search with known protein database, 34,084 (57.5%) showed significant similarity to known proteins in Nr database, and 28,875 (48.7%) had BLAST hits in Swiss-Prot database. 19,562 and 23,037 unigenes were assigned into gene ontology categories and clusters of orthologous group, respectively. 9138 unigenes were mapped to 211 KEGG pathways. For functional marker development, 13,322 candidate simple sequence repeats were identified in the transcriptome and 7235 primer pairs were successfully designed. Among 72 primer pairs selected for validation, 67 (93.1%) were successful in PCR amplification and 14 (19.4%) exhibited obvious repeat length polymorphisms in a culture spotted halibut population. The transcriptomic data and microsatellite markers will provide valuable resources for future functional gene analyses, genetic map construction, and quantitative trait loci mapping in V. variegatus.

참고문헌 (43)

참고문헌 신청

Chen S / 2006 / Study on developmental characters in early stage of spotted halibut Verasper variegatus / Period Ocean Univ China 36:281~286

Chen S / 2014 / Whole-genome sequence of a flatfish provides insights into ZW sex chromosome evolution and adaptation to a benthic lifestyle / Nat Genet 46:253~260

Chen X / 2016 / De novo assembly and characterization of foot transcriptome and microsatellite marker development for Paphia textile / Gene 576:537~543

Conesa A / 2005 / Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research / Bioinformatics 21:3674~3676

Ellis JR / 2007 / EST-SSRs as a resource for population genetic analyses / Heredity 99:125~132

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