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KMID : 0381120170390030307
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Genes and Genomics
2017 Volume.39 No. 3 p.307 ~ p.316
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Characterization of the global transcriptome and microsatellite marker information for spotted halibut Verasper variegatus
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Ge Jianlong
Chen Siqing
Liu Changlin
Bian Li
Sun Huiling
Tan Jie
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Abstract
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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.
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KEYWORD
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Verasper variegatus, Illumina sequencing, Transcriptome analysis, SSR markers
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