Draft sequencing and analysis of the genome of pufferfish Takifugu flavidus.
Bottom Line: The combined length of repetitive sequences was 26.5 Mb, which accounted for 6.87% of the genome, indicating that the compactness of T. flavidus genome was approximative with that of T. rubripes genome.A total of 1,253 non-coding RNA genes and 30,285 protein-encoding genes were assigned to the genome.This draft genome provides a valuable resource for understanding and improving both fundamental and applied research with pufferfish in the future.
Affiliation: The Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong 266071, China University of Chinese Academy of Sciences, Shijingshan, Beijing 100049, China.Show MeSH
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Mentions: Scaffolding and gap filling were performed using the mate-pair information to interlink the contigs and cover the gaps as many as possible. As a result, 31,086 gaps from low similarity regions were successfully filled among the total 208,550 gaps (Supplementary Table S1). There were 50,947 scaffolds with the combined length of 384,451,902 bp and N50 size of 305,741 bp, which covered >95% of the whole genome (Table 1 and Supplementary Table S2). Thirty-five scaffolds were with length longer than 1 Mb, among which the longest was 2,799,124 bp. The average GC content of T. flavidus genome was 45.2% (Fig. 1), which was very close to that of T. rubripes genome (45.5%) and slightly lower than that of Tetraodon nigroviridis genome (46.3%). In addition, the GC-rich and GC-poor regions in the genome of T. flavidus were slightly less than those of T. rubripes and Tetraodon nigroviridis (Fig. 1).Figure 1.
Affiliation: The Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong 266071, China University of Chinese Academy of Sciences, Shijingshan, Beijing 100049, China.