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Draft sequencing and analysis of the genome of pufferfish Takifugu flavidus.

Gao Y, Gao Q, Zhang H, Wang L, Zhang F, Yang C, Song L - DNA Res. (2014)

Bottom Line: There were 132,775 and 394 presumptive genes playing roles in the colour pattern variation, the relatively slow growth and the lipid metabolism, respectively.Among them, genes involved in the microtubule-dependent transport system, angiogenesis, decapentaplegic pathway and lipid mobilization were significantly expanded in the T. flavidus genome.This draft genome provides a valuable resource for understanding and improving both fundamental and applied research with pufferfish in the future.

View Article: PubMed Central - PubMed

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.

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The GC contents of the T. flavidus genome. The size of sliding window was 500 bp. The horizontal axis was the percentage of GC in the windows, whereas the vertical axis showed the frequency of windows. The GC contents of genomes of T. rubripes and Tetraodon nigroviridis were shown for comparison. This figure appears in colour in the online version of DNA Research.
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DSU025F1: The GC contents of the T. flavidus genome. The size of sliding window was 500 bp. The horizontal axis was the percentage of GC in the windows, whereas the vertical axis showed the frequency of windows. The GC contents of genomes of T. rubripes and Tetraodon nigroviridis were shown for comparison. This figure appears in colour in the online version of DNA Research.

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.


Draft sequencing and analysis of the genome of pufferfish Takifugu flavidus.

Gao Y, Gao Q, Zhang H, Wang L, Zhang F, Yang C, Song L - DNA Res. (2014)

The GC contents of the T. flavidus genome. The size of sliding window was 500 bp. The horizontal axis was the percentage of GC in the windows, whereas the vertical axis showed the frequency of windows. The GC contents of genomes of T. rubripes and Tetraodon nigroviridis were shown for comparison. This figure appears in colour in the online version of DNA Research.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4263296&req=5

DSU025F1: The GC contents of the T. flavidus genome. The size of sliding window was 500 bp. The horizontal axis was the percentage of GC in the windows, whereas the vertical axis showed the frequency of windows. The GC contents of genomes of T. rubripes and Tetraodon nigroviridis were shown for comparison. This figure appears in colour in the online version of DNA Research.
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.

Bottom Line: There were 132,775 and 394 presumptive genes playing roles in the colour pattern variation, the relatively slow growth and the lipid metabolism, respectively.Among them, genes involved in the microtubule-dependent transport system, angiogenesis, decapentaplegic pathway and lipid mobilization were significantly expanded in the T. flavidus genome.This draft genome provides a valuable resource for understanding and improving both fundamental and applied research with pufferfish in the future.

View Article: PubMed Central - PubMed

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