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Survey of genome sequences in a wild sweet potato, Ipomoea trifida (H. B. K.) G. Don.

Hirakawa H, Okada Y, Tabuchi H, Shirasawa K, Watanabe A, Tsuruoka H, Minami C, Nakayama S, Sasamoto S, Kohara M, Kishida Y, Fujishiro T, Kato M, Nanri K, Komaki A, Yoshinaga M, Takahata Y, Tanaka M, Tabata S, Isobe SN - DNA Res. (2015)

Bottom Line: Of the assembled sequences, 240 Mb (Mx23Hm) and 353 Mb (0431-1) were classified into core candidate sequences.A total of 62,407 (62.4 Mb) and 109,449 (87.2 Mb) putative genes were identified, respectively, in the genomes of Mx23Hm and 0431-1, of which 11,823 were derived from core sequences of Mx23Hm, while 28,831 were from the core candidate sequence of 0431-1.The results presented here are expected to contribute to the progress of genomic and genetic studies of I. trifida, as well as studies of the sweet potato and the genus Ipomoea in general.

View Article: PubMed Central - PubMed

Affiliation: Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan.

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Total lengths of core candidates and line-specific sequences of ITR_r1.0 (Mx23Hm) and ITRk_r1.0 (0431-1).
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DSV002F1: Total lengths of core candidates and line-specific sequences of ITR_r1.0 (Mx23Hm) and ITRk_r1.0 (0431-1).

Mentions: The assembled sequences were then classified into ‘core candidates' and ‘line-specific’ sequences using the LAST program. The total lengths of core candidates were 239.6 Mb (Mx23Hm) and 353.5 Mb (0431-1), whereas those of line-specific sequences were 273.4 Mb (Mx23Hm) and 358.6 Mb (0431-1) (Fig. 1 and Supplementary Table S4). In both assembled sequences, most of the N bases were classified as line-specific sequences: the N% of Mx23Hm and 0431-1 was 64.2 and 63.6%, respectively.Figure 1.


Survey of genome sequences in a wild sweet potato, Ipomoea trifida (H. B. K.) G. Don.

Hirakawa H, Okada Y, Tabuchi H, Shirasawa K, Watanabe A, Tsuruoka H, Minami C, Nakayama S, Sasamoto S, Kohara M, Kishida Y, Fujishiro T, Kato M, Nanri K, Komaki A, Yoshinaga M, Takahata Y, Tanaka M, Tabata S, Isobe SN - DNA Res. (2015)

Total lengths of core candidates and line-specific sequences of ITR_r1.0 (Mx23Hm) and ITRk_r1.0 (0431-1).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4401327&req=5

DSV002F1: Total lengths of core candidates and line-specific sequences of ITR_r1.0 (Mx23Hm) and ITRk_r1.0 (0431-1).
Mentions: The assembled sequences were then classified into ‘core candidates' and ‘line-specific’ sequences using the LAST program. The total lengths of core candidates were 239.6 Mb (Mx23Hm) and 353.5 Mb (0431-1), whereas those of line-specific sequences were 273.4 Mb (Mx23Hm) and 358.6 Mb (0431-1) (Fig. 1 and Supplementary Table S4). In both assembled sequences, most of the N bases were classified as line-specific sequences: the N% of Mx23Hm and 0431-1 was 64.2 and 63.6%, respectively.Figure 1.

Bottom Line: Of the assembled sequences, 240 Mb (Mx23Hm) and 353 Mb (0431-1) were classified into core candidate sequences.A total of 62,407 (62.4 Mb) and 109,449 (87.2 Mb) putative genes were identified, respectively, in the genomes of Mx23Hm and 0431-1, of which 11,823 were derived from core sequences of Mx23Hm, while 28,831 were from the core candidate sequence of 0431-1.The results presented here are expected to contribute to the progress of genomic and genetic studies of I. trifida, as well as studies of the sweet potato and the genus Ipomoea in general.

View Article: PubMed Central - PubMed

Affiliation: Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan.

Show MeSH
Related in: MedlinePlus