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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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Venn diagram showing the numbers of gene clusters in Ipomoea trifida and other plant species, i.e. Arabidopsis thaliana, potato (Solanum tuberosum), and cassava (Manihot esculenta). The black and white numbers in parenthesis represent the numbers of non-clustered sequences and sequences clustered with other species, respectively. The green, purple, orange, aqua, and red numbers in parenthesis represent the total numbers of putative genes subjected to clustering.
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DSV002F2: Venn diagram showing the numbers of gene clusters in Ipomoea trifida and other plant species, i.e. Arabidopsis thaliana, potato (Solanum tuberosum), and cassava (Manihot esculenta). The black and white numbers in parenthesis represent the numbers of non-clustered sequences and sequences clustered with other species, respectively. The green, purple, orange, aqua, and red numbers in parenthesis represent the total numbers of putative genes subjected to clustering.

Mentions: The intrinsic and partial genes were subjected to clustering with a total of 57,354 predicted genes containing 35,386 genes in A. thaliana as a dicot model and 56,218 genes in potato and 34,151 genes in cassava as tuber crops by similarity searches using the CD-hit program. Of the putative I. trifida genes, 15,184 (Mx23Hm) and 26,243 (0431-1) could be clustered with predicted genes identified in other species, whereas the remaining 5,849 (Mx23Hm) and 15,020 (0431-1) were not clustered and therefore considered as I. trifida-specific genes (Fig. 2; Supplementary Tables S14 and S15).Figure 2.


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)

Venn diagram showing the numbers of gene clusters in Ipomoea trifida and other plant species, i.e. Arabidopsis thaliana, potato (Solanum tuberosum), and cassava (Manihot esculenta). The black and white numbers in parenthesis represent the numbers of non-clustered sequences and sequences clustered with other species, respectively. The green, purple, orange, aqua, and red numbers in parenthesis represent the total numbers of putative genes subjected to clustering.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

DSV002F2: Venn diagram showing the numbers of gene clusters in Ipomoea trifida and other plant species, i.e. Arabidopsis thaliana, potato (Solanum tuberosum), and cassava (Manihot esculenta). The black and white numbers in parenthesis represent the numbers of non-clustered sequences and sequences clustered with other species, respectively. The green, purple, orange, aqua, and red numbers in parenthesis represent the total numbers of putative genes subjected to clustering.
Mentions: The intrinsic and partial genes were subjected to clustering with a total of 57,354 predicted genes containing 35,386 genes in A. thaliana as a dicot model and 56,218 genes in potato and 34,151 genes in cassava as tuber crops by similarity searches using the CD-hit program. Of the putative I. trifida genes, 15,184 (Mx23Hm) and 26,243 (0431-1) could be clustered with predicted genes identified in other species, whereas the remaining 5,849 (Mx23Hm) and 15,020 (0431-1) were not clustered and therefore considered as I. trifida-specific genes (Fig. 2; Supplementary Tables S14 and S15).Figure 2.

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