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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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Related in: MedlinePlus

CNV distributions and corresponding positions of core candidates and line-specific sequences of scaffold Itr_sc000048.1 (1,177,009 bases in length). Red dots show the log2 ratios of CNVs between Mx23Hm and 0431-1. The upper bar represents core candidate (red) and line-specific (blue) sequences in their corresponding positions.
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DSV002F3: CNV distributions and corresponding positions of core candidates and line-specific sequences of scaffold Itr_sc000048.1 (1,177,009 bases in length). Red dots show the log2 ratios of CNVs between Mx23Hm and 0431-1. The upper bar represents core candidate (red) and line-specific (blue) sequences in their corresponding positions.

Mentions: CNVs in the genomes of Mx23Hm and 0431-1 were detected using the CNV-seq program. CNVs between Mx23Hm and 0431-1 longer than 50 kb in length were identified on 2,095 scaffolds. The numbers of detected CNVs varied in accordance with the threshold values of the log2 ratio (log-transformed ratio of the number of mapped reads in 0431-1 to the number in Mx23Hm) and CNV sizes. For example, 54 CNVs with a mean length of 12,444 bases were identified under the stringent condition (log2 ratio >10 and CNV size >10,000 bases) (Supplementary Fig. S9). Under a more relaxed condition (i.e. log2 ratio of >1 and CNV size >1,000 bases), 16,682 CNVs with a mean length of 1,918 bases were detected. Under both stringent and relaxed conditions, the CNVs occupied 671,974 bases (0.3%) and 44,892,563 bases (18.8%), respectively, of the total length of the 2,095 contigs (239,146,348 bases). The mean absolute values of log2 ratios in the core candidate and line-specific sequences were 0.63 and 1.72, respectively, indicating that CNVs were significantly enriched in the line-specific regions relative to the core candidate regions of the genomes (P < 0.001) (Fig. 3; Supplementary Fig. S10).Figure 3.


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)

CNV distributions and corresponding positions of core candidates and line-specific sequences of scaffold Itr_sc000048.1 (1,177,009 bases in length). Red dots show the log2 ratios of CNVs between Mx23Hm and 0431-1. The upper bar represents core candidate (red) and line-specific (blue) sequences in their corresponding positions.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4401327&req=5

DSV002F3: CNV distributions and corresponding positions of core candidates and line-specific sequences of scaffold Itr_sc000048.1 (1,177,009 bases in length). Red dots show the log2 ratios of CNVs between Mx23Hm and 0431-1. The upper bar represents core candidate (red) and line-specific (blue) sequences in their corresponding positions.
Mentions: CNVs in the genomes of Mx23Hm and 0431-1 were detected using the CNV-seq program. CNVs between Mx23Hm and 0431-1 longer than 50 kb in length were identified on 2,095 scaffolds. The numbers of detected CNVs varied in accordance with the threshold values of the log2 ratio (log-transformed ratio of the number of mapped reads in 0431-1 to the number in Mx23Hm) and CNV sizes. For example, 54 CNVs with a mean length of 12,444 bases were identified under the stringent condition (log2 ratio >10 and CNV size >10,000 bases) (Supplementary Fig. S9). Under a more relaxed condition (i.e. log2 ratio of >1 and CNV size >1,000 bases), 16,682 CNVs with a mean length of 1,918 bases were detected. Under both stringent and relaxed conditions, the CNVs occupied 671,974 bases (0.3%) and 44,892,563 bases (18.8%), respectively, of the total length of the 2,095 contigs (239,146,348 bases). The mean absolute values of log2 ratios in the core candidate and line-specific sequences were 0.63 and 1.72, respectively, indicating that CNVs were significantly enriched in the line-specific regions relative to the core candidate regions of the genomes (P < 0.001) (Fig. 3; Supplementary Fig. S10).Figure 3.

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