title: Survey of genome sequences in a wild sweet potato, Ipomoea trifida (H. B. K.) G. Don.
abstract: Ipomoea trifida (H. B. K.) G. Don. is the most likely diploid ancestor of the hexaploid sweet potato, I. batatas (L.) Lam. To assist in analysis of the sweet potato genome, de novo whole-genome sequencing was performed with two lines of I. trifida, namely the selfed line Mx23Hm and the highly heterozygous line 0431-1, using the Illumina HiSeq platform. We classified the sequences thus obtained as either 'core candidates' (common to the two lines) or 'line specific'. The total lengths of the assembled sequences of Mx23Hm (ITR_r1.0) was 513 Mb, while that of 0431-1 (ITRk_r1.0) was 712 Mb. 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. There were a total of 1,464,173 single-nucleotide polymorphisms and 16,682 copy number variations (CNVs) in the two assembled genomic sequences (under the condition of log2 ratio of >1 and CNV size >1,000 bases). 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.
authors: Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan.
authors: Hideki
authors: H
authors: Hirakawa
authors: Crop and Agribusiness Research Division, Kyushu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization (NARO/KARC), Itoman, Okinawa 901-0336, Japan.
authors: Yoshihiro
authors: Y
authors: Okada
authors: Upland Farming Research Division, Kyushu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization (NARO/KARC), Miyakonojo, Miyazaki 885-0091, Japan.
authors: Hiroaki
authors: H
authors: Tabuchi
authors: Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan.
authors: Kenta
authors: K
authors: Shirasawa
authors: Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan.
authors: Akiko
authors: A
authors: Watanabe
authors: Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan.
authors: Hisano
authors: H
authors: Tsuruoka
authors: Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan.
authors: Chiharu
authors: C
authors: Minami
authors: Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan.
authors: Shinobu
authors: S
authors: Nakayama
authors: Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan.
authors: Shigemi
authors: S
authors: Sasamoto
authors: Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan.
authors: Mitsuyo
authors: M
authors: Kohara
authors: Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan.
authors: Yoshie
authors: Y
authors: Kishida
authors: Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan.
authors: Tsunakazu
authors: T
authors: Fujishiro
authors: Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan.
authors: Midori
authors: M
authors: Kato
authors: Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan.
authors: Keiko
authors: K
authors: Nanri
authors: Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan.
authors: Akiko
authors: A
authors: Komaki
authors: Upland Farming Research Division, Kyushu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization (NARO/KARC), Miyakonojo, Miyazaki 885-0091, Japan.
authors: Masaru
authors: M
authors: Yoshinaga
authors: Upland Farming Research Division, Kyushu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization (NARO/KARC), Miyakonojo, Miyazaki 885-0091, Japan.
authors: Yasuhiro
authors: Y
authors: Takahata
authors: Upland Farming Research Division, Kyushu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization (NARO/KARC), Miyakonojo, Miyazaki 885-0091, Japan.
authors: Masaru
authors: M
authors: Tanaka
authors: Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan.
authors: Satoshi
authors: S
authors: Tabata
authors: Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan sisobe@kazusa.or.jp.
authors: Sachiko N
authors: SN
authors: Isobe
mesh_terms: D001483:Base Sequence; D056915:DNA Copy Number Variations; D017343:Genes, Plant; D018745:Genome, Plant; D023281:Genomics; D027741:Ipomoea / Q000235:genetics*; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA
keywords: CNVs; Ipomoea trifida; SNPs; core- and line-specific sequences; genome sequence assembly