title: Draft genome sequence of bitter gourd (Momordica charantia), a vegetable and medicinal plant in tropical and subtropical regions.
abstract: Bitter gourd (Momordica charantia) is an important vegetable and medicinal plant in tropical and subtropical regions globally. In this study, the draft genome sequence of a monoecious bitter gourd inbred line, OHB3-1, was analyzed. Through Illumina sequencing and de novo assembly, scaffolds of 285.5 Mb in length were generated, corresponding to ∼84% of the estimated genome size of bitter gourd (339 Mb). In this draft genome sequence, 45,859 protein-coding gene loci were identified, and transposable elements accounted for 15.3% of the whole genome. According to synteny mapping and phylogenetic analysis of conserved genes, bitter gourd was more related to watermelon (Citrullus lanatus) than to cucumber (Cucumis sativus) or melon (C. melo). Using RAD-seq analysis, 1507 marker loci were genotyped in an F2 progeny of two bitter gourd lines, resulting in an improved linkage map, comprising 11 linkage groups. By anchoring RAD tag markers, 255 scaffolds were assigned to the linkage map. Comparative analysis of genome sequences and predicted genes determined that putative trypsin-inhibitor and ribosome-inactivating genes were distinctive in the bitter gourd genome. These genes could characterize the bitter gourd as a medicinal plant.
authors.affiliation: Okinawa Prefectural Agricultural Research Center, Itoman, Okinawa 901-0336, Japan.
authors.forename: Naoya
authors.initials: N
authors.lastname: Urasaki
authors.affiliation: Iwate Biotechnology Research Center, Kitakami, Iwate 024-0003, Japan.
authors.forename: Hiroki
authors.initials: H
authors.lastname: Takagi
authors.affiliation: Iwate Biotechnology Research Center, Kitakami, Iwate 024-0003, Japan.
authors.forename: Satoshi
authors.initials: S
authors.lastname: Natsume
authors.affiliation: Iwate Biotechnology Research Center, Kitakami, Iwate 024-0003, Japan.
authors.forename: Aiko
authors.initials: A
authors.lastname: Uemura
authors.affiliation: Okinawa Prefectural Agricultural Research Center, Itoman, Okinawa 901-0336, Japan.
authors.forename: Naoki
authors.initials: N
authors.lastname: Taniai
authors.affiliation: Okinawa Prefectural Agricultural Research Center, Itoman, Okinawa 901-0336, Japan.
authors.forename: Norimichi
authors.initials: N
authors.lastname: Miyagi
authors.affiliation: Shinshu university, Ueda, Nagano 386-8567, Japan.
authors.forename: Mai
authors.initials: M
authors.lastname: Fukushima
authors.affiliation: Shinshu university, Ueda, Nagano 386-8567, Japan.
authors.forename: Shouta
authors.initials: S
authors.lastname: Suzuki
authors.affiliation: Okinawa Prefectural Agricultural Research Center, Itoman, Okinawa 901-0336, Japan.
authors.forename: Kazuhiko
authors.initials: K
authors.lastname: Tarora
authors.affiliation: Okinawa Prefectural Agricultural Research Center, Itoman, Okinawa 901-0336, Japan.
authors.forename: Moritoshi
authors.initials: M
authors.lastname: Tamaki
authors.affiliation: Okinawa Prefectural Agricultural Research Center, Itoman, Okinawa 901-0336, Japan.
authors.forename: Moriaki
authors.initials: M
authors.lastname: Sakamoto
authors.affiliation: Iwate Biotechnology Research Center, Kitakami, Iwate 024-0003, Japan.
authors.forename: Ryohei
authors.initials: R
authors.lastname: Terauchi
authors.affiliation: Shinshu university, Ueda, Nagano 386-8567, Japan.
authors.forename: Hideo
authors.initials: H
authors.lastname: Matsumura
mesh_terms: D004251:DNA Transposable Elements; D018745:Genome, Plant; D029777:Momordica charantia / Q000235:genetics*; D010802:Phylogeny; D010946:Plants, Medicinal / Q000235:genetics*; D054788:Ribosome Inactivating Proteins / Q000235:genetics; D014329:Tropical Climate; D014361:Trypsin Inhibitors / Q000378:metabolism
chemical_list: D004251:DNA Transposable Elements; D014361:Trypsin Inhibitors; D054788:Ribosome Inactivating Proteins
keywords: Cucurbitaceae; Momordica charantia; bitter gourd; de novo sequencing; draft genome