Draft genome sequence of bitter gourd (<i>Momordica charantia</i>), a vegetable and medicinal plant in tropical and subtropical regions

Urasaki, Naoya; Takagi, Hiroki; Natsume, Satoshi; Uemura, Aiko; Taniai, Naoki; Miyagi, Norimichi; Fukushima, Mai; Suzuki, Shouta; Tarora, Kazuhiko; Tamaki, Maro; Sakamoto, Moriaki; Terauchi, Ryohei; Matsumura, Hideo

doi:10.1093/dnares/dsw047

Cited by 81 publications

(97 citation statements)

References 48 publications

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“…To provide the protein homology evidence, protein sequences from Arabidopsis, watermelon, cucumber, and melon, as well as the UniProt (Swiss-Prot plant division) database were aligned to the bottle gourd genome using Spaln (Iwata and Gotoh, 2012). The same annotation pipeline was applied to the bitter gourd genome (Urasaki et al, 2017), which predicted 20 778 protein-coding genes that were used in the comparative genomics analyses in this study.…”

Section: Protein-coding Gene Prediction and Functional Annotationmentioning

confidence: 99%

The bottle gourd genome provides insights into Cucurbitaceae evolution and facilitates mapping of a Papaya ring‐spot virus resistance locus

et al. 2017

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Bottle gourd (Lagenaria siceraria) is an important vegetable crop as well as a rootstock for other cucurbit crops. In this study, we report a high-quality 313.4-Mb genome sequence of a bottle gourd inbred line, USVL1VR-Ls, with a scaffold N50 of 8.7 Mb and the longest of 19.0 Mb. About 98.3% of the assembled scaffolds are anchored to the 11 pseudomolecules. Our comparative genomic analysis identifies chromosome-level syntenic relationships between bottle gourd and other cucurbits, as well as lineage-specific gene family expansions in bottle gourd. We reconstructed the genome of the most recent common ancestor of Cucurbitaceae, which revealed that the ancestral Cucurbitaceae karyotypes consisted of 12 protochromosomes with 18 534 protogenes. The 12 protochromosomes are largely retained in the modern melon genome, while have undergone different degrees of shuffling events in other investigated cucurbit genomes. The 11 bottle gourd chromosomes derive from the ancestral Cucurbitaceae karyotypes followed by 19 chromosomal fissions and 20 fusions. The bottle gourd genome sequence has facilitated the mapping of a dominant monogenic locus, Prs, conferring Papaya ring-spot virus (PRSV) resistance in bottle gourd, to a 317.8-kb region on chromosome 1. We have developed a cleaved amplified polymorphic sequence (CAPS) marker tightly linked to the Prs locus and demonstrated its potential application in marker-assisted selection of PRSV resistance in bottle gourd. This study provides insights into the paleohistory of Cucurbitaceae genome evolution, and the high-quality genome sequence of bottle gourd provides a useful resource for plant comparative genomics studies and cucurbit improvement.

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Section: Protein-coding Gene Prediction and Functional Annotationmentioning

confidence: 99%

The bottle gourd genome provides insights into Cucurbitaceae evolution and facilitates mapping of a Papaya ring‐spot virus resistance locus

et al. 2017

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“…Protein sequences from Arabidopsis 69 , watermelon 15 , cucumber 16 , and melon 14 and the UniProt (Swiss-Prot plant division) database were aligned to the genomes using Spaln 70 to provide the protein homology evidence. The same annotation pipeline was also applied to the bitter gourd genome 71 , which predicted 20,778 protein-coding genes that were used in the analyses in this study.…”

Section: Protein Coding Gene Prediction and Functional Annotationmentioning

confidence: 99%

Karyotype stability and unbiased fractionation in the paleo-allotetraploidCucurbitagenomes

Sun

Zhang

et al. 2017

Preprint

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The Cucurbita genus contains several economically important species in the Cucurbitaceae family. Interspecific hybrids between C. maxima and C. moschata are widely used as rootstocks for other cucurbit crops. We report high-quality genome sequences of C. maxima and C. moschata and provide evidence supporting an allotetraploidization event in Cucurbita. We are able to partition the genome into two homoeologous subgenomes based on different genetic distances to melon, cucumber and watermelon in the Benincaseae tribe. We estimate that the two diploid progenitors successively diverged from Benincaseae around 31 and 26 million years ago (Mya), and the allotetraploidization happened earlier than 3 Mya, when C. maxima and C. moschata diverged. The subgenomes have largely maintained the chromosome structures of their diploid progenitors. Such long-term karyotype stability after polyploidization is uncommon in plant polyploids. The two subgenomes have retained similar numbers of genes, and neither subgenome is globally dominant in gene expression. Allele-specific expression analysis in the C. maxima × C. moschata interspecific F1 hybrid and the two parents indicates the predominance of trans-regulatory effects underlying expression divergence of the parents, and detects transgressive gene expression changes in the hybrid correlated with heterosis in important agronomic traits. Our study provides insights into plant genome evolution and valuable resources for genetic improvement of cucurbit crops.peer-reviewed)

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“…hardwickii, was also analyzed for its genome sequencing (Qi et al 2013). Similarly, genomes of some other important crops of the Cucurbitaceae family such as Cucumis melo (melon), Citrullus lanatus (watermelon) and Momordica charantia (bitter gourd) have also been sequenced (Garcia-Mas et al 2012;Guo et al 2013;Urasaki et al 2016). Recently, genome sequences of bottle gourd (Lagenaria siceraria) and pumpkin species (Cucurbita maxima and Cucurbita moschata) became available (Wu et al 2017; http://cucurbitgenomics.org/).…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification of the Dehydrin Genes in the Cucurbitaceae Species

Lee

Ali

et al. 2017

Plant Breed. Biotech.

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This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. ABSTRACT Dehydrins (DHNs) are hydrophilic proteins with conserved lysine-rich K-segment, which belong to Group II of the late embryogenesis abundant (LEA) protein family. DHNs are considered as molecular chaperons playing important roles in abiotic stress tolerance. In this study, DHN genes were identified through genome-wide searches in five Cucurbitaceae species, including cucumber, wild cucumber, melon, watermelon, and bitter gourd. Three to five DHN genes were found in each of the five species, which were further divided into several protein architecture types based on the presence and order of the major conserved motifs such as K-, Y-, and S-segments. In silico expression profiling using RNA-Seq data revealed high expression of SK3-type DHN gene and low expression of other type DHN genes in cucumber and melon. In silico promoter analysis identified a number of cis-acting element-like sequences related to abiotic stress-response such as DRE and ABRE in 2-kb putative promoter sequences. DHN genes identified in this study will be valuable for understanding the stress response mechanism as well as assisting molecular breeding in Cucurbitaceae crops.

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Draft genome sequence of bitter gourd (Momordica charantia), a vegetable and medicinal plant in tropical and subtropical regions

Cited by 81 publications

References 48 publications

The bottle gourd genome provides insights into Cucurbitaceae evolution and facilitates mapping of a Papaya ring‐spot virus resistance locus

The bottle gourd genome provides insights into Cucurbitaceae evolution and facilitates mapping of a Papaya ring‐spot virus resistance locus

Karyotype stability and unbiased fractionation in the paleo-allotetraploidCucurbitagenomes

Genome-Wide Identification of the Dehydrin Genes in the Cucurbitaceae Species

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