Dataset Information

The genome of melon (Cucumis melo L.).

ABSTRACT: We report the genome sequence of melon, an important horticultural crop worldwide. We assembled 375 Mb of the double-haploid line DHL92, representing 83.3% of the estimated melon genome. We predicted 27,427 protein-coding genes, which we analyzed by reconstructing 22,218 phylogenetic trees, allowing mapping of the orthology and paralogy relationships of sequenced plant genomes. We observed the absence of recent whole-genome duplications in the melon lineage since the ancient eudicot triplication, and our data suggest that transposon amplification may in part explain the increased size of the melon genome compared with the close relative cucumber. A low number of nucleotide-binding site-leucine-rich repeat disease resistance genes were annotated, suggesting the existence of specific defense mechanisms in this species. The DHL92 genome was compared with that of its parental lines allowing the quantification of sequence variability in the species. The use of the genome sequence in future investigations will facilitate the understanding of evolution of cucurbits and the improvement of breeding strategies.

SUBMITTER: Garcia-Mas J

PROVIDER: S-EPMC3406823 | biostudies-literature | 2012 Jul

REPOSITORIES: biostudies-literature

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The genome of melon (Cucumis melo L.).

Garcia-Mas Jordi J Benjak Andrej A Sanseverino Walter W Bourgeois Michael M Mir Gisela G González Víctor M VM Hénaff Elizabeth E Câmara Francisco F Cozzuto Luca L Lowy Ernesto E Alioto Tyler T Capella-Gutiérrez Salvador S Blanca Jose J Cañizares Joaquín J Ziarsolo Pello P Gonzalez-Ibeas Daniel D Rodríguez-Moreno Luis L Droege Marcus M Du Lei L Alvarez-Tejado Miguel M Lorente-Galdos Belen B Melé Marta M Yang Luming L Weng Yiqun Y Navarro Arcadi A Marques-Bonet Tomas T Aranda Miguel A MA Nuez Fernando F Picó Belén B Gabaldón Toni T Roma Guglielmo G Guigó Roderic R Casacuberta Josep M JM Arús Pere P Puigdomènech Pere P

Proceedings of the National Academy of Sciences of the United States of America 20120702 29

We report the genome sequence of melon, an important horticultural crop worldwide. We assembled 375 Mb of the double-haploid line DHL92, representing 83.3% of the estimated melon genome. We predicted 27,427 protein-coding genes, which we analyzed by reconstructing 22,218 phylogenetic trees, allowing mapping of the orthology and paralogy relationships of sequenced plant genomes. We observed the absence of recent whole-genome duplications in the melon lineage since the ancient eudicot triplication ...[more]

PMID: 22753475

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Project description:BackgroundThe genome of the melon (Cucumis melo L.) double-haploid line DHL92 was recently sequenced, with 87.5 and 80.8% of the scaffold assembly anchored and oriented to the 12 linkage groups, respectively. However, insufficient marker coverage and a lack of recombination left several large, gene rich scaffolds unanchored, and some anchored scaffolds unoriented. To improve the anchoring and orientation of the melon genome assembly, we used resequencing data between the parental lines of DHL92 to develop a new set of SNP markers from unanchored scaffolds.ResultsA high-resolution genetic map composed of 580 SNPs was used to anchor 354.8 Mb of sequence, contained in 141 scaffolds (average size 2.5 Mb) and corresponding to 98.2% of the scaffold assembly, to the 12 melon chromosomes. Over 325.4 Mb (90%) of the assembly was oriented. The genetic map revealed regions of segregation distortion favoring SC alleles as well as recombination suppression regions coinciding with putative centromere, 45S, and 5S rDNA sites. New chromosome-scale pseudomolecules were created by incorporating to the previous v3.5 version an additional 38.3 Mb of anchored sequence representing 1,837 predicted genes contained in 55 scaffolds. Using fluorescent in situ hybridization (FISH) with BACs that produced chromosome-specific signals, melon chromosomes that correspond to the twelve linkage groups were identified, and a standardized karyotype of melon inbred line T111 was developed.ConclusionsBy utilizing resequencing data and targeted SNP selection combined with a large F2 mapping population, we significantly improved the quantity of anchored and oriented melon scaffold genome assembly. Using genome information combined with FISH mapping provided the first cytogenetic map of an inodorus melon type. With these results it was possible to make inferences on melon chromosome structure by relating zones of recombination suppression to centromeres and 45S and 5S heterochromatic regions. This study represents the first steps towards the integration of the high-resolution genetic and cytogenetic maps with the genomic sequence in melon that will provide more information on genome organization and allow for the improvement of the melon genome draft sequence.

Dataset Information

The genome of melon (Cucumis melo L.).

Publications

The genome of melon (Cucumis melo L.).

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