Publication:20161121154410
From Bioinformatics Core Wiki
| Publication | |
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| URL | http://www.ncbi.nlm.nih.gov/pubmed/22753475 |
| Title | The genome of melon (Cucumis melo L.)
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| Authors | Jordi Garcia-Mas, Andrej Benjak, Walter Sanseverino, Michael Bourgeois, Gisela Mir, Víctor M. González, Elizabeth Hénaff, Francisco Câmara, Luca Cozzuto, Ernesto Lowy, Tyler Alioto, Salvador Capella-Gutiérrez, Jose Blanca, Joaquín Cañizares, Pello Ziarsolo, Daniel Gonzalez-Ibeas, Luis Rodríguez-Moreno, Marcus Droege, Lei Du, Miguel Alvarez-Tejado, Belen Lorente-Galdos, Marta Melé, Luming Yang, Yiqun Weng, Arcadi Navarro, Tomas Marques-Bonet, Miguel A. Aranda, Fernando Nuez, Belén Picó, Toni Gabaldón, Guglielmo Roma, Roderic Guigó, Josep M. Casacuberta, Pere Arús, Pere Puigdomènech |
| Date | 2012-07-17
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| Publisher | Proceedings of the National Academy of Sciences of the United States of America |
| DOI | 10.1073/pnas.1205415109 |
| Tag | Base Sequence, Biological Evolution, Chromosome Mapping, Chromosomes, Artificial, Bacterial, Cucumis melo, DNA Transposable Elements, Disease Resistance, Genes, Duplicate, Genes, Plant, Genome, Plant, Genomics, Likelihood Functions, Models, Genetic, Molecular Sequence Annotation, Molecular Sequence Data, Phylogeny, Sequence Alignment, Sequence Analysis, DNA |
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.
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.
| Annotation | To decipher the melon genome, the governmental foundation Genoma España funded the project MELONOMICS, to which the BioCore contributed by predicting small non-coding RNAs and pathogen resistant genes. |
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