Mir G

References (2)

Title : The genome of melon (Cucumis melo L.) - Garcia-Mas_2012_Proc.Natl.Acad.Sci.U.S.A_109_11872
Author(s) : Garcia-Mas J , Benjak A , Sanseverino W , Bourgeois M , Mir G , Gonzalez VM , Henaff E , Camara F , Cozzuto L , Lowy E , Alioto T , Capella-Gutierrez S , Blanca J , Canizares J , Ziarsolo P , Gonzalez-Ibeas D , Rodriguez-Moreno L , Droege M , Du L , Alvarez-Tejado M , Lorente-Galdos B , Mele M , Yang L , Weng Y , Navarro A , Marques-Bonet T , Aranda MA , Nuez F , Pico B , Gabaldon T , Roma G , Guigo R , Casacuberta JM , Arus P , Puigdomenech P
Ref : Proc Natl Acad Sci U S A , 109 :11872 , 2012
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.
ESTHER : Garcia-Mas_2012_Proc.Natl.Acad.Sci.U.S.A_109_11872
PubMedSearch : Garcia-Mas_2012_Proc.Natl.Acad.Sci.U.S.A_109_11872
PubMedID: 22753475
Gene_locus related to this paper: cucme-a0a1s3cge4 , cucme-a0a1s3ct47 , cucme-a0a1s3bcl7 , cucsa-a0a0a0m228 , cucme-a0a1s3bnl4 , cucme-a0a1s3b1c9 , cucme-a0a1s3b1d4 , cucme-a0a1s3buy0 , cucme-a0a1s3bva9 , cucme-a0a1s3c6j4 , cucme-a0a1s3cky2 , cucme-a0a1s3clz8 , cucme-a0a1s3buy6 , cucme-a0a1s3bp26

Title : Sequencing of 6.7 Mb of the melon genome using a BAC pooling strategy - Gonzalez_2010_BMC.Plant.Biol_10_246
Author(s) : Gonzalez VM , Benjak A , Henaff EM , Mir G , Casacuberta JM , Garcia-Mas J , Puigdomenech P
Ref : BMC Plant Biol , 10 :246 , 2010
Abstract : BACKGROUND: Cucumis melo (melon) belongs to the Cucurbitaceae family, whose economic importance among horticulture crops is second only to Solanaceae. Melon has a high intra-specific genetic variation, morphologic diversity and a small genome size (454 Mb), which make it suitable for a great variety of molecular and genetic studies. A number of genetic and genomic resources have already been developed, such as several genetic maps, BAC genomic libraries, a BAC-based physical map and EST collections. Sequence information would be invaluable to complete the picture of the melon genomic landscape, furthering our understanding of this species' evolution from its relatives and providing an important genetic tool. However, to this day there is little sequence data available, only a few melon genes and genomic regions are deposited in public databases. The development of massively parallel sequencing methods allows envisaging new strategies to obtain long fragments of genomic sequence at higher speed and lower cost than previous Sanger-based methods.
RESULTS: In order to gain insight into the structure of a significant portion of the melon genome we set out to perform massive sequencing of pools of BAC clones. For this, a set of 57 BAC clones from a double haploid line was sequenced in two pools with the 454 system using both shotgun and paired-end approaches. The final assembly consists of an estimated 95% of the actual size of the melon BAC clones, with most likely complete sequences for 50 of the BACs, and a total sequence coverage of 39x. The accuracy of the assembly was assessed by comparing the previously available Sanger sequence of one of the BACs against its 454 sequence, and the polymorphisms found involved only 1.7 differences every 10,000 bp that were localized in 15 homopolymeric regions and two dinucleotide tandem repeats. Overall, the study provides approximately 6.7 Mb or 1.5% of the melon genome. The analysis of this new data has allowed us to gain further insight into characteristics of the melon genome such as gene density, average protein length, or microsatellite and transposon content. The annotation of the BAC sequences revealed a high degree of collinearity and protein sequence identity between melon and its close relative Cucumis sativus (cucumber). Transposon content analysis of the syntenic regions suggests that transposition activity after the split of both cucurbit species has been low in cucumber but very high in melon.
CONCLUSIONS: The results presented here show that the strategy followed, which combines shotgun and BAC-end sequencing together with anchored marker information, is an excellent method for sequencing specific genomic regions, especially from relatively compact genomes such as that of melon. However, in agreement with other results, this map-based, BAC approach is confirmed to be an expensive way of sequencing a whole plant genome. Our results also provide a partial description of the melon genome's structure. Namely, our analysis shows that the melon genome is highly collinear with the smaller one of cucumber, the size difference being mainly due to the expansion of intergenic regions and proliferation of transposable elements.
ESTHER : Gonzalez_2010_BMC.Plant.Biol_10_246
PubMedSearch : Gonzalez_2010_BMC.Plant.Biol_10_246
PubMedID: 21073723