Sequencing of 6.7 Mb of the melon genome using a BAC pooling strategy
González Miguel, Víctor Manuel (Centre de Recerca en Agrigenòmica)
Benjak, Andrej (Centre de Recerca en Agrigenòmica)
Hénaff, Elizabeth (Centre de Recerca en Agrigenòmica)
Mir, Gisela (Centre de Recerca en Agrigenòmica)
Casacuberta i Suñer, Josep M. 1962- (Centre de Recerca en Agrigenòmica)
Garcia-Mas, Jordi (Centre de Recerca en Agrigenòmica)
Puigdomènech, Pere, 1948- (Centre de Recerca en Agrigenòmica)

Fecha:	2010
Resumen:	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.
Ayudas:	Ministerio de Economía y Competitividad BIO2007-61789 Ministerio de Ciencia y Tecnología AGL2006-12780-C02-01 Ministerio de Ciencia e Innovación CSD2007-00036
Derechos:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Lengua:	Anglès
Documento:	Article ; recerca ; Versió publicada
Publicado en:	BMC plant biology, Vol. 10 Núm. 246 (novembre 2010) , p. 1-15, ISSN 1471-2229

DOI: 10.1186/1471-2229-10-246
PMID: 21073723

15 p, 788.7 KB

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