Sequencing of 6.7 Mb of the melon genome using a BAC pooling strategy
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Autor/a
González, Víctor M
Benjak, Andrej
Hénaff, Elizabeth Marie
Casacuberta, Josep M
Puigdomènech, Pere
Fecha de publicación
2010-11-12ISSN
1471-2229
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.
Tipo de documento
Artículo
Versión del documento
Versión publicada
Lengua
English
Materias (CDU)
575 - Genética general. Citogenética general. Inmunogenética. Evolución. Filogenia
633 - Cultivos y producciones
Páginas
15
Publicado por
BMC
Publicado en
BMC Plant Biology
Citación
González, Víctor M, Andrej Benjak, Elizabeth Marie Hénaff, Gisela Mir, Josep M Casacuberta, Jordi Garcia-Mas, and Pere Puigdomènech. 2010. “Sequencing of 6.7 Mb of the Melon Genome Using a BAC Pooling Strategy.” BMC Plant Biology 10 (1): 246. doi: 10.1186/1471-2229-10-246
Número del acuerdo de la subvención
MEC/ /BIO2007-61789/ES/Ampliación del mapa fisico y aplicación al análisis de los caracteres de forma del fruto del melón (Cucumis melo)/
MEC/ /AGL2006-12780-C02-01/ES/Caracterización agronómica y con herramientas genómicas de QTLS implicados en calidad de fruto y desarrollo de herramientas basadas en el silenciamiento génico/AGR
MEC/Programa nacional de medios de transporte/CSD2007-00036/ES/Centro de Genómica Básica y de orientación Agroalimentaria/
Program
Genòmica i Biotecnologia
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