RT Journal Article
SR Electronic
T1 <em>De-novo</em> assembly of zucchini genome reveals a whole genome duplication associated with the origin of the <em>Cucurbita</em> genus
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 147702
DO 10.1101/147702
A1 Javier Montero-Pau
A1 José Blanca
A1 Aureliano Bombarely
A1 Peio Ziarsolo
A1 Cristina Esteras
A1 Carlos Martí-Gómez
A1 María Ferriol
A1 Pedro Gómez
A1 Manuel Jamilena
A1 Lukas Mueller
A1 Belén Picó
A1 Joaquín Cañizares
YR 2017
UL http://biorxiv.org/content/early/2017/06/09/147702.abstract
AB The Cucurbita genus (squashes, pumpkins, gourds) includes important domesticated species such as C. pepo, C. maxima and C. moschata. In this study, we present a high-quality draft of the zucchini (C. pepo) genome. The assembly has a size of 263 Mb, a scaffold N50 of 1.8 Mb, 34,240 gene models, includes 92% of the conserved BUSCO core gene set, and it is estimated to cover 93.0% of the genome. The genome is organized in 20 pseudomolecules, that represent 81.4% of the assembly, and it is integrated with a genetic map of 7,718 SNPs. Despite its small genome size three independent evidences support that the C. pepo genome is the result of a Whole Genome Duplication: the topology of the gene family phylogenies, the karyotype organization, and the distribution of 4DTv distances. Additionally, 40 transcriptomes of 12 species of the genus were assembled and analyzed together with all the other published genomes of the Cucurbitaceae family. The duplication was detected in all the Cucurbita species analyzed, including C. maxima and C. moschata, but not in the more distant cucurbits belonging to the Cucumis and Citrullus genera, and it is likely to have happened 30 ± 4 Mya in the ancestral species that gave rise to the genus.