An improved melon reference genome with single-molecule sequencing uncovers a recent burst of transposable elements with potential impact on genes
Casacuberta, Josep M.
The published melon (Cucumis melo L.) reference genome assembly (v3.6.1) has still 41.6 Mb (Megabases) of sequences unassigned to pseudo-chromosomes and about 57 Mb of gaps. Although different approaches have been undertaken to improve the melon genome assembly in recent years, the high percentage of repeats (~40%) and limitations due to read length have made it difficult to resolve gaps and scaffold's misassignments to pseudomolecules, especially in the heterochromatic regions. Taking advantage of the PacBio single- molecule real-time (SMRT) sequencing technology, an improvement of the melon genome was achieved. About 90% of the gaps were filled and the unassigned sequences were drastically reduced. A lift-over of the latest annotation v4.0 allowed to re-collocate protein-coding genes belonging to the unassigned sequences to the pseudomolecules. A direct proof of the improvement reached in the new melon assembly was highlighted looking at the improved annotation of the transposable element fraction. By screening the new assembly, we discovered many young (inserted less than 2Mya), polymorphic LTR-retrotransposons that were not captured in the previous reference genome. These elements sit mostly in the pericentromeric regions, but some of them are inserted in the upstream region of genes suggesting that they can have regulatory potential. This improved reference genome will provide an invaluable tool for identifying new gene or transposon variants associated with important phenotypes.
633 - Cultius i produccions
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Frontiers in Plant Science
Castanera, Raúl, Valentino Ruggieri, Marta Pujol, Jordi Garcia-Mas, and Josep M. Casacuberta. 2020. "An Improved Melon Reference Genome With Single-Molecule Sequencing Uncovers A Recent Burst Of Transposable Elements With Potential Impact On Genes". Frontiers In Plant Science 10. Frontiers Media SA. doi:10.3389/fpls.2019.01815.
Grant agreement number
MINECO/Programa Estatal de I+D+I orientada a los retos de la sociedad/AGL2015-64625-C2-1-R/ES/DISECCION GENETICA DE DOS CARACTERES DE INTERES AGRONOMICO EN MELON: RESISTENCIA A CUCUMBER MOSAIC VIRUS Y MADURACION CLIMATERICA DE FRUTO/RESMELORIP
MINECO/ /SEV-2015-0533/ES/ /
MINECO-FEDER/Programa Estatal de I+D+I orientada a los retos de la Sociedad/AGL2016-78992-R/ES/INPACTO DE LOS TRANSPOSONES EN LA EVOLUCION DE LOS GENOMAS DE PLANTAS CULTIVADAS/
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