An improved assembly and annotation of the melon (Cucumis melo L.) reference genome
Ruggieri, Valentino (Centre de Recerca en Agrigenòmica)
Alexiou, Konstantinos G. (Institut de Recerca i Tecnologia Agroalimentàries)
Morata, Jordi (Centre de Recerca en Agrigenòmica)
Argyris, Jason (Centre de Recerca en Agrigenòmica)
Pujol Abajo, Marta (Institut de Recerca i Tecnologia Agroalimentàries)
Yano, Ryoichi (University of Tsukuba. Faculty of Life and Environmental Sciences)
Nonaka, Satoko (University of Tsukuba. Faculty of Life and Environmental Sciences)
Ezura, Hiroshi (University of Tsukuba. Faculty of Life and Environmental Sciences)
Latrasse, David (University of Evry. Institute of Plant Sciences Paris-Saclay (IPS2))
Boualem, Adnane (University of Evry. Institute of Plant Sciences Paris-Saclay (IPS2))
Benhamed, Moussa (University of Evry. Institute of Plant Sciences Paris-Saclay (IPS2))
Bendahmane, Abdelhafid (University of Evry. Institute of Plant Sciences Paris-Saclay (IPS2))
Aiese Cigliano, Riccardo (Sequentia Biotech SL)
Sanseverino, Walter (Sequentia Biotech SL)
Puigdomènech, Pere, 1948- (Centre de Recerca en Agrigenòmica)
Casacuberta i Suñer, Josep M. 1962- (Centre de Recerca en Agrigenòmica)
Garcia-Mas, Jordi (Centre de Recerca en Agrigenòmica)

Date:	2018
Abstract:	We report an improved assembly (v3. 6. 1) of the melon (Cucumis melo L. ) genome and a new genome annotation (v4. 0). The optical mapping approach allowed correcting the order and the orientation of 21 previous scaffolds and permitted to correctly define the gap-size extension along the 12 pseudomolecules. A new comprehensive annotation was also built in order to update the previous annotation v3. 5. 1, released more than six years ago. Using an integrative annotation pipeline, based on exhaustive RNA-Seq collections and ad-hoc transposable element annotation, we identified 29,980 protein-coding loci. Compared to the previous version, the v4. 0 annotation improved gene models in terms of completeness of gene structure, UTR regions definition, intron-exon junctions and reduction of fragmented genes. More than 8,000 new genes were identified, one third of them being well supported by RNA-Seq data. To make all the new resources easily exploitable and completely available for the scientific community, a redesigned Melonomics genomic platform was released at http://melonomics. net. The resources produced in this work considerably increase the reliability of the melon genome assembly and resolution of the gene models paving the way for further studies in melon and related species.
Grants:	Ministerio de Economía y Competitividad AGL2015-64625-C2-1-R Ministerio de Economía y Competitividad SEV-2015-0533 European Commission 6655919
Rights:	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.
Language:	Anglès
Document:	Article ; recerca ; Versió publicada
Published in:	Scientific reports, Vol. 8 (May 2018) , art. 8088, ISSN 2045-2322

DOI: 10.1038/s41598-018-26416-2
PMID: 29795526

9 p, 1.8 MB

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Research literature > UAB research groups literature > Research Centres and Groups (research output) > Experimental sciences > CRAG (Centre for Research in Agricultural Genomics)
Articles > Research articles
Articles > Published articles