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Sci Rep. 2018 May 24;8(1):8088. doi: 10.1038/s41598-018-26416-2.

An improved assembly and annotation of the melon (Cucumis melo L.) reference genome.

Author information

1
Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Barcelona, 08193, Spain.
2
IRTA (Institut de Recerca i Tecnologia Agroalimentàries), Barcelona, 08193, Spain.
3
Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan.
4
Institute of Plant Sciences Paris-Saclay (IPS2), INRA, CNRS, University of Paris-Sud, University of Evry, University Paris-Diderot, Sorbone Paris-Cite, University of Paris-Saclay, Orsay, 91192, France.
5
Sequentia Biotech SL, Barcelona, 08193, Spain.
6
Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Barcelona, 08193, Spain. jordi.garcia@irta.cat.
7
IRTA (Institut de Recerca i Tecnologia Agroalimentàries), Barcelona, 08193, Spain. jordi.garcia@irta.cat.

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.

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