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.
Highlights
We report an improved assembly (v3.6.1) of the melon (Cucumis melo L.) genome and a new genome annotation (v4.0)
A genomic platform was built in order to host the genome sequence
Taking advantage of the continuous improvement of the genomics technologies and bioinformatics approaches[4,7] here we describe an improved version of the melon genome assembly (v3.6.1), which includes an optical mapping correction and re-orientation of some scaffolds along the 12 pseudomolecules
Summary
An optical mapping approach allowed improving pseudomolecules. To improve the melon genome assembly v3.5.1, an optical mapping approach[19,20,21] was undertaken in collaboration with the company OpGen. The integration of the transcriptome assembly, the evidence derived from the liftover of the previous annotations and the HMM models coming from the ab initio gene discovery allowed the annotation of 43,564 protein-coding genes. Among these genes, 13,584 were masked since they overlapped with repeat elements, leaving 29,980 protein-coding genes into a final comprehensive v4.0 melon annotation. The reference genome sequence axis, the browser incorporates 15 tracks including the v4.0 gene models, two TE annotations (MeloV4_Repet and MeloV4_RM_ Masking), a cumulative RNA-Seq expression track, epigenetic marks derived from methylation of leaf and root tissues jointly with the corresponding RNA-Seq tracks and a variome set including the re-sequencing of seven melon accessions (Fig. 4). A Download section allows the users to retrieve all the data and resources related to the new melon genome assembly and annotation
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