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

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.

High Contiguity de novo Genome Sequence Assembly of Trifoliate Yam (Dioscorea dumetorum) Using Long Read Sequencing

“…The release of genome sequences of many model and crop plants has provided new opportunities for gene identification and studies of genome evolution, both ultimately serving the process of plant breeding [45] by allowing discovery of genes responsible for important agronomic traits and the development of molecular markers associated with these traits. Here, we present the first genome sequence for D. dumetorum, an important crop for Central and Western Africa, and the second genome sequence for the genus.…”

Transcriptome profiling of non-climacteric ‘yellow’ melon during ripening: insights on sugar metabolism

“…The expression for each gene and differential expression (DE) analyses were calculated by statistical test evaluating the negative binomial distribution, being considered significant padj ≤0.05 (see Methods). In this analysis, over 15,000 expressed genes were detected in each sample ( Table 2 and Additional file 1: Table S2) of the 29,980 annotated in the Cucumis melo genome [22,23]. However, a total of 1804 genes showed significant DE between the evaluated stages of fruit maturation (Additional file 1: Table S2).…”

“…The results generated~59 million clean single reads of~100 bp in length. A total of~53 million filtered reads were mapped to the Cucumis melo reference genome (https://www.melonomics.net) [22,23] using Bowtie2 [24]. Most sample reads (79.65-97.88%) were successfully aligned and for RNA-seq analysis, only the reads with overlapping in a single gene were considered ( Table 2 and Additional file 1: Table S1).…”

High contiguity de novo genome sequence assembly of Trifoliate yam (Dioscorea dumetorum) using long read sequencing

“…The release of genome sequences of many model and crop plants has provided new opportunities for gene identification and studies of genome evolution, both ultimately serving the process of plant breeding [45] by allowing discovery of genes responsible for important agronomic traits and the development of molecular markers associated with these traits. Here, we present the first genome sequence for Dioscorea dumetorum , an important crop for Central and Western Africa, and the second genome sequence for the genus.…”