Cucumis melo Assembly and Gene Annotation

About Cucumis melo

Cucumis melo (melon) is a eudicot diploid plant species (2n=2x=24) of interest for its specific biological properties and for its economic importance. It belongs to the Cucurbitaceae family, which also includes cucumber, watermelon and squash. Although originally thought to originate in Africa, recent data suggest that melon and cucumber may be of Asian origin. Melon is an attractive model for studying fruit ripening, sex determination and phloem physiology. It is also an important fruit crop, particularly in Mediterranean and East Asian countries, where hybrid varieties have a significant and growing economic value. This is a project of the Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB.

Assembly

Genomic DNA was extracted from the double-haploid line DHL92, the same line sequenced to obtain the previous version of the genome. A total of 2.5M PacBio long reads were generated, which corresponds to 50x coverage of the estimated genome, and using the hierarchical genome-assembly process 4 (HGAP4) pipeline. The resulting contigs were ordered and oriented based on the previous assembly (v3.6.1) with RaGOO to produce pseudomolecules. The new consensus sequences were polished with 20x Illumina paired-end reads (2x150 bp) and error corrected with the Pilon pipeline. The completeness of the final assembly was evaluated with BUSCO yielding 94.8% of complete and 1.7% of fragmented BUSCOs at the genome level.

Annotation

Gene annotation was performed by transferring through a liftover process the latest published gene models to the new PacBio-based genome assembly using Maker v2. Completeness analysis reported 91.1% of complete and 2.4% fragmented BUSCOs at the gene model level.

Repeats were annotated with the Ensembl Genomes repeat feature pipeline. There are: 840,447 Low complexity (Dust) features, covering 33 Mb (9.2% of the genome); 265,681 RepeatMasker features (with the nrTEplants library), covering 175 Mb (48.8% of the genome); 102,852 RepeatMasker features (with the REdat library), covering 41 Mb (11.3% of the genome); 296,952 Tandem repeats (TRF) features, covering 27 Mb (7.4% of the genome).

References

1. An Improved Melon Reference Genome With Single-Molecule Sequencing Uncovers a Recent Burst of Transposable Elements With Potential Impact on Genes.
   Castanera R, Ruggieri V, Pujol M, Garcia-Mas J, Casacuberta JM..
2. An improved assembly and annotation of the melon (Cucumis melo L.) reference genome.
   Ruggieri V, Alexiou KG, Morata J, Argyris J, Pujol M, Yano R, Nonaka S, Ezura H, Latrasse D, Boualem A, Benhamed M, Bendahmane A, Cigliano RA, Sanseverino W, Puigdomènech P, Casacuberta JM, Garcia-Mas J..
3. The genome of melon (Cucumis melo L.).
   Garcia-Mas J, Benjak A, Sanseverino W, Bourgeois M, Mir G, González VM, Hénaff E, Câmara F, Cozzuto L, Lowy E, Alioto T, Capella-Gutiérrez S, Blanca J, Cañizares J, Ziarsolo P, Gonzalez-Ibeas D, Rodríguez-Moreno L, Droege M, Du L, Alvarez-Tejado M, Lorente-Galdos B, Melé M, Yang L, Weng Y, Navarro A, Marques-Bonet T, Aranda MA, Nuez F, Picó B, Gabaldón T, Roma G, Guigó R, Casacuberta JM, Arús P, Puigdomènech P..

Picture credit: www.melonomics.net

Links

melonomics

More information

General information about this species can be found in Wikipedia.