De Novo Transcriptome Analysis of Cucumis melo L. var. makuwa

Abstract

Oriental melon (Cucumis melo L. var. makuwa) is one of six subspecies of melon and is cultivated widely in East Asia, including China, Japan, and Korea. Although oriental melon is economically valuable in Asia and is genetically distinct from other subspecies, few reports of genome-scale research on oriental melon have been published. We generated 30.5 and 36.8 Gb of raw RNA sequence data from the female and male flowers, leaves, roots, and fruit of two oriental melon varieties, Korean landrace (KM) and Breeding line of NongWoo Bio Co. (NW), respectively. From the raw reads, 64,998 transcripts from KM and 100,234 transcripts from NW were de novo assembled. The assembled transcripts were used to identify molecular markers (e.g., single-nucleotide polymorphisms and simple sequence repeats), detect tissue-specific expressed genes, and construct a genetic linkage map. In total, 234 single-nucleotide polymorphisms and 25 simple sequence repeats were screened from 7,871 and 8,052 candidates, respectively, between the KM and NW varieties and used for construction of a genetic map with 94 F2 population specimens. The genetic linkage map consisted of 12 linkage groups, and 248 markers were assigned. These transcriptome and molecular marker data provide information useful for molecular breeding of oriental melon and further comparative studies of the Cucurbitaceae family.

Keywords: Korean melon; genetic linkage map; simple sequence repeat; single-nucleotide polymorphism; transcriptome analysis.

Fig. 1.

Schematic illustrating transcriptome assembly and the analysis of oriental melon sequence data. Transcriptome assembly and the transcript sequence data analysis proceeded as a workflow. Sequence data quality analysis, data trimming, and read-length sorting were carried out using the SolexaQA, DynamicTrim, and LengthSort programs, respectively. Transcripts were de novo assembled using Velvet and Oases, with the optimum K-mer value set at 59. The assembled transcripts were annotated using BLASTX (evalue ≤ 1e⁻⁰⁵) with the SEEDERS plant annotation database.

Fig. 2.

GO classification of the assembled unigenes. Oriental melon unigenes were classified into three functional categories: ‘biological process’, ‘cellular component’, and ‘molecular function’. Bars indicate the number of genes in each GO term category.

Fig. 3.

Number of SNPs. Synonymous and non-synonymous SNPs were distributed into 12 linkage groups using the published melon genome (Cucumis melo. L) as the reference.

Fig. 4.

Distribution of genetic markers in the oriental melon genetic map. Linkage groups are numbered at the top, and markers are listed to the right of each linkage group. Map distances are given in cM from the top of each linkage group on the left.