Draft genome sequences of two oriental melons, Cucumis melo L. var. makuwa.

Oriental melon (Cucumis melo L. var. makuwa) is one of the most important cultivated cucurbits, and is grown widely in Northeast Asian countries. With increasing interest in its biological properties and economic importance, oriental melon has become an attractive model crop for studying various horticultural traits. A previous genome sequence of the melon was constructed from a homozygous double-haploid line. Thus, individual reference genomes are required to perform functional studies and further breeding applications. Here, we report draft genome sequences of two oriental melons, Chang Bougi and SW3. The assembled 344 Mb genome of Chang Bougi was obtained with scaffold N50 1.0 Mb, and 36,235 genes were annotated. The 354 Mb genome of SW3 was assembled with scaffold N50 1.6 Mb, and has 38,173 genes. These newly constructed genomes will enable studies of fruit development, disease resistance, and breeding applications in the oriental melon.

Shin AY ，Koo N ，Kim S ，Sim YM ，Choi D ，Kim YM ，Kwon SY ... -  《Scientific Data》

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

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.

Kim HA ，Shin AY ，Lee MS ，Lee HJ ，Lee HR ，Ahn J ，Nahm S ，Jo SH ，Park JM ，Kwon SY ... -  《-》

Development of SSR markers by next-generation sequencing of Korean landraces of chamoe (Cucumis melo var. makuwa).

The oriental melon (Cucumis melo var. makuwa), called 'chamoe' in Korean, is a popular fruit crop cultivated mainly in Asia and a high-market value crop in Korea. To provide molecular breeding resources for chamoe, we developed and characterized genomic SSR markers from the preliminary Illumina read assemblies of Gotgam chamoe (one of the major landraces; KM) and SW3 (the breeding parent). Mononucleotide motifs were the most abundant type of markers, followed by di-, tri-, tetra-, and pentanucleotide motifs. The most abundant dinucleotide was AT, followed by AG and AC, and AAT was the most abundant trinucleotide motif in both assemblies. Following our SSR-marker development strategy, we designed a total of 370 primer sets. Of these, 236 primer sets were tested, exhibiting 93 % polymorphism between KM and SW3. Those polymorphic SSRs were successfully amplified in the netted and Kirkagac melons, which respectively exhibited 81 and 76 % polymorphism relative to KM, and 32 and 38 % polymorphism relative to SW3. Seven selected SSR markers with a total of 17 alleles (2-3 alleles per locus) were used to distinguish between KM, SW3, and four chamoe cultivars. Our results represent the first attempt to provide genomic resources for Korean landraces for the purposes of chamoe breeding, as well as to discover a set of SSR markers capable of discriminating chamoe varieties from Korea and the rest of Asia, which possess little genetic diversity. This study establishes a highly efficient strategy for developing SSR markers from preliminary Illumina assemblies of AT-rich genomes.

Park I ，Kim J ，Lee J ，Kim S ，Cho O ，Yang K ，Ahn J ，Nahm S ，Kim H ... -  《-》

The genome of melon (Cucumis melo L.).

We report the genome sequence of melon, an important horticultural crop worldwide. We assembled 375 Mb of the double-haploid line DHL92, representing 83.3% of the estimated melon genome. We predicted 27,427 protein-coding genes, which we analyzed by reconstructing 22,218 phylogenetic trees, allowing mapping of the orthology and paralogy relationships of sequenced plant genomes. We observed the absence of recent whole-genome duplications in the melon lineage since the ancient eudicot triplication, and our data suggest that transposon amplification may in part explain the increased size of the melon genome compared with the close relative cucumber. A low number of nucleotide-binding site-leucine-rich repeat disease resistance genes were annotated, suggesting the existence of specific defense mechanisms in this species. The DHL92 genome was compared with that of its parental lines allowing the quantification of sequence variability in the species. The use of the genome sequence in future investigations will facilitate the understanding of evolution of cucurbits and the improvement of breeding strategies.

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 ... -  《-》

Genome-Wide SNP Markers for Genotypic and Phenotypic Differentiation of Melon (Cucumis melo L.) Varieties Using Genotyping-by-Sequencing.

Melon ( L.) is an economically important horticultural crop with abundant morphological and genetic variability. Complex genetic variations exist even among melon varieties and remain unclear to date. Therefore, unraveling the genetic variability among the three different melon varieties, muskmelon ( subsp. ), makuwa ( L. var. ), and cantaloupes ( subsp. var. ), could provide a basis for evolutionary research. In this study, we attempted a systematic approach with genotyping-by-sequencing (GBS)-derived single nucleotide polymorphisms (SNPs) to reveal the genetic structure and diversity, haplotype differences, and marker-based varieties differentiation. A total of 6406 GBS-derived SNPs were selected for the diversity analysis, in which the muskmelon varieties showed higher heterozygote SNPs. Linkage disequilibrium (LD) decay varied significantly among the three melon varieties, in which more rapid LD decay was observed in muskmelon ( = 0.25) varieties. The Bayesian phylogenetic tree provided the intraspecific relationships among the three melon varieties that formed, as expected, individual clusters exhibiting the greatest genetic distance based on the posterior probability. The haplotype analysis also supported the phylogeny result by generating three major networks for 48 haplotypes. Further investigation for varieties discrimination allowed us to detect a total of 52 SNP markers that discriminated muskmelon from makuwa varieties, of which two SNPs were converted into cleaved amplified polymorphic sequence markers for practical use. In addition to these markers, the genome-wide association study identified two SNPs located in the genes on chromosome 6, which were significantly associated with the phenotypic traits of melon seed. This study demonstrated that a systematic approach using GBS-derived SNPs could serve to efficiently classify and manage the melon varieties in the genebank.

Hyun DY ，Sebastin R ，Lee GA ，Lee KJ ，Kim SH ，Yoo E ，Lee S ，Kang MJ ，Lee SB ，Jang I ，Ro NY ，Cho GT ... -  《INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES》