1E). Bartek has three variations of fruits; Long-Green, Ellips-Green, and Yellow. We assembled 375 Mb of the double-haploid line DHL92, representing 83.3% of the estimated melon genome. Conflict of interest statement: L.D., M.D., and M.A.-T. are Roche employees, and the work was partly funded by Roche. Genes were preferentially distributed near the telomeres for most of the chromosomes (Fig. This represents the first steps towards the integration of the high-resolution genetic and cytogenetic map with the genomic sequence in melon that will provide more information on genome organization and allow for the improvement of the melon genome draft Cucumber is believed to have evolved from melon through chromosome fusion, but the details of this process are largely unknown. Africa is considered to be the centre of origin for melon because of the frequent occurrence of wild species of Cucumis with the same basic chromosome number n=12.5 The secondary center of origin of melon is in Turkey, Syria, Iran, However, loss of chromosome fragments during chromosome fusion in cucumber may also explain the larger melon genome. S11 and S12), which contain a total of 17 recombination events, with an average of 1.4 recombinations per linkage group. The total of duplicated sequences identified by depth of coverage could still be an underestimate, given that the genome is highly fractionated. Shoot primordium aggregates were induced from shoot-tips cultured in liquid medium and shaken at low speed (2 rpm). (F) Melon genome duplications. In addition, both melon and cucumber are believed to be of Asian origin, which were derived from a common ancestor approximately nine million years ago [12].The genome size of melon (12 chromosome pairs) is estimated to be 454 Mb, and cucumber (7 chromosome pairs) i). A total of 22,218 maximum-likelihood (ML) phylogenetic trees were reconstructed and deposited at PhylomeDB (24) (http://phylomedb.org). Compared with use of NGS technology, SMRT sequencing exhibited superiority in To assess whether DNA transposons have also been more active in the melon lineage than that of cucumber, we annotated in the Gy14 cucumber genome the three most represented superfamilies in both species (i.e., CACTA, MULE, and PIF/Harbinger) (SI Appendix, Table S8) (19), showing that all three have been amplified in the melon lineage (10 for CACTA, 47 for MULE, and 3.8 for PIF) (SI Appendix, Table S9). Direct blocks are represented in red and inverted blocks in green. In melon, high-copy-number satellite DNAs (SatDNAs) were found at various chromosomal locations such as centromeric, pericentromeric, and subtelomeric regions. According to total number of chromosome, Bartek is more related to melon. The quality of the assembly was assessed by mapping it to four BACs that were previously sequenced using a shotgun Sanger approach. inodorus) (PS), was chosen to obtain a better assembly of the genome sequence. is supported by European Research Council Starting Grant StG_20091118. Bars represent the total number of genes for each species (scale on the top). *This Direct Submission article had a prearranged editor. A total of 102 ncRNA were identified as forming 26 potential clusters (SI Appendix, Table S14). Comparative genomics of 23 fully sequenced plant species where phylogeny is based on maximum-likelihood analysis of a concatenated alignment of 60 widespread single-copy proteins. The melon genome assembly can be considered of good quality compared with other sequenced plant genomes based on next-generation sequencing (NGS) (SI Appendix, Table S3). Four clusters containing 13 TNL genes and spanning a region of 570 kb are located in the same region of the melon Vat resistance gene (35). The bitter melon more typical of India has a narrower shape with pointed ends, and a surface covered with jagged, triangular "teeth" and ridges. Matsum. Melon LG IV and LG VI were fused into cucumber chromosome 3, but with several rearrangements and a reduction in total size in cucumber (30.4 and 29.8 Mb vs. 39.7 Mb) (Fig. However, it is probably an underestimate as a result of the high stringency of our searches and the presence of additional transposon sequences in the unassembled fraction of the genome. We do not capture any email address. The number of genes in the CNL II cluster was comparable between cucumber (22) and C. hystrix (25), but the number in melon (13) was half the number in the other two species. By continuing you agree to the use of cookies. d. Infection by a primate virus created a new chromosome when the viral DNA became a permanent part of the genome. Enter multiple addresses on separate lines or separate them with commas. The melon and cucumber genome sequences are excellent tools for understanding the genome structure and evolution of two important species of the same genus with different chromosome number (melon, 2n = 2x = 24; cucumber, 2n = 2x = 14). Online ISSN 1091-6490. 4A; SI Appendix, Table S18). Search. In both cases the usual 7 pairs of chromosomes were found (fig. Among the major processes that occur during fruit ripening, two are particularly interesting from the breeding point of view: accumulation of sugars, which is responsible for the characteristic sweet taste, and carotenoid accumulation, which is responsible for the flesh color. Total number of diploid chromosomes (2n) = 24 in Bartek - "Chromosome Characterization of Bartek (Cucumis Melo L. var. ones, the pollen mother cells of the varieties Lemon and Long Green were examined. Cultivated melon was domesticated from wild melons, which produce small fruits with non-edible fruit flesh. The DHL92 melon genome. According In general it can be stated that each band represents a distinct gene. Bartek), Local Melon Variety from Pemalang" Skip to search form Skip to main content > Semantic Scholar's Logo. His classification was based on not only morphology but also other taxonomic keys comprising chromosome number, type of cucurbitacin, type of flavonoid, isozymes, DNA and crossability. In this case, melon used as the comparison of Bartek because their similarity in chromosome number (2n=2x=24). It is particularly important in Mediterranean and East Asian countries, where hybrid varieties have a significant and growing economic value. Melon and cucumber belong to the same genus, although cucumber has seven chromosomes and melon has 12. The annotation of the assembled genome after masking repetitive regions resulted in a prediction of 27,427 genes with 34,848 predicted transcripts encoding 32,487 predicted polypeptides (SI Appendix, Table S10). From a total of 19 MIR169 members identified, 12 were located in the same scaffold in a range of 35 kb. Recent experiments and simulations are starting to answer some fundamental questions about how life came to be. At least 30 other species of Cucumis have had their chromosomes counted, all but one from Africa and all having 2n = 24 or multiples thereof . The annotation of the assembled genome predicted 27,427 genes, a number similar to other plant species. (E) Distribution of NBSLRR R-genes (brown). Bartek has three variations of fruits; Long-Green, Ellips-Green, and Yellow. There was no direct correlation between chromosome size and number of cross-species SSR markers. Another cluster with seven TNL genes spanning 135 kb colocalized with the region harboring the Fom-1 resistance gene (36). Cucumis, as traditionally conceived, is geographically centered in Africa, with C. sativus and C. hystrix thought to be the only Cucumis species in Asia. According to the total number of chromosome, Bartek is closer to melon than cucumber. 3). agrestis (HS, a few-sucrose accumulator and GSB-resistant landrace). 4B). Likewise, the level of polymorphism of melon agrestis) (SC) and the Piel de Sapo T111 line (ssp. 1). This analysis showed that, although different families had distinct patterns of amplification over time, most retrotransposons were inserted recently, with a peak of activity around 2 million years ago (Mya) (Fig. conomon (pickling melon), dudaim (mango melon or pomegranate melon) and momordica (snap melon). Orange: widespread but plant-specific genes that are found in at least 20 of the 23 plant species. Transposable elements have accumulated to a greater extent in melon compared with cucumber with a peak of activity around 2 Mya, suggesting that the larger genome size of melon, probably to a large extent, may be due to transposon amplification. This percentage is similar to the one reported for genomes of similar size such as cacao (18). Length of chromosome was drawn based on number of marker loci used for inference of syntenic blocks which is an approximation of actual length of each chromosome. Two rounds of WGD have been reported for Arabidopsis and soybean, whereas no WGD has been found in Fragaria. 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. Data deposition: The sequence data from this study have been deposited in the ENA Short Read Archive under accession no. acknowledge the Spanish National Bioinformatics Institute for funding. Melon is a valuable human food source cultivated in arid and semiarid regions of the world [4]. Different background colors indicate taxonomic groupings within the species used to make the tree. C. sativus has a chromosome number of 2n = 14, whereas C. melo has a chromosome number of 2n = 24. Similar varietal chromosome number differences are found also in Cucumis melo, in which species pollen mother cells have been ex-amined from the ordinary melon (var. These expansions provide useful clues to establishing genetic links to the phenotypic particularities of these species. This question is for testing whether or not you are a human visitor and to prevent automated spam submissions. Bartek is one of local melon varieties mainly cultivated in Pemalang, Central Java. created a genome of 46 chromosomes without the loss of any genetic information. The increasing availability of genome sequences from higher plants provides us with an important tool for understanding plant evolution and the genetic variability existing within cultivated species. 1B). agrestis (HS, a few-sucrose accumulator and GSB-resistant landrace). A cell-wall invertase (CmCIN-LIKE1) was annotated, probably resulting from the duplication of CmCIN2 in the ancestor of melon and cucumber (SI Appendix, Fig. This taxonomy forms the basis for all ongoing Cucumis breeding and genomics efforts. The reconstructed phylogenies of some of these families revealed interesting scenarios: three lineage-specific independent RLK expansions involving several rounds of tandem duplications at three corresponding ancestral loci were identified (SI Appendix, Fig. The resulting intersection between WSSD and WGAC is a good measure of the quality of duplicated content in a given assembly, detecting both artifact duplications and general collapse. Similar results were obtained when the annotation pipeline was applied to the 9930 cucumber genome (19). The mitotic analysis exhibited that the Bartek has similar karyotype formula, 2n = 2x = 24m. The DHL92 genome was compared with that of its parental lines allowing the quantification of sequence variability in the species. Expansion of the lipoxygenase gene family has been suggested as a complementary mechanism to challenge biotic stress in cucumber (19), but we did not observe such an expansion in melon. The availability of the genome sequence will be very valuable in studying this question that is also of importance for breeding biotic resistance. Melon has a key position in the Cucurbitaceae family for its high economic value and as a model to study biologically relevant characters, so the melon genome sequence has the added value of providing breeders with an additional tool in breeding programs. R-genes were nonrandomly distributed in the melon genome, but organized in clusters (SI Appendix, Fig. Chromosome number is showed at the right end of each chromosome diagram. 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. Since there are 5000 bands in D. melanogaster it is believed that there are about 5,000 genes in this species. (A) Physical map of the 12 melon pseudochromosomes, represented clockwise starting from center above. A set of 57 BACs sequenced with 454 using a pooling strategy (10) was also compared with the assembly, which confirmed 92.3% of the BAC assemblies as being consistent with the genome assembly (SI Appendix, Table S6). On the left of each chromosome, the distance in Mb and the melon gene member (with a Cm prefix) are shown. The results showed that all of Bartek observed in this study have similar diploid (2n) chromosome number = 24. This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1205415109/-/DCSupplemental. polytene chromosomes has shown a total number of ve long polytene elements (10 polytene arms) KEY WORDS Bactrocera cucurbitae, melon y, polytene chromosomes, chromosome inversions, Tephritidae The melon y, Bactrocera cucurbitae Coquillett (Dip-tera: Tephritidae), is a species of signicant agricul-tural importance. Chromosome characterization of the Bartek was investigated to determine the genetic variation. There are other examples of more complex chromosomal rearrangements, but the total number of small inversions cannot be easily determined due to lack of orientation of some scaffolds in both species. A low number of nucleotide-binding siteleucine-rich repeat disease resistance genes were annotated, suggesting the existence of specific defense mechanisms in this species. Our phylogenetic analysis is in agreement with the assignment of Populus in the Malvidae clade (28). A total of 1,253 noncoding RNA (ncRNA) genes were identified in the melon genome, similar to Arabidopsis (SI Appendix, Table S13; Dataset S2). A cluster of six CNL genes spanning 56 kb and not described previously was located in LG I. (D) Distribution of transposable elements (blue). A phylogenetic analysis of gene families greatly helped in the quality of the prediction. Heavy hydrogen makes heavy water more dense and raises its boiling point. Blocks of the same color correspond to syntenic regions. Red arrow indicates when the melon and cucumber lineages diverged. By using homology and structure-based searches, we identified 323 transposable element representatives belonging to the major superfamilies previously described in plants. The quality of the assembly has an impact on further uses of the genome sequence, providing an efficient reference genome for resequencing analysis. We dated the insertion time of all LTR retrotransposons belonging to families containing at least 10 complete elements by intraelement comparison of LTRs (SI Appendix, SI Text). Both 454 and Sanger reads were assembled with Newbler 2.5 into 1,594 scaffolds and 29,865 contigs, totaling 375 Mb of assembled genome (Table 1; SI Appendix, SI Text). They were maintained by subculturing small pieces (5mm<) every 4 weeks. Bartek is one of local melon varieties mainly cultivated in Pemalang, Central Java. Although originally thought to originate in Africa, recent data suggest that melon and cucumber may be of Asian origin (1). Bartek has three variations of fruits; Long-Green, Ellips-Green, and Yellow. Eight of them were found in pairs in a range of around 300 bases in the same DNA strand (SI Appendix, Fig. The difference between the estimated and the assembled genome size could be due to unassembled regions of repetitive DNA, similar to what has been found in genomes obtained with NGS (16). 40 Cucumis species with chromosome counts, C. sativus is the only species with 2n = 14 chromosomes; all other species have 2n = 24, and occasionally 2n = 48 or 72 chromosomes (Kirkbride 1993). Melon LG IV and LG VI were fused into cucumber chromosome 3, but with several rearrangements and a reduction in total size in cucumber (30.4 and 29.8 Mb vs. 39.7 Mb) ( Fig. R.G. The 12 pseudo-chromosomes of melon genome, reconstructed from HS x XH and PS x SC genetic maps. The N50 scaffold size was 4.68 Mb, and 90% of the assembly was contained in 78 scaffolds (SI Appendix, Table S2). has x=7 chromosome numbers, Cucumis subgen. and melon diverged from a common ancestor ~12 million years ago (MYA); cucumber and C. hystrix diverged ~5 MYA (Sebastian et al. Jonathon Yuly, David Beratan, and Peng Zhang investigate how electron bifurcation reactions work. The first distal 8.5 and 5 Mb of melon LG IV and cucumber chromosome 3, respectively, are highly collinear but with a progressive increase in size in melon toward the heterochomatic fraction (Fig. The ratio between genetic and physical distances localized a region of recombination suppression in each pseudochromosome, which may correspond to the position of the centromeres (SI Appendix, Fig. Overall, 92.5% of the BAC sequences were well represented in the genome assembly, aligning contiguously and with more than 99% similarity (SI Appendix, Fig. & Nakai], and squash (Cucurbita spp.). (B) Distribution of ncRNAs (orange). Comparative analysis of the melon and cucumber genomes. (C) Distribution of predicted genes (light green). Author contributions: J.G.-M., M.A.A., F.N., B.P., T.G., G.R., R.G., J.M.C., P.A., and P.P. designed research; A.B., W.S., M.B., G.M., V.M.G., E.H., F.C., L.C., E.L., T.A., S.C.-G., J.C., P.Z., D.G.-I., L.R.-M., M.D., L.D., M.A.-T., B.L.-G., M.M., L.Y., and Y.W. This is called the diploid number (di meaning two, as in dissect cut in two). Twenty-one of these genes were not previously reported in melon (37, 38), of which 8 had EST support. A total of 411 putative disease resistance R-genes (32) were identified in the melon genome (SI Appendix, Table S15). Further information is accessible through the MELONOMICS website (http://melonomics.net). We found an excess of possible collapses in the assembly (11.63 Mb) as a result of its construction based on short reads (43). In the present study, utilizing the published draft genome sequence of melon, The Cucurbitaceae is, after the Solanaceae, the most economically important group of vegetable crops, especially in Mediterranean countries. The resequencing of the parents of the DHL92 reference genome allowed a first measure of the polymorphism in melon, as more than 2 million putative SNPs were identified. 2010) (Figure 1). Here, we report a chromosomelevel genome assembly for C. metuliferus, with a 316 Mb genome sequence comprising 29,039 genes. The number of SNPs and indels between SC and PS resulted in a frequency of one SNP every 176 bp and one indel every 907 bp. In this study, we employed the PacBio SMRT long reads and high-throughput chromosome conformation capture (Hi-C) technologies to assemble for the genome of melon subspecies of C. melo spp. All LTR retrotransposon families with 10 or more copies were considered. It belongs to the Cucurbitaceae family, which also includes cucumber (Cucumis sativus L.), watermelon [Citrullus lanatus (Thunb.) Karyotype of Yellow Bartek. Passion fruit (Passiflora edulis) 18 Setaria viridis (Setaria viridis) Though the chromosome X had the least number of 45 common markers, the chromosome V had the lowest density of 2.0 SSR/Mb. With this even number, cell division is highly regular and produces pollen and egg cells with 11 chromosomes that recombine to produce seed with the usual 22 chromosomes. e. Humans have the correct number of chromosomes. Bartek is one of local melon varieties mainly cultivated in Pemalang, Central Java. Of these, 81 may exert their disease resistance function as cytoplasmatic proteins through canonical resistance domains, such as the NBS, the LRR, and the TIR domains (Fig. A gene putatively encoding a UDP-glc phyrophosphorylase (CmUGP-LIKE1), for which a single gene was described (CmUGP), was annotated (SI Appendix, Fig.