Abstract
BackgroundThe melon belongs to the Cucurbitaceae family, whose economic importance among vegetable crops is second only to Solanaceae. The melon has a small genome size (454 Mb), which makes it suitable for molecular and genetic studies. Despite similar nuclear and chloroplast genome sizes, cucurbits show great variation when their mitochondrial genomes are compared. The melon possesses the largest plant mitochondrial genome, as much as eight times larger than that of other cucurbits.ResultsThe nucleotide sequences of the melon chloroplast and mitochondrial genomes were determined. The chloroplast genome (156,017 bp) included 132 genes, with 98 single-copy genes dispersed between the small (SSC) and large (LSC) single-copy regions and 17 duplicated genes in the inverted repeat regions (IRa and IRb). A comparison of the cucumber and melon chloroplast genomes showed differences in only approximately 5% of nucleotides, mainly due to short indels and SNPs. Additionally, 2.74 Mb of mitochondrial sequence, accounting for 95% of the estimated mitochondrial genome size, were assembled into five scaffolds and four additional unscaffolded contigs. An 84% of the mitochondrial genome is contained in a single scaffold. The gene-coding region accounted for 1.7% (45,926 bp) of the total sequence, including 51 protein-coding genes, 4 conserved ORFs, 3 rRNA genes and 24 tRNA genes. Despite the differences observed in the mitochondrial genome sizes of cucurbit species, Citrullus lanatus (379 kb), Cucurbita pepo (983 kb) and Cucumis melo (2,740 kb) share 120 kb of sequence, including the predicted protein-coding regions. Nevertheless, melon contained a high number of repetitive sequences and a high content of DNA of nuclear origin, which represented 42% and 47% of the total sequence, respectively.ConclusionsWhereas the size and gene organisation of chloroplast genomes are similar among the cucurbit species, mitochondrial genomes show a wide variety of sizes, with a non-conserved structure both in gene number and organisation, as well as in the features of the noncoding DNA. The transfer of nuclear DNA to the melon mitochondrial genome and the high proportion of repetitive DNA appear to explain the size of the largest mitochondrial genome reported so far.
Highlights
The melon belongs to the Cucurbitaceae family, whose economic importance among vegetable crops is second only to Solanaceae
We report the complete sequence of the melon chloroplast genome obtained from BAC end sequences (BES), and we report an estimated 95% of the melon mitochondrial genome determined using Roche-454 sequencing technology
The genome was 156,017 bp long and included a pair of inverted repeats (IRa and IRb) of 25,797 bp separated by small (SSC) and large (LSC) single-copy regions of 18,090 and 86,334 bp, respectively (Figure 1, Table 1)
Summary
The melon belongs to the Cucurbitaceae family, whose economic importance among vegetable crops is second only to Solanaceae. The melon has a small genome size (454 Mb), which makes it suitable for molecular and genetic studies. The melon (Cucumis melo L.) is an important vegetable crop grown in temperate, subtropical and tropical regions worldwide. The melon belongs to the Cucurbitaceae family, which comprises other vegetable crops such as cucumber, watermelon, pumpkin and squash, and whose economic importance among vegetable crops is second only to Solanaceae. Extensive research has been performed in melon to elucidate fruit ripening processes, carotene accumulation and aroma production [2]. Recent research has increased the availability of genetic and genomic resources for melon [7], such as the sequencing of ESTs [8,9], the development of an oligonucleotide-based microarray [10], the construction of BAC libraries [11,12,13], the production of mutant collections for TILLING analyses [14,15,16], the development of a collection of near-isogenic lines (NILs) [17], the construction of several genetic maps [9,18,19,20,21,22] and the development of a genetically anchored BAC-based physical map [23]
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