Determination of the melon chloroplast and mitochondrial genome sequences reveals that the largest reported mitochondrial genome in plants contains a significant amount of DNA having a nuclear origin

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.

The complete chloroplast genome sequence of the Citrullus lanatus L. Subsp. Vulgaris (Cucurbitaceae)

“…KY014105). Its structure was similar to most of the described chloroplast genomes from cucurbit plants (Kim et al 2006;Chung et al 2007;Pla˛der et al 2007;Rodriguez-Moreno et al 2011), composed of two inverted repeated regions (IRa and IRb) of 25,150 bp, which was divided by a large single-copy (SSC) region of 70,063 bp and a small single-copy (LSC) region of 17,895 bp. The genome was typical of AT-rich, and its GC contents were 37.2%.…”

“…The genomic DNA was extracted from young leaves of C. lanatus collected from and cultivated in the farm field of Whole genome sequence data of 20 Gb were generated and trimmed, high quality PE reads of 0.4 Gb were randomly extracted and assembled with the BAC end sequences (Guo et al 2013) using SPAdes (v3.6.2) (Bankevich et al 2012), as described in Rodriguez-Moreno et al (Rodriguez-Moreno et al 2011). Contigs representing the chloroplast genome were retrieved, ordered and joined into a single draft sequence by comparison with the chloroplast genome of Cucumis sativus (GenBank accession no.…”

Plant Mitochondrial Genome Evolution and Cytoplasmic Male Sterility

“…By contrast, vertebrate animal mitogenomes are rather small (»14-20 kb) and highly conserved in both size and structure (Boore, 1999;Lavrov et al, 2016), and plant mitochondrial genomes exhibit substantial variation in both these features (Kitazaki and Kubo, 2010;Galtier, 2011;Mower et al, 2012b), although exceptions exist in nonflowering plants Guo et al, 2016). Plant mitochondrial genomes may vary enormously in size even within single plant families; in the Cucurbitaceae, for example, mitochondrial genomes vary over 7-fold in size, from 379 kb in Citrullus lanatus to 2,740 kb in Cucumis melo (Rodriguez-Moreno et al, 2011). Even more spectacularly, within the single genus Silene, mitogenome sizes vary over 40-fold in size, from 253 kb in Silene latifolia (Sloan et al, 2010) to more than 11 Mb in Silene conica (Sloan et al, 2010).…”

“…2010; Kitazaki and Kubo, 2010;Rodriguez-Moreno et al, 2011). As an indication of the scale of this process, between 0.1 and 10.3% of mtDNA has an origin tracing back to the chloroplast genome (Kitazaki and Kubo, 2010;Sloan and Wu, 2014); again, this likely underestimates the upper end of the range .…”

“…Exogenous sequence uptake into plant mitochondrial is common and ongoing, occurring throughout land plants (Kitazaki and Kubo, 2010;Rodriguez-Moreno, 2011). There is, however, a notable difference in the propensity for chloroplast DNA (e.g.…”