Abstract
We assembled three complete mitochondrial genomes (mitogenomes), two of Solanum lycopersicum and one of Solanum pennellii, and analyzed their intra- and interspecific variations. The mitogenomes were 423,596–446,257 bp in length. Despite numerous rearrangements between the S. lycopersicum and S. pennellii mitogenomes, over 97% of the mitogenomes were similar to each other. These mitogenomes were compared with plastid and nuclear genomes to investigate genetic material transfers among DNA-containing organelles in tomato. In all mitogenomes, 9,598 bp of plastome sequences were found. Numerous nuclear copies of mitochondrial DNA (NUMTs) and plastid DNA (NUPTs) were observed in the S. lycopersicum and S. pennellii nuclear genomes. Several long organellar DNA fragments were tightly clustered in the nuclear genome; however, the NUMT and NUPT locations differed between the two species. Our results demonstrate the recent occurrence of frequent endosymbiotic gene transfers in tomato genomes.
Highlights
The plant cell organelles, the plastid and mitochondrion, are known to have originated from prokaryotes via endosymbiosis, and it is possible that the origin of the mitochondrion was contemporaneous with that of the eukaryotic cell, because there is no evidence of an amitochondriate phase in eukaryotic evolution [1]
Mapped reads were assembled de novo with zero mismatch and gap to generate reference contigs, before we annotated the reference contigs using Geneious [60] to confirm whether all of the ribosomal RNAs, transfer RNAs, and protein-coding regions included in the other Solanaceae mitogenomes were included in these contigs
The three mitogenome sequences were 423,596–446,257 bp in length (Fig 1 and Table 1). Their lengths were similar to the length of the MSA1 mitogenome which were generated by cell fusion between the tomato and potato [58] but were longer than that of the first draft of the tomato mitogenome [73]
Summary
The plant cell organelles, the plastid and mitochondrion, are known to have originated from prokaryotes via endosymbiosis, and it is possible that the origin of the mitochondrion was contemporaneous with that of the eukaryotic cell, because there is no evidence of an amitochondriate phase in eukaryotic evolution [1] Both organelles exist together in the plant cell, the evolutionary histories of the two organellar genomes in land plants differ slightly. Plastid genomes (plastomes) from bryophytes to angiosperms are normally 120–170 kb in length [2,3,4,5], excluding certain contracted or expanded genomes [6, 7] They are highly conserved in terms of gene content and arrangement, which is typically circular [4]. Certain plant species contain multichromosomal mitogenomes [19, 20]
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