Organellar genome analysis reveals endosymbiotic gene transfers in tomato

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.

Nuclear Integrants of Organellar DNA Contribute to Genome Structure and Evolution in Plants

“…The nuclear integrants of organellar DNA were first discovered in a study in which a mitochondrial ATPase subunit gene was found in the nuclear genome, as well as in the mitochondrial genome of Neurospora crassa [25]. Since then, organelle-derived sequences were examined in the nuclear genome of a number of animals [26][27][28][29][30][31][32] and plants [15][16][17][18][19][20][21]. The availability of a large amount of plant organelle and nuclear genome data has made it possible to investigate the prevalence and characteristics of NUMTs and NUPTs in plants.…”

“…NUPTs/NUMTs are usually distributed unevenly in the analyzed plant genomes [20,21,39]. NUPTs and NUMTs are more preferred to distribute in centromeric and pericentromeric regions [36,39], which have few genes and a high level of heterochromatin content [42][43][44].…”

“…This makes the large-scale analysis of NUPTs and NUMTs in plants be possible. Currently, NUPTs and NUMTs in some plant genomes have been characterized [15][16][17][18][19][20][21]. The characterization of nuclear organellar DNAs in plants adds new insights into the role of NUPTs and NUMTs in genome structure and evolution.…”

Molecular and functional diversity of organelle RNA editing mediated by RNA recognition motif‐containing protein ORRM4 in tomato

“…In our previous study, given the limited information available about the tomato mitochondrial genome, we identified only a few sites as being affected by SlORRM4 mutations (Yang et al ., 2017). Here, however, based on recently published tomato mitochondrial genome information (Kim & Lee, 2018), we were able to carry out the high‐throughput analysis mentioned earlier to identify mitochondrial C‐to‐U RNA editing sites in tomato fruit genome wide. Consequently, we identified a total of 552 mitochondrial C‐to‐U editing sites in tomato (Fig.…”

“…Sequencing reads were trimmed to remove barcode and adaptor sequences. The clean reads from each library were aligned with the complete tomato mitochondrion reference genome, NC_035963.1 (Kim & Lee, 2018), or chloroplast reference genome, NC_007898.3, using Star (v.2.5.0a, https://github.com/alexdobin/STAR). Then the RNA editing sites and editing extents were analyzed by REDiscover (v.0.14b, https://github.com/lpryszcz/REDiscover).…”