Organellar genome analysis reveals endosymbiotic gene transfers in tomato

PLoS One. 2018 Sep 5;13(9):e0202279. doi: 10.1371/journal.pone.0202279. eCollection 2018.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Cell Nucleus / genetics
  • DNA, Mitochondrial / chemistry
  • DNA, Mitochondrial / genetics*
  • Evolution, Molecular
  • Genome, Mitochondrial / genetics*
  • Genome, Plant / genetics
  • Sequence Analysis, DNA
  • Sequence Homology, Nucleic Acid
  • Solanum / genetics*
  • Solanum lycopersicum / classification
  • Solanum lycopersicum / genetics*
  • Symbiosis / genetics*

Substances

  • DNA, Mitochondrial

Grants and funding

This work was supported by the National Research Foundation of Korea under grant 2018R1A2B6002620 (JML) and 2017R1A6A3A01007551 (HTK); and the Golden Seed Project (Center for Horticultural Seed Development), the Ministry of Agriculture, Food and Rural Affairs, Republic of Korea (JML).