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A custom-built program (Patrick Charlebois, Claude Lemieux and Monique Turmel, unpublished data) was used to identify the gene clusters that are conserved in selected pairs of streptophyte mtDNAs.
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Mesorhizobium loti genes whose homologs are conserved in three rhizobia were selected according to the criteria described by Kaneko et al. The lower threshold of acceptability was set at 0.25 of the BLASTP bit score reported by self-comparison.
Details of the 71 rice accessions are in Additional file 2. The majority of the MIRNAs selected are conserved in other species to ensure they are bona fide MIRNAs.
Genes whose homologs are conserved in other rhizobium genomes were selected by comparing the genome sequences of three rhizobium species, M. loti strain MAFF303099 (symbiont for Lotus japonicus), Sinorhizobium meliloti strain 1021 (alfalfa symbiont), and Bradyrhizobium japonicum strain USDA110 (soybean symbiont), whose complete genome sequences were available when this study was initiated.
The vast majority (31 out of 33) of these positively selected sites are conserved in the feruloyl esterase A group but not in the lipase group.
We set the threshold for the conservation score to 0.70 to select target sites that are conserved in mammals.
Poxins are conserved in mammalian poxviruses.
Violet: components that are conserved in Amoebozoa and Excavata, blue: conserved in Amoebozoa, Teal or pink, conserved in only dictyostelia or Excavata, respectively.
We find that these mechanisms are conserved in human neocortex.
The carbamylated lysines are conserved in all five peroxidases.
Moreover, these functions are conserved in human cells.
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