Protein and RNA gene content in sequenced seed plant mitochondrial genomes.

<p>Dark shading indicates the presence of an intact reading frame or folding structure, whereas light shading indicates the presence of only a putative pseudogene. The numbers at the bottom of each group indicate the total number of intact genes for that species. Note that the <i>ccmFc</i> gene, which is universally present in all other seed plants surveyed to date <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001241#pbio.1001241-Adams1" target="_blank">[104]</a>, is classified as a pseudogene in <i>S. conica</i>. It has experienced numerous structural mutations in this lineage, including multiple frame shifts in the second exon that introduce premature stop codons. However, cDNA sequencing confirmed that this gene is transcribed, spliced, and RNA edited in <i>S. conica</i> (unpublished data), so it is possible that the gene is still functional in its truncated form. In some cases, the presence of an intact gene may not indicate functionality. This is particularly true for tRNA genes embedded within recently transferred regions of plastid DNA <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001241#pbio.1001241-Alverson1" target="_blank">[20]</a>,<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001241#pbio.1001241-Leon1" target="_blank">[105]</a>. For example, the <i>trnN(guu)</i> and <i>trnR(acg)</i> genes in <i>S. vulgaris</i> may not be functional, as they are within a 2.6-kb region that appears to have been recently transferred from the plastid genome (on the basis of its perfect sequence identity with the exception of a single 18-bp deletion). These two tRNA genes are not orthologous to the plastid-derived copies of <i>trnN(guu)</i> and <i>trnR(acg)</i> in other seed plant mitochondria. Intron-containing plastid-derived tRNA genes such as <i>trnA(ugc)</i> in <i>Bambusa</i>, <i>trnV(uac)</i> in <i>Cycas</i>, <i>trnK(uuu)</i> in <i>Vitis</i>, and <i>trnI(gau)</i> in <i>Zea</i> are also unlikely to be functional. In <i>Cycas</i>, the <i>trnL(uaa)</i>, <i>trnP(ugg)</i>, <i>trnQ(uug)</i>, <i>trnR(ucu)</i>, and <i>trnV(uac)-</i> Ψ genes are classified on the basis of sequence homology to other land plant tRNAs even though their genomically encoded anticodons differ (CAA, CGG, CUG, CCU, and CAC, respectively). It is possible that these anticodons undergo C-to-U RNA editing to restore the ancestral codon as has been observed in other vascular plants <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001241#pbio.1001241-Grewe1" target="_blank">[106]</a>,<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001241#pbio.1001241-Grewe2" target="_blank">[107]</a>. Plastid-derived tRNAs with substitutions in their anticodons, such as <i>Citrullus trnT(ugu)</i> and <i>Silene latifolia trnP(ugg)</i>, are also classified (as pseudogenes) on the basis of homology.