Ribosomal protein L10 is encoded in the mitochondrial genome of many land plants and green algae

Background: The mitochondrial genomes of plants generally encode 30-40 identified protein-coding genes and a large number of lineage-specific ORFs. The lack of wide conservation for most ORFs suggests they are unlikely to be functional. However, an ORF, termed orf-bryo1, was recently found to be conserved among bryophytes suggesting that it might indeed encode a functional mitochondrial protein. Results: From a broad survey of land plants, we have found that the orf-bryo1 gene is also conserved in the mitochondria of vascular plants and charophycean green algae. This gene is actively transcribed and RNA edited in many flowering plants. Comparative sequence analysis and distribution of editing suggests that it encodes ribosomal protein L10 of the large subunit of the ribosome. In several lineages, such as crucifers and grasses, where the rpl10 gene has been lost from the mitochondrion, we suggest that a copy of the nucleus-encoded chloroplast-derived rpl10 gene may serve as a functional replacement. Conclusion: Despite the fact that there are now over 20 mitochondrial genome sequences for land plants and green algae, this gene has remained unidentified and largely undetected until now because of the unlikely coincidence that most of the earlier sequences were from the few lineages that lack the intact gene. These results illustrate the power of comparative sequencing to identify novel genomic features

The wheat mitochondrial gene for subunit I of the NADH dehydrogenase complex : A trans-splicing model for this gene-in-pieces

NRC publication: Ye

RT–PCR and cRT–PCR detection of lariat (and/or circularized) versus linear wheat mitochondrial intron molecules

<p><b>Copyright information:</b></p><p>Taken from "Multiple physical forms of excised group II intron RNAs in wheat mitochondria"</p><p>Nucleic Acids Research 2006;34(9):2782-2790.</p><p>Published online 22 May 2006</p><p>PMCID:PMC1464410.</p><p>© The Author 2006. Published by Oxford University Press. All rights reserved</p> () RT–PCR across the excised intron junction using 24 h wheat mitochondrial RNA as template, either pre-treated with ligase (+L; lanes 2, 5, 7 and 9) or untreated (−L; lanes 1, 4, 6 and 8) generated products of sizes 450, 520, 630 and 400 bp (denoted by arrowheads) for mRNA, intron 4, intron and intron 2, respectively. Size markers are shown in lane 3. () Southern blot of gels (shown in A, lanes 4–9) using intron-specific oligomer probes for intron 4, intron and intron 2. () Schematic showing positions of primers (arrows 1 and 2) used for RT–PCR and cRT–PCR in panels (A) and (B). Branchpoint is shown by A. Dotted lines indicate regions of amplification. () Direct sequencing of RT–PCR products for (D) intron (+L), (E) intron 2 (−L) and (F) intron 2 (+L) using oligomers 6, 11 and 16, respectively (Supplementary data). Note that an inverted orientation of the sequencing gel is shown for (E). Arrows show positions of the 5′ terminal nucleotide of the introns, stars highlight short non-encoded A-rich stretches and the discrete non-encoded insert sequence is boxed in (E)

Shared signatures of parasitism and phylogenomics unite Cryptomycota and microsporidia.

Fungi grow within their food, externally digesting it and absorbing nutrients across a semirigid chitinous cell wall. Members of the new phylum Cryptomycota were proposed to represent intermediate fungal forms, lacking a chitinous cell wall during feeding and known almost exclusively from ubiquitous environmental ribosomal RNA sequences that cluster at the base of the fungal tree [1, 2]. Here, we sequence the first Cryptomycotan genome (the water mold endoparasite Rozella allomycis) and unite the Cryptomycota with another group of endoparasites, the microsporidia, based on phylogenomics and shared genomic traits. We propose that Cryptomycota and microsporidia share a common endoparasitic ancestor, with the clade unified by a chitinous cell wall used to develop turgor pressure in the infection process [3, 4]. Shared genomic elements include a nucleotide transporter that is used by microsporidia for stealing energy in the form of ATP from their hosts [5]. Rozella harbors a mitochondrion that contains a very rapidly evolving genome and lacks complex I of the respiratory chain. These degenerate features are offset by the presence of nuclear genes for alternative respiratory pathways. The Rozella proteome has not undergone major contraction like microsporidia; instead, several classes have undergone expansion, such as host-effector, signal-transduction, and folding proteins

Shared signatures of parasitism and phylogenomics unite Cryptomycota and microsporidia.

Fungi grow within their food, externally digesting it and absorbing nutrients across a semirigid chitinous cell wall. Members of the new phylum Cryptomycota were proposed to represent intermediate fungal forms, lacking a chitinous cell wall during feeding and known almost exclusively from ubiquitous environmental ribosomal RNA sequences that cluster at the base of the fungal tree [1, 2]. Here, we sequence the first Cryptomycotan genome (the water mold endoparasite Rozella allomycis) and unite the Cryptomycota with another group of endoparasites, the microsporidia, based on phylogenomics and shared genomic traits. We propose that Cryptomycota and microsporidia share a common endoparasitic ancestor, with the clade unified by a chitinous cell wall used to develop turgor pressure in the infection process [3, 4]. Shared genomic elements include a nucleotide transporter that is used by microsporidia for stealing energy in the form of ATP from their hosts [5]. Rozella harbors a mitochondrion that contains a very rapidly evolving genome and lacks complex I of the respiratory chain. These degenerate features are offset by the presence of nuclear genes for alternative respiratory pathways. The Rozella proteome has not undergone major contraction like microsporidia; instead, several classes have undergone expansion, such as host-effector, signal-transduction, and folding proteins