Did RNA editing in plant organellar genomes originate under natural selection or through genetic drift?

<p>Abstract</p> <p>Background</p> <p>The C↔U substitution types of RNA editing have been observed frequently in organellar genomes of land plants. Although various attempts have been made to explain why such a seemingly inefficient genetic mechanism would have evolved, no satisfactory explanation exists in our view. In this study, we examined editing patterns in chloroplast genomes of the hornwort <it>Anthoceros formosae </it>and the fern <it>Adiantum capillus-veneris </it>and in mitochondrial genomes of the angiosperms <it>Arabidopsis thaliana</it>, <it>Beta vulgaris </it>and <it>Oryza sativa</it>, to gain an understanding of the question of how RNA editing originated.</p> <p>Results</p> <p>We found that 1) most editing sites were distributed at the 2^ndand 1^stcodon positions, 2) editing affected codons that resulted in larger hydrophobicity and molecular size changes much more frequently than those with little change involved, 3) editing uniformly increased protein hydrophobicity, 4) editing occurred more frequently in ancestrally T-rich sequences, which were more abundant in genes encoding membrane-bound proteins with many hydrophobic amino acids than in genes encoding soluble proteins, and 5) editing occurred most often in genes found to be under strong selective constraint.</p> <p>Conclusion</p> <p>These analyses show that editing mostly affects functionally important and evolutionarily conserved codon positions, codons and genes encoding membrane-bound proteins. In particular, abundance of RNA editing in plant organellar genomes may be associated with disproportionately large percentages of genes in these two genomes that encode membrane-bound proteins, which are rich in hydrophobic amino acids and selectively constrained. These data support a hypothesis that natural selection imposed by protein functional constraints has contributed to selective fixation of certain editing sites and maintenance of the editing activity in plant organelles over a period of more than four hundred millions years. The retention of genes encoding RNA editing activity may be driven by forces that shape nucleotide composition equilibrium in two organellar genomes of these plants. Nevertheless, the causes of lineage-specific occurrence of a large portion of RNA editing sites remain to be determined.</p> <p>Reviewers</p> <p>This article was reviewed by Michael Gray (nominated by Laurence Hurst), Kirsten Krause (nominated by Martin Lercher), and Jeffery Mower (nominated by David Ardell).</p

Phylogenetic inference in Rafflesiales: the influence of rate heterogeneity and horizontal gene transfer

BACKGROUND: The phylogenetic relationships among the holoparasites of Rafflesiales have remained enigmatic for over a century. Recent molecular phylogenetic studies using the mitochondrial matR gene placed Rafflesia, Rhizanthes and Sapria (Rafflesiaceae s. str.) in the angiosperm order Malpighiales and Mitrastema (Mitrastemonaceae) in Ericales. These phylogenetic studies did not, however, sample two additional groups traditionally classified within Rafflesiales (Apodantheaceae and Cytinaceae). Here we provide molecular phylogenetic evidence using DNA sequence data from mitochondrial and nuclear genes for representatives of all genera in Rafflesiales. RESULTS: Our analyses indicate that the phylogenetic affinities of the large-flowered clade and Mitrastema, ascertained using mitochondrial matR, are congruent with results from nuclear SSU rDNA when these data are analyzed using maximum likelihood and Bayesian methods. The relationship of Cytinaceae to Malvales was recovered in all analyses. Relationships between Apodanthaceae and photosynthetic angiosperms varied depending upon the data partition: Malvales (3-gene), Cucurbitales (matR) or Fabales (atp1). The latter incongruencies suggest that horizontal gene transfer (HGT) may be affecting the mitochondrial gene topologies. The lack of association between Mitrastema and Ericales using atp1 is suggestive of HGT, but greater sampling within eudicots is needed to test this hypothesis further. CONCLUSIONS: Rafflesiales are not monophyletic but composed of three or four independent lineages (families): Rafflesiaceae, Mitrastemonaceae, Apodanthaceae and Cytinaceae. Long-branch attraction appears to be misleading parsimony analyses of nuclear small-subunit rDNA data, but model-based methods (maximum likelihood and Bayesian analyses) recover a topology that is congruent with the mitochondrial matR gene tree, thus providing compelling evidence for organismal relationships. Horizontal gene transfer appears to be influencing only some taxa and some mitochondrial genes, thus indicating that the process is acting at the single gene (not whole genome) level

The Mitochondrial Genomes of the Early Land Plants Treubia lacunosa and Anomodon rugelii: Dynamic and Conservative Evolution

Early land plant mitochondrial genomes captured important changes of mitochondrial genome evolution when plants colonized land. The chondromes of seed plants show several derived characteristics, e.g., large genome size variation, rapid intra-genomic rearrangement, abundant introns, and highly variable levels of RNA editing. On the other hand, the chondromes of charophytic algae are still largely ancestral in these aspects, resembling those of early eukaryotes. When the transition happened has been a long-standing question in studies of mitochondrial genome evolution. Here we report complete mitochondrial genome sequences from an early-diverging liverwort, Treubia lacunosa, and a late-evolving moss, Anomodon rugelii. The two genomes, 151,983 and 104,239 base pairs in size respectively, contain standard sets of protein coding genes for respiration and protein synthesis, as well as nearly full sets of rRNA and tRNA genes found in the chondromes of the liverworts Marchantia polymorpha and Pleurozia purpurea and the moss Physcomitrella patens. The gene orders of these two chondromes are identical to those of the other liverworts and moss. Their intron contents, with all cis-spliced group I or group II introns, are also similar to those in the previously sequenced liverwort and moss chondromes. These five chondromes plus the two from the hornworts Phaeoceros laevis and Megaceros aenigmaticus for the first time allowed comprehensive comparative analyses of structure and organization of mitochondrial genomes both within and across the three major lineages of bryophytes. These analyses led to the conclusion that the mitochondrial genome experienced dynamic evolution in genome size, gene content, intron acquisition, gene order, and RNA editing during the origins of land plants and their major clades. However, evolution of this organellar genome has remained rather conservative since the origin and initial radiation of early land plants, except within vascular plants

A phylogenetic analysis of Apostasioideae (Orchidaceae) based on ITS, trn L-F and mat K sequences

The orchid subfamily Apostasioideae consists of two genera, Apostasia and Neuwiedia . To study the position of Apostasioideae within Orchidaceae and their intra- and intergeneric relationships, a molecular phylogenetic analysis has been conducted on the nuclear ITS region and the two plastid DNA regions trn L-F intron and mat K. The two genera traditionally ascribed to Apostasioideae are each monophyletic. In Apostasia , A. nuda , with two stamens and no staminode, is sister to a clade comprising three species characterised by two stamens and one staminode. Within Neuwiedia , maximum parsimony analyses place N. zollingeri as sister to the clade formed by N. borneensis and N. veratrifolia . A family-wide phylogenetic analysis of mat K sequences representing all proposed subfamilies of Orchidaceae produced five moderately to well-supported clades. One of these clades, Apostasioideae, is sister to the clade formed by Vanilloideae, Cypripedioideae, Orchidoideae and Epidendroideae. High transition-transversion ratio and the absence of stop codons in the individual sequences suggest that mat K is at the transition from a possibly functional gene to a pseudogene in Apostasioideae, contrary to what is found in some other groups of Orchidaceae.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/41641/1/606_2004_Article_133.pd

Lycophyte plastid genomics: extreme variation in GC, gene and intron content and multiple inversions between a direct and inverted orientation of the rRNA repeat

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/148375/1/nph15650_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/148375/2/nph15650.pd

Lycophyte plastid genomics: extreme variation in GC, gene and intron content and multiple inversions between a direct and inverted orientation of the rRNA repeat

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/148375/1/nph15650_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/148375/2/nph15650.pd

Imaging Features of Pediatric Pentastomiasis Infection: a Case Report

We report here a case of pentastomiasis infection in a 3-year-old girl who had high fever, abdominal pain, abdominal tension and anemia. Ultrasound scanning of the abdomen revealed disseminated hyperechoic nodules in the liver and a small amount of ascites. Abdominal MRI showed marked hepatomegaly with disseminated miliary nodules of high signal intensity throughout the hepatic parenchyma on T2-weighted images; retroperitoneal lymphadenopathy and disseminated miliary nodules on the peritoneum were also noted. Chest CT showed scattered small hyperdense nodules on both sides of the lungs. The laparoscopy demonstrated diffuse white nodules on the liver surface and the peritoneum. After the small intestinal wall and peritoneal biopsy, histological examination revealed parenchymal tubercles containing several larvae of pentastomids and a large amount of inflammatory cell infiltration around them. The pathological diagnosis was parasitic granuloma from pentastomiasis infection

Mitochondrial matR sequences help to resolve deep phylogenetic relationships in rosids

<p>Abstract</p> <p>Background</p> <p>Rosids are a major clade in the angiosperms containing 13 orders and about one-third of angiosperm species. Recent molecular analyses recognized two major groups (i.e., fabids with seven orders and malvids with three orders). However, phylogenetic relationships within the two groups and among fabids, malvids, and potentially basal rosids including Geraniales, Myrtales, and Crossosomatales remain to be resolved with more data and a broader taxon sampling. In this study, we obtained DNA sequences of the mitochondrial <it>matR </it>gene from 174 species representing 72 families of putative rosids and examined phylogenetic relationships and phylogenetic utility of <it>matR </it>in rosids. We also inferred phylogenetic relationships within the "rosid clade" based on a combined data set of 91 taxa and four genes including <it>matR</it>, two plastid genes (<it>rbcL</it>, <it>atpB</it>), and one nuclear gene (18S rDNA).</p> <p>Results</p> <p>Comparison of mitochondrial <it>matR </it>and two plastid genes (<it>rbcL </it>and <it>atpB</it>) showed that the synonymous substitution rate in <it>matR </it>was approximately four times slower than those of <it>rbcL </it>and <it>atpB</it>; however, the nonsynonymous substitution rate in <it>matR </it>was relatively high, close to its synonymous substitution rate, indicating that the <it>matR </it>has experienced a relaxed evolutionary history. Analyses of our <it>matR </it>sequences supported the monophyly of malvids and most orders of the rosids. However, fabids did not form a clade; instead, the COM clade of fabids (Celastrales, Oxalidales, Malpighiales, and Huaceae) was sister to malvids. Analyses of the four-gene data set suggested that Geraniales and Myrtales were successively sister to other rosids, and that Crossosomatales were sister to malvids.</p> <p>Conclusion</p> <p>Compared to plastid genes such as <it>rbcL </it>and <it>atpB</it>, slowly evolving <it>matR </it>produced less homoplasious but not less informative substitutions. Thus, <it>matR </it>appears useful in higher-level angiosperm phylogenetics. Analysis of <it>matR </it>alone identified a novel deep relationship within rosids, the grouping of the COM clade of fabids and malvids, which was not resolved by any previous molecular analyses but recently suggested by floral structural features. Our four-gene analysis supported the placements of Geraniales, Myrtales at basal nodes of the rosid clade and placed Crossosomatales as sister to malvids. We also suggest that the core part of rosids should include fabids, malvids and Crossosomatales.</p

Multiple major increases and decreases in mitochondrial substitution rates in the plant family Geraniaceae

Background: Rates of synonymous nucleotide substitutions are, in general, exceptionally low in plant mitochondrial genomes, several times lower than in chloroplast genomes, 10-20 times lower than in plant nuclear genomes, and 50-100 times lower than in many animal mitochondrial genomes. Several cases of moderate variation in mitochondrial substitution rates have been reported in plants, but these mostly involve correlated changes in chloroplast and/or nuclear substitution rates and are therefore thought to reflect whole-organism forces rather than ones impinging directly on the mitochondrial mutation rate. Only a single case of extensive, mitochondrial-specific rate changes has been described, in the angiosperm genus Plantago. Results: We explored a second potential case of highly accelerated mitochondrial sequence evolution in plants. This case was first suggested by relatively poor hybridization of mitochondrial gene probes to DNA of Pelargonium hortorum (the common geranium). We found that all eight mitochondrial genes sequenced from P. hortorum are exceptionally divergent, whereas chloroplast and nuclear divergence is unexceptional in P. hortorum. Two mitochondrial genes were sequenced from a broad range of taxa of variable relatedness to P. hortorum, and absolute rates of mitochondrial synonymous substitutions were calculated on each branch of a phylogenetic tree of these taxa. We infer one major, similar to 10-fold increase in the mitochondrial synonymous substitution rate at the base of the Pelargonium family Geraniaceae, and a subsequent similar to 10-fold rate increase early in the evolution of Pelargonium. We also infer several moderate to major rate decreases following these initial rate increases, such that the mitochondrial substitution rate has returned to normally low levels in many members of the Geraniaceae. Finally, we find unusually little RNA editing of Geraniaceae mitochondrial genes, suggesting high levels of retroprocessing in their history. Conclusion: The existence of major, mitochondrial-specific changes in rates of synonymous substitutions in the Geraniaceae implies major and reversible underlying changes in the mitochondrial mutation rate in this family. Together with the recent report of a similar pattern of rate heterogeneity in Plantago, these findings indicate that the mitochondrial mutation rate is a more plastic character in plants than previously realized. Many molecular factors could be responsible for these dramatic changes in the mitochondrial mutation rate, including nuclear gene mutations affecting the fidelity and efficacy of mitochondrial DNA replication and/or repair and consistent with the lack of RNA editing - exceptionally high levels of mutagenic retroprocessing. That the mitochondrial mutation rate has returned to normally low levels in many Geraniaceae raises the possibility that, akin to the ephemerality of mutator strains in bacteria, selection favors a low mutation rate in plant mitochondria