Evolutionary transfer of ORF-containing group I introns between different subcellular compartments (chloroplast and mitochondrion).


:We describe here a case of homologous introns containing homologous open reading frames (ORFs) that are inserted at the same site in the large subunit (LSU) rRNA gene of different organelles in distantly related organisms. We show that the chloroplast LSU rRNA gene of the green alga Chlamydomonas pallidostigmatica contains a group I intron (CpLSU.2) encoding a site-specific endonuclease (I-CpaI). This intron is inserted at the identical site (corresponding to position 1931-1932 of the Escherichia coli 23S rRNA sequence) as a group I intron (AcLSU.m1) in the mitochondrial LSU rRNA gene of the amoeboid protozoon Acanthamoeba castellanii. The CpLSU.2 intron displays a remarkable degree of nucleotide similarity in both primary sequence and secondary structure to the AcLSU.m1 intron; moreover, the Acanthamoeba intron contains an ORF in the same location within its secondary structure as the CpLSU.2 ORF and shares with it a strikingly high level of amino acid similarity (65%; 42% identity). A comprehensive survey of intron distribution at site 1931 of the chloroplast LSU rRNA gene reveals a rather restricted occurrence within the polyphyletic genus Chlamydomonas, with no evidence of this intron among a number of non-Chlamydomonad green algae surveyed, nor in land plants. A parallel survey of homologues of a previously described and similar intron/ORF pair (C. reinhardtii chloroplast CrLSU/A. castellanii mitochondrial AcLSU.m3) also shows a restricted occurrence of this intron (site 2593) among chloroplasts, although the intron distribution is somewhat broader than that observed at site 1931, with site-2593 introns appearing in several green algal branches outside of the Chlamydomonas lineage. The available data, while not definitive, are most consistent with a relatively recent horizontal transfer of both site-1931 and site-2593 introns (and their contained ORFs) between the chloroplast of a Chlamydomonas-type organism and the mitochondrion of an Acanthamoeba-like organism, probably in the direction chloroplast to mitochondrion. The data also suggest that both introns could have been acquired in a single event.


Mol Biol Evol


Turmel M,Côté V,Otis C,Mercier JP,Gray MW,Lonergan KM,Lemieux C




Has Abstract


1995-07-01 00:00:00












  • The mysterious evolutionary origin for the GNE gene and the root of bilateria.

    abstract::Phylogenomic analyses have revealed several important metazoan clades, such as the Ecdysozoa and the Lophotrochozoa. However, the phylogenetic positions of a few taxa, such as ctenophores, chaetognaths, acoelomorphs, and Xenoturbella, remain contentious. Thus, the findings of qualitative markers or "rare genomic chang...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: de Mendoza A,Ruiz-Trillo I

    更新日期:2011-11-01 00:00:00

  • Selective sweeps at the organophosphorus insecticide resistance locus, Rop-1, have affected variation across and beyond the α-esterase gene cluster in the Australian sheep blowfly, Lucilia cuprina.

    abstract::A major theoretical consequence of selection at a locus is the genetic hitchhiking of linked sites (selective sweep). The extent of hitchhiking around a gene is related to the strength of selection and the rate of recombination, with its impact diminishing with distance from the selected site. At the Rop-1 locus of th...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Rose CJ,Chapman JR,Marshall SD,Lee SF,Batterham P,Ross HA,Newcomb RD

    更新日期:2011-06-01 00:00:00

  • Phylogenomic analysis supports the monophyly of cryptophytes and haptophytes and the association of rhizaria with chromalveolates.

    abstract::Here we use phylogenomics with expressed sequence tag (EST) data from the ecologically important coccolithophore-forming alga Emiliania huxleyi and the plastid-lacking cryptophyte Goniomonas cf. pacifica to establish their phylogenetic positions in the eukaryotic tree. Haptophytes and cryptophytes are members of the p...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Hackett JD,Yoon HS,Li S,Reyes-Prieto A,Rümmele SE,Bhattacharya D

    更新日期:2007-08-01 00:00:00

  • Divergent evolution and evolution by the birth-and-death process in the immunoglobulin VH gene family.

    abstract::Immunoglobulin diversity is generated primarily by the heavy- and light-chain variable-region gene families. To understand the pattern of long-term evolution of the heavy-chain variable-region (VH) gene family, which is composed of a large number of member genes, the evolutionary relationships of representative VH gen...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Ota T,Nei M

    更新日期:1994-05-01 00:00:00

  • ModelTeller: Model Selection for Optimal Phylogenetic Reconstruction Using Machine Learning.

    abstract::Statistical criteria have long been the standard for selecting the best model for phylogenetic reconstruction and downstream statistical inference. Although model selection is regarded as a fundamental step in phylogenetics, existing methods for this task consume computational resources for long processing time, they ...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Abadi S,Avram O,Rosset S,Pupko T,Mayrose I

    更新日期:2020-11-01 00:00:00

  • Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Genome-wide search of gene conversions in duplicated genes of mouse and rat.

    abstract::Gene conversion is considered to play important roles in the formation of genomic makeup such as homogenization of multigene families and diversification of alleles. We devised two statistical tests on quartets for detecting gene conversion events. Each "quartet" consists of two pairs of orthologous sequences supposed...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Ezawa K,OOta S,Saitou N,SMBE Tri-National Young Investigators.

    更新日期:2006-05-01 00:00:00

  • A model of directional selection applied to the evolution of drug resistance in HIV-1.

    abstract::Understanding how pathogens acquire resistance to drugs is important for the design of treatment strategies, particularly for rapidly evolving viruses such as HIV-1. Drug treatment can exert strong selective pressures and sites within targeted genes that confer resistance frequently evolve far more rapidly than the ne...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Seoighe C,Ketwaroo F,Pillay V,Scheffler K,Wood N,Duffet R,Zvelebil M,Martinson N,McIntyre J,Morris L,Hide W

    更新日期:2007-04-01 00:00:00

  • Purifying selection modulates the estimates of population differentiation and confounds genome-wide comparisons across single-nucleotide polymorphisms.

    abstract::An improved understanding of the biological and numerical properties of measures of population differentiation across loci is becoming increasingly more important because of their growing use in analyzing genome-wide polymorphism data for detecting population structures, inferring the rates of migration, and identifyi...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Maruki T,Kumar S,Kim Y

    更新日期:2012-12-01 00:00:00

  • Arsenite oxidase, an ancient bioenergetic enzyme.

    abstract::Operons coding for the enzyme arsenite oxidase have been detected in the genomes from Archaea and Bacteria by Blast searches using the amino acid sequences of the respective enzyme characterized in two different beta-proteobacteria as templates. Sequence analyses show that in all these species, arsenite oxidase is tra...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Lebrun E,Brugna M,Baymann F,Muller D,Lièvremont D,Lett MC,Nitschke W

    更新日期:2003-05-01 00:00:00

  • The phylogenetic position of Rhopalura ophiocomae (Orthonectida) based on 18S ribosomal DNA sequence analysis.

    abstract::The Orthonectida is a small, poorly known phylum of parasites of marine invertebrates. Their phylogenetic placement is obscure; they have been considered to be multicellular protozoans, primitive animals at a "mesozoan" grade of organization, or secondarily simplified flatworm-like organisms. The best known species in...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Hanelt B,Van Schyndel D,Adema CM,Lewis LA,Loker ES

    更新日期:1996-11-01 00:00:00

  • Numerous transposed sequences of mitochondrial cytochrome oxidase I-II in aphids of the genus Sitobion (Hemiptera: Aphididae).

    abstract::Polymerase chain reaction (PCR) products corresponding to 803 bp of the cytochrome oxidase subunits I and II region of mitochondrial DNA (mtDNA COI-II) were deduced to consist of multiple haplotypes in three Sitobion species. We investigated the molecular basis of these observations. PCR products were cloned, and six ...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Sunnucks P,Hales DF

    更新日期:1996-03-01 00:00:00

  • Cross-Study Comparison Reveals Common Genomic, Network, and Functional Signatures of Desiccation Resistance in Drosophila melanogaster.

    abstract::Repeated attempts to map the genomic basis of complex traits often yield different outcomes because of the influence of genetic background, gene-by-environment interactions, and/or statistical limitations. However, where repeatability is low at the level of individual genes, overlap often occurs in gene ontology categ...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Telonis-Scott M,Sgrò CM,Hoffmann AA,Griffin PC

    更新日期:2016-04-01 00:00:00

  • Sequencing errors and molecular evolutionary analysis.

    abstract::Heuristic approaches were used to quantify the influence that sequencing errors have on estimates of nucleotide diversity, substitution rate, and the construction of genealogies. Error rates of less than 1 nucleotide/kb probably have little affect on conclusions about the evolutionary history of highly polymorphic org...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Clark AG,Whittam TS

    更新日期:1992-07-01 00:00:00

  • Evolution of immunoglobulin VH pseudogenes in chickens.

    abstract::In chickens, there is a single functional gene (VH1) coding for the heavy chain variable region of immunoglobulins, and immunoglobulin diversity is generated by gene conversion of the VH1 gene by many variable region pseudogenes (psi VH's) that exist on the 5' side of the VH1 gene. To understand the evolution of this ...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Ota T,Nei M

    更新日期:1995-01-01 00:00:00

  • Odorant Receptors for Detecting Flowering Plant Cues Are Functionally Conserved across Moths and Butterflies.

    abstract::Odorant receptors (ORs) are essential for plant-insect interactions. However, despite the global impacts of Lepidoptera (moths and butterflies) as major herbivores and pollinators, little functional data is available about Lepidoptera ORs involved in plant volatile detection. Here, we initially characterized the plant...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Guo M,Du L,Chen Q,Feng Y,Zhang J,Zhang X,Tian K,Cao S,Huang T,Jacquin-Joly E,Wang G,Liu Y

    更新日期:2020-11-24 00:00:00

  • Large-scale coding sequence change underlies the evolution of postdevelopmental novelty in honey bees.

    abstract::Whether coding or regulatory sequence change is more important to the evolution of phenotypic novelty is one of biology's major unresolved questions. The field of evo-devo has shown that in early development changes to regulatory regions are the dominant mode of genetic change, but whether this extends to the evolutio...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Jasper WC,Linksvayer TA,Atallah J,Friedman D,Chiu JC,Johnson BR

    更新日期:2015-02-01 00:00:00

  • First-Step Mutations during Adaptation Restore the Expression of Hundreds of Genes.

    abstract::The temporal change of phenotypes during the adaptive process remains largely unexplored, as do the genetic changes that affect these phenotypic changes. Here we focused on three mutations that rose to high frequency in the early stages of adaptation within 12 Escherichia coli populations subjected to thermal stress (...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Rodríguez-Verdugo A,Tenaillon O,Gaut BS

    更新日期:2016-01-01 00:00:00

  • The shoot stem cell niche in angiosperms: expression patterns of WUS orthologues in rice and maize imply major modifications in the course of mono- and dicot evolution.

    abstract::In Arabidopsis, stem cell homeostasis in the shoot apical meristem (SAM) is controlled by a feedback loop between WUS and CLV functions. We have identified WUS orthologues in maize and rice by a detailed phylogenetic analysis of the WOX gene family and subsequent cloning. A single WUS orthologue is present in the rice...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Nardmann J,Werr W

    更新日期:2006-12-01 00:00:00

  • Evolution of isochores in rodents.

    abstract::The most deviant isochore pattern within mammals was found in rat and mouse; most other mammals possess a different kind of isochore organization called the "general pattern." However, isochore patterns remain largely unknown in rodents other than mouse and rat. To investigate the taxonomic distribution of isochore pa...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Robinson M,Gautier C,Mouchiroud D

    更新日期:1997-08-01 00:00:00

  • Decreases in activation energy and substrate affinity in cold-adapted A4-lactate dehydrogenase: evidence from the Antarctic notothenioid fish Chaenocephalus aceratus.

    abstract::Enzyme function is strongly affected by temperature, and orthologs from species adapted to different thermal environments often show temperature compensation in kinetic properties. Antarctic notothenioid fishes live in a habitat of constant, extreme cold (-1.86 +/- 2 degrees C), and orthologs of the enzyme A4-lactate ...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Fields PA,Houseman DE

    更新日期:2004-12-01 00:00:00

  • A novel family of short interspersed repetitive elements (SINEs) from cichlids: the patterns of insertion of SINEs at orthologous loci support the proposed monophyly of four major groups of cichlid fishes in Lake Tanganyika.

    abstract::Short interspersed repetitive elements (SINEs) have been shown to be excellent markers of molecular phylogeny, since the integration of a SINE at a particular position in a genome can be considered an unambiguous derived homologous character. In the present study, we isolated a new family of SINEs from cichlids in Lak...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Takahashi K,Terai Y,Nishida M,Okada N

    更新日期:1998-04-01 00:00:00

  • Origin of a giant sex chromosome.

    abstract::Chromosome size and morphology vary within and among species, but little is known about the proximate or ultimate causes of these differences. Cichlid fish species in the tribe Oreochromini share an unusual giant chromosome that is ∼3 times longer than the other chromosomes. This giant chromosome functions as a sex ch...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Conte MA,Clark FE,Roberts RB,Xu L,Tao W,Zhou Q,Wang D,Kocher TD

    更新日期:2020-12-10 00:00:00

  • Phenotypic Plasticity Contributes to Maize Adaptation and Heterosis.

    abstract::Plant phenotypic plasticity describes altered phenotypic performance of an individual when grown in different environments. Exploring genetic architecture underlying plant plasticity variation may help mitigate the detrimental effects of a rapidly changing climate on agriculture, but little research has been done in t...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Liu N,Du Y,Warburton ML,Xiao Y,Yan J

    更新日期:2020-11-03 00:00:00

  • Mosaic origin of the heme biosynthesis pathway in photosynthetic eukaryotes.

    abstract::Heme biosynthesis represents one of the most essential metabolic pathways in living organisms, providing the precursors for cytochrome prosthetic groups, photosynthetic pigments, and vitamin B(12). Using genomic data, we have compared the heme pathway in the diatom Thalassiosira pseudonana and the red alga Cyanidiosch...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Oborník M,Green BR

    更新日期:2005-12-01 00:00:00

  • Conditional gene genealogies under strong purifying selection.

    abstract::The ancestral selection graph, conditioned on the allelic types in the sample, is used to obtain a limiting gene genealogical process under strong selection. In an equilibrium, two-allele system with strong selection, neutral gene genealogies are predicted for random samples and for samples containing at most one unfa...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Wakeley J

    更新日期:2008-12-01 00:00:00

  • Evolution of the TIR domain-containing adaptors in humans: swinging between constraint and adaptation.

    abstract::Natural selection is expected to act strongly on immune system genes as hosts adapt to novel, diverse, and coevolving pathogens. Population genetic studies of host defense genes with parallel functions in model organisms have revealed distinct evolutionary histories among the different components-receptors, adaptors, ...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Fornarino S,Laval G,Barreiro LB,Manry J,Vasseur E,Quintana-Murci L

    更新日期:2011-11-01 00:00:00

  • Complex evolution of light-dependent protochlorophyllide oxidoreductases in aerobic anoxygenic phototrophs: origin, phylogeny and function.

    abstract::Light-dependent and dark-operative protochlorophyllide oxidoreductases (LPORs and DPORs) are evolutionary and structurally distinct enzymes that are essential for the synthesis of (bacterio)chlorophyll, the primary pigment needed for both anoxygenic and oxygenic photosynthesis. In contrast to the long-held hypothesis ...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Chernomor O,Peters L,Schneidewind J,Loeschcke A,Knieps-Grünhagen E,Schmitz F,von Lieres E,Kutta RJ,Svensson V,Jaeger KE,Drepper T,von Haeseler A,Krauss U

    更新日期:2020-09-15 00:00:00

  • More Than One-to-Four via 2R: Evidence of an Independent Amphioxus Expansion and Two-Gene Ancestral Vertebrate State for MyoD-Related Myogenic Regulatory Factors (MRFs).

    abstract::The evolutionary transition from invertebrates to vertebrates involved extensive gene duplication, but understanding precisely how such duplications contributed to this transition requires more detailed knowledge of specific cases of genes and gene families. Myogenic differentiation (MyoD) has long been recognized as ...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Aase-Remedios ME,Coll-Lladó C,Ferrier DEK

    更新日期:2020-10-01 00:00:00

  • DNA-DNA hybridization evidence of the rapid rate of muroid rodent DNA evolution.

    abstract::Single-copy nuclear DNAs (scnDNAs) of eight species of arvicoline and six species of murine rodents were compared using DNA-DNA hybridization. The branching pattern derived from the DNA comparisons is congruent with the fossil evidence and supported by comparative biochemical, chromosomal, and morphological studies. T...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Catzeflis FM,Sheldon FH,Ahlquist JE,Sibley CG

    更新日期:1987-05-01 00:00:00

  • Analysis of piRNA-mediated silencing of active TEs in Drosophila melanogaster suggests limits on the evolution of host genome defense.

    abstract::The Piwi-interacting RNA (piRNA) pathway defends animal genomes against the harmful consequences of transposable element (TE) infection by imposing small-RNA-mediated silencing. Because silencing is targeted by TE-derived piRNAs, piRNA production is posited to be central to the evolution of genome defense. We harnesse...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Kelleher ES,Barbash DA

    更新日期:2013-08-01 00:00:00