Constraints on the evolution of plastid introns: the group II intron in the gene encoding tRNA-Val(UAC).


:The evolution of the group II intron in the plastid gene encoding tRNA(Val)UAC (trnV) from seven plant taxa was studied by aligning secondary and other structural features. Levels of evolutionary divergence between six angiosperms and a liverwort, Marchantia polymorpha, were compared for the six domains commonly demonstrated for group II introns and were shown to be statistically heterogeneous. Evolutionary rates varied substantially among various domains and other features. Domain II showed the highest evolutionary rate, approaching the synonymous substitution rate reported for cpDNA-encoded genes, while domain VI and the helix and loop region bearing EBS1 evolved at rates similar to those for nonsynonymous substitutions of a number of cpDNA-encoded genes. The minimum free-energy structure of domain I varied among the seven taxa, suggesting that possible protein-RNA or tertiary interactions are important for intron processing.


Mol Biol Evol


Learn GH Jr,Shore JS,Furnier GR,Zurawski G,Clegg MT




Has Abstract


1992-09-01 00:00:00












  • Evidence that the human X chromosome is enriched for male-specific but not female-specific genes.

    abstract::There is increasing evidence that X chromosomes have an unusual complement of genes, especially genes that have sex-specific expression. However, whereas in worm and fly the X chromosome has a dearth of male-specific genes, in mice genes that are uniquely expressed in spermatogonia are especially abundant on the X chr...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Lercher MJ,Urrutia AO,Hurst LD

    更新日期:2003-07-01 00:00:00

  • Protein function, connectivity, and duplicability in yeast.

    abstract::Protein-protein interaction networks have evolved mainly through connectivity rewiring and gene duplication. However, how protein function influences these processes and how a network grows in time have not been well studied. Using protein-protein interaction data and genomic data from the budding yeast, we first exam...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Prachumwat A,Li WH

    更新日期:2006-01-01 00:00:00

  • Horizontal transfer and selection in the evolution of P elements.

    abstract::The roles of selection and horizontal transfer in the evolution of the canonical subfamily of P: elements were studied in the saltans and willistoni species groups of the genus Drosophila (subgenus Sophophora). We estimate that the common ancestor of the canonical P: subfamily dates back 2-3 Myr at the most, despite t...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Silva JC,Kidwell MG

    更新日期:2000-10-01 00:00:00

  • Conservation of alternative splicing and genomic organization of the myosin alkali light-chain (Mlc1) gene among Drosophila species.

    abstract::The Mlc1 gene of Drosophila melanogaster encodes two MLC1 isoforms via developmentally regulated alternative pre-mRNA splicing. In larval muscle and tubular and abdominal muscles of adults, all of the six exons are included in the spliced mRNA, whereas, in the fibrillar indirect flight muscle of adult, exon 5 is exclu...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Leicht BG,Lyckegaard EM,Benedict CM,Clark AG

    更新日期:1993-07-01 00:00:00

  • Determinants of adaptive evolution at the molecular level: the extended complexity hypothesis.

    abstract::To explain why informational genes (i.e., those involved in transcription, translation, and related processes) are less likely than housekeeping genes to be horizontally transferred, Jain and coworkers proposed the complexity hypothesis. The underlying idea is that informational genes belong to large, complex systems ...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Aris-Brosou S

    更新日期:2005-02-01 00:00:00

  • Conserved motifs reveal details of ancestry and structure in the small TIM chaperones of the mitochondrial intermembrane space.

    abstract::The mitochondrial inner and outer membranes are composed of a variety of integral membrane proteins, assembled into the membranes posttranslationally. The small translocase of the inner mitochondrial membranes (TIMs) are a group of approximately 10 kDa proteins that function as chaperones to ferry the imported protein...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Gentle IE,Perry AJ,Alcock FH,Likić VA,Dolezal P,Ng ET,Purcell AW,McConnville M,Naderer T,Chanez AL,Charrière F,Aschinger C,Schneider A,Tokatlidis K,Lithgow T

    更新日期:2007-05-01 00:00:00

  • The evolutionary history of archaeal MCM helicases: a case study of vertical evolution combined with hitchhiking of mobile genetic elements.

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    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Krupovic M,Gribaldo S,Bamford DH,Forterre P

    更新日期:2010-12-01 00:00:00

  • G+C content variation along and among Saccharomyces cerevisiae chromosomes.

    abstract::Past analyses of the genome of the yeast Saccharomyces cerevisiae have revealed substantial regional variation in G+C content. Important questions remain, though, as to the origin, nature, significance, and generality of this variation. We conducted an extensive analysis of the yeast genome to try to answer these ques...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Bradnam KR,Seoighe C,Sharp PM,Wolfe KH

    更新日期:1999-05-01 00:00:00

  • A role for selection in regulating the evolutionary emergence of disease-causing and other coding CAG repeats in humans and mice.

    abstract::The evolutionary expansion of CAG repeats in human triplet expansion disease genes is intriguing because of their deleterious phenotype. In the past, this expansion has been suggested to reflect a broad genomewide expansion of repeats, which would imply that mutational and evolutionary processes acting on repeats diff...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Hancock JM,Worthey EA,Santibáñez-Koref MF

    更新日期:2001-06-01 00:00:00

  • The Genotype-Phenotype Relationships in the Light of Natural Selection.

    abstract::Although any genotype-phenotype relationships are a result of evolution, little is known about how natural selection and neutral drift, two distinct driving forces of evolution, operate to shape the relationships. By analyzing ∼500 yeast quantitative traits, we reveal a basic "supervisor-worker" gene architecture unde...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Chen H,Wu CI,He X

    更新日期:2018-03-01 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

  • Empirical assessment of RAD sequencing for interspecific phylogeny.

    abstract::Next-generation sequencing opened up new possibilities in phylogenetics; however, choosing an appropriate method of sample preparation remains challenging. Here, we demonstrate that restriction-site-associated DNA sequencing (RAD-seq) generates useful data for phylogenomics. Analysis of our RAD library using current b...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Cruaud A,Gautier M,Galan M,Foucaud J,Sauné L,Genson G,Dubois E,Nidelet S,Deuve T,Rasplus JY

    更新日期:2014-05-01 00:00:00

  • Estimation of hominoid ancestral population sizes under bayesian coalescent models incorporating mutation rate variation and sequencing errors.

    abstract::Estimation of population parameters for the common ancestors of humans and the great apes is important in understanding our evolutionary history. In particular, inference of population size for the human-chimpanzee common ancestor may shed light on the process by which the 2 species separated and on whether the human ...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Burgess R,Yang Z

    更新日期:2008-09-01 00:00:00

  • Evolutionary relationships of class II major-histocompatibility-complex genes in mammals.

    abstract::The major histocompatibility complex (MHC) class II molecule consists of noncovalently associated alpha and beta chains. In mammals studied so far, the class II MHC can be divided into a number of regions, each containing one or more alpha-chain genes (A genes) and beta-chain genes (B genes), and it has been known for...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Hughes AL,Nei M

    更新日期:1990-11-01 00:00:00

  • Tracing the Austronesian footprint in Mainland Southeast Asia: a perspective from mitochondrial DNA.

    abstract::As the relic of the ancient Champa Kingdom, the Cham people represent the major Austronesian speakers in Mainland Southeast Asia (MSEA) and their origin is evidently associated with the Austronesian diffusion in MSEA. Hitherto, hypotheses stemming mainly from linguistic and cultural viewpoints on the origin of the Cha...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Peng MS,Quang HH,Dang KP,Trieu AV,Wang HW,Yao YG,Kong QP,Zhang YP

    更新日期:2010-10-01 00:00:00

  • Nontoxic strains of cyanobacteria are the result of major gene deletion events induced by a transposable element.

    abstract::Blooms that are formed by cyanobacteria consist of toxic and nontoxic strains. The mechanisms that result in the occurrence of nontoxic strains are enigmatic. All the nontoxic strains of the filamentous cyanobacterium Planktothrix that were isolated from 9 European countries were found to have lost 90% of a large micr...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Christiansen G,Molitor C,Philmus B,Kurmayer R

    更新日期:2008-08-01 00:00:00

  • MitoFish and MiFish Pipeline: A Mitochondrial Genome Database of Fish with an Analysis Pipeline for Environmental DNA Metabarcoding.

    abstract::Fish mitochondrial genome (mitogenome) data form a fundamental basis for revealing vertebrate evolution and hydrosphere ecology. Here, we report recent functional updates of MitoFish, which is a database of fish mitogenomes with a precise annotation pipeline MitoAnnotator. Most importantly, we describe implementation ...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Sato Y,Miya M,Fukunaga T,Sado T,Iwasaki W

    更新日期:2018-06-01 00:00:00

  • Positions of multiple insertions in SSU rDNA of lichen-forming fungi.

    abstract::Lichen-forming fungi, in symbiotic associations with algae, frequently have nuclear small subunit ribosomal DNA (SSU rDNA) longer than the 1,800 nucleotides typical for eukaryotes. The lichen-forming ascomycetous fungus Lecanora dispersa contains insertions at eight distinct positions of its SSU rDNA; the lichen-formi...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Gargas A,DePriest PT,Taylor JW

    更新日期:1995-03-01 00:00:00

  • Widespread evolutionary conservation of alternatively spliced exons in Caenorhabditis.

    abstract::Alternative splicing (AS) contributes to increased transcriptome and proteome diversity in various eukaryotic lineages. Previous studies showed low levels of conservation of alternatively spliced (cassette) exons within mammals and within dipterans. We report a strikingly different pattern in Caenorhabditis nematodes-...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Irimia M,Rukov JL,Penny D,Garcia-Fernandez J,Vinther J,Roy SW

    更新日期:2008-02-01 00:00:00

  • Splicing and transcription differ between spore and intracellular life stages in the parasitic microsporidia.

    abstract::Microsporidia are a diverse group of highly derived fungal relatives that are intracellular parasites of many animals. Both transcription and introns have been shown to be unusual in microsporidia: The complete genome of the human parasite Encephalitozoon cuniculi has only a few very short introns, and two distantly r...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Gill EE,Lee RC,Corradi N,Grisdale CJ,Limpright VO,Keeling PJ,Fast NM

    更新日期:2010-07-01 00:00:00

  • Accelerated evolution of functional plastid rRNA and elongation factor genes due to reduced protein synthetic load after the loss of photosynthesis in the chlorophyte alga Polytoma.

    abstract::Polytoma obtusum and Polytoma uvella are members of a clade of nonphotosynthetic chlorophyte algae closely related to Chlamydomonas humicola and other photosynthetic members of the Chlamydomonadaceae. Descended from a nonphotosynthetic mutant, these obligate heterotrophs retain a plastid (leucoplast) with a functional...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Vernon D,Gutell RR,Cannone JJ,Rumpf RW,Birky CW Jr

    更新日期:2001-09-01 00:00:00

  • Elucidation of Codon Usage Signatures across the Domains of Life.

    abstract::Because of the degeneracy of the genetic code, multiple codons are translated into the same amino acid. Despite being "synonymous," these codons are not equally used. Selective pressures are thought to drive the choice among synonymous codons within a genome, while GC content, which is typically attributed to mutation...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Novoa EM,Jungreis I,Jaillon O,Kellis M

    更新日期:2019-10-01 00:00:00

  • The covariation between TpA deficiency, CpG deficiency, and G+C content of human isochores is due to a mathematical artifact.

    abstract::CpG and TpA dinucleotides are underrepresented in the human genome. The CpG deficiency is due to the high mutation rate from C to T in methylated CpG's. The TpA suppression was thought to reflect a counterselection against TpA's destabilizing effect in RNA. Unexpectedly, the TpA and CpG deficiencies vary according to ...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Duret L,Galtier N

    更新日期:2000-11-01 00:00:00

  • Small RNAs Reflect Grandparental Environments in Apomictic Dandelion.

    abstract::Plants can show long-term effects of environmental stresses and in some cases a stress "memory" has been reported to persist across generations, potentially mediated by epigenetic mechanisms. However, few documented cases exist of transgenerational effects that persist for multiple generations and it remains unclear i...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Morgado L,Preite V,Oplaat C,Anava S,Ferreira de Carvalho J,Rechavi O,Johannes F,Verhoeven KJF

    更新日期:2017-08-01 00:00:00

  • Asymmetric evolution in two fish-specifically duplicated receptor tyrosine kinase paralogons involved in teleost coloration.

    abstract::The occurrence of a fish-specific genome duplication (FSGD) in the lineage leading to teleost fishes is widely accepted, but the consequences of this event remain elusive. Teleosts, and the cichlid fishes from the species flocks in the East African Great Lakes in particular, evolved a unique complexity and diversity o...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Braasch I,Salzburger W,Meyer A

    更新日期:2006-06-01 00:00:00

  • The effect of single nucleotide polymorphism identification strategies on estimates of linkage disequilibrium.

    abstract::At present there is tremendous interest in characterizing the magnitude and distribution of linkage disequilibrium (LD) throughout the human genome, which will provide the necessary foundation for genome-wide LD analyses and facilitate detailed evolutionary studies. To this end, a human high-density single-nucleotide ...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Akey JM,Zhang K,Xiong M,Jin L

    更新日期:2003-02-01 00:00:00

  • Isolation of homeodomain-leucine zipper genes from the moss Physcomitrella patens and the evolution of homeodomain-leucine zipper genes in land plants.

    abstract::Homeobox genes encode transcription factors involved in many aspects of developmental processes. The homeodomain-leucine zipper (HD-Zip) genes, which are characterized by the presence of both a homeodomain and a leucine zipper motif, form a clade within the homeobox superfamily and were previously reported only from v...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Sakakibara K,Nishiyama T,Kato M,Hasebe M

    更新日期:2001-04-01 00:00:00

  • Improving Bayesian population dynamics inference: a coalescent-based model for multiple loci.

    abstract::Effective population size is fundamental in population genetics and characterizes genetic diversity. To infer past population dynamics from molecular sequence data, coalescent-based models have been developed for Bayesian nonparametric estimation of effective population size over time. Among the most successful is a G...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Gill MS,Lemey P,Faria NR,Rambaut A,Shapiro B,Suchard MA

    更新日期:2013-03-01 00:00:00

  • Spread of the autonomous transposable element hobo in the genome of Drosophila melanogaster.

    abstract::The transposable element hobo has been introduced into the previously empty Drosophila melanogaster strain Hikone so that its dynamics can be followed and it can be compared with the P element. Five transformed lines were followed over 58 generations. The results were highly dependent on the culture temperature, the s...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Galindo MI,Ladevèze V,Lemeunier F,Kalmes R,Periquet G,Pascual L

    更新日期:1995-09-01 00:00:00

  • Sequential evolution of a symbiont inferred from the host: Wolbachia and Drosophila simulans.

    abstract::This study aims to unravel the biogeography of a model symbiont/host system by exploiting the prediction that a symbiont will leave a signature of infection on the host. Specifically, a global sample of 1,442 Drosophila simulans from 33 countries and 64 sampling localities was employed to infer the phylogeography of t...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Ballard JW

    更新日期:2004-03-01 00:00:00