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The mtDNA rns gene landscape in the Ophiostomatales and other fungal taxa: Twintrons, introns, and intron-encoded proteins

https://doi.org/10.1016/j.fgb.2013.01.005

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Group II twintron: an intron within an intron in a chloroplast cytochrome b‐559 gene.

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Function of the Neurospora crassa mitochondrial tyrosyl-tRNA synthetase in RNA splicing. Role of the idiosyncratic N-terminal extension and different modes of interaction with different group I introns

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Direct RNA motif definition and identification from multiple sequence alignments using secondary structure profiles 1 1Edited by J. Doudna

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Homing Endonucleases and Inteins

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Group I Introns and Their Maturases: Uninvited, but Welcome Guests

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Mitochondrial Excision-Amplification Plasmids in Senescent and Long-Lived Cultures of Podospora Anserina

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Organelle genetics : evolution of organelle genomes and gene expression

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Introns, Mobile Elements, and Plasmids

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Intercistronic group III introns in polycistronic ribosomal protein operons of chloroplasts

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Twintrons are not unique to the Euglena chloroplast genome: structure and evolution of a plastome cpn60 gene from a cryptomonad

inferredcites →https://doi.org/10.1007/bf00311881openalex-snapshot

Nucleotide-sequence analysis indicates that a DNA plasmid in a diseased isolate of Ophiostoma novo-ulmi is derived by recombination between two long repeat sequences in the mitochondrial large subunit ribosomal RNA gene

inferredcites →https://doi.org/10.1007/bf00418495openalex-snapshot

Analysis of class I introns in a mitochondrial plasmid associated with senescence of Podospora anserina reveals extraordinary resemblance to the Tetrahymena ribosomal intron

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A monograph of ceratocystis and ceratocystiopsis

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Evolutionary Dynamics of the mS952 Intron: A Novel Mitochondrial Group II Intron Encoding a LAGLIDADG Homing Endonuclease Gene

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Plasticity of the mitochondrial genome in Podospora. Polymorphism for 15 optional sequences: group-I, group-II introns, intronic ORFs and an intergenic region

inferredcites →https://doi.org/10.1007/s10267-012-0183-2openalex-snapshot

The mtDNA rps3 locus has been invaded by a group I intron in some species of Grosmannia

inferredcites →https://doi.org/10.1016/0022-2836(90)90386-zopenalex-snapshot

Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis

inferredcites →https://doi.org/10.1016/0378-1119(89)90026-7openalex-snapshot

Comparative and functional anatomy of group II catalytic introns — a review

inferredcites →https://doi.org/10.1016/0378-1119(89)90034-6openalex-snapshot

Group I introns as mobile genetic elements: Facts and mechanistic speculations — a review

inferredcites →https://doi.org/10.1016/0968-0004(93)90008-bopenalex-snapshot

Group II and group III introns of twintrons: potential relationships with nuclear pre-mRNA introns

inferredcites →https://doi.org/10.1016/j.femsyr.2003.12.005openalex-snapshot

Speciation in the large-spored clade and establishment of a new species, comb. nov.

inferredcites →https://doi.org/10.1016/j.fgb.2009.07.005openalex-snapshot

The Cryphonectria parasitica mitochondrial rns gene: Plasmid-like elements, introns and homing endonucleases

inferredcites →https://doi.org/10.1016/j.fgb.2011.05.006openalex-snapshot

A 971-bp insertion in the rns gene is associated with mitochondrial hypovirulence in a strain of Cryphonectria parasitica isolated from nature

inferredcites →https://doi.org/10.1016/j.funbio.2011.07.007openalex-snapshot

The highly variable mitochondrial small-subunit ribosomal RNA gene of Ophiostoma minus

inferredcites →https://doi.org/10.1016/j.funbio.2011.10.005openalex-snapshot

Identification of group I introns within the SSU rDNA gene in species of Ceratocystiopsis and related taxa

inferredcites →https://doi.org/10.1016/j.jmb.2010.02.001openalex-snapshot

Protein-Facilitated Folding of Group II Intron Ribozymes

inferredcites →https://doi.org/10.1016/j.mycres.2007.11.017openalex-snapshot

The sporadic occurrence of a group I intron-like element in the mtDNA rnl gene of Ophiostoma novo-ulmi subsp. americana

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Homing Endonucleases: From Microbial Genetic Invaders to Reagents for Targeted DNA Modification

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Folding of group II introns: a model system for large, multidomain RNAs?

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The ribozyme core of group II introns: a structure in want of partners

inferredcites →https://doi.org/10.1016/j.tig.2004.12.007openalex-snapshot

The natural history of group I introns

inferredcites →https://doi.org/10.1016/j.tig.2007.01.006openalex-snapshot

Mitochondrial introns: a critical view

inferredcites →https://doi.org/10.1016/j.tree.2004.07.002openalex-snapshot

Bayesian inference of character evolution

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Distribution of rRNA Introns in the Three-dimensional Structure of the Ribosome

inferredcites →https://doi.org/10.1016/s0065-2660(08)60460-5openalex-snapshot

The Variable Mitochondrial Genome of Ascomycetes: Organization, Mutational Alterations, and Expression

inferredcites →https://doi.org/10.1016/s0168-1656(98)00104-7openalex-snapshot

Group I twintrons: Genetic elements in myxomycete and schizopyrenid amoeboflagellate ribosomal DNAs

inferredcites →https://doi.org/10.1016/s0168-9525(01)02324-1openalex-snapshot

The ins and outs of group II introns

inferredcites →https://doi.org/10.1016/s0953-7562(09)81188-xopenalex-snapshot

Ceratocystiopsis: a reappraisal based on molecular criteria

inferredcites →https://doi.org/10.1016/s0953-7562(96)80171-7openalex-snapshot

Multiple insertions and deletions determine the size differences between the mitochondrial DNAs of the EAN and NAN races of Ophiostoma novo-ulmi

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The Closest Unicellular Relatives of Animals

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Mobile introns: Retrohoming by complete reverse splicing

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New loop-loop tertiary interactions in self-splicing introns of subgroup IC and ID: a complete 3D model of the Tetrahymena thermophila ribozyme

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A Reverse Transcriptase/Maturase Promotes Splicing by Binding at Its Own Coding Segment in a Group II Intron RNA

inferredcites →https://doi.org/10.1017/s0033583505004063openalex-snapshot

Homing endonuclease structure and function

inferredcites →https://doi.org/10.1017/s095375620500376xopenalex-snapshot

Optional mitochondrial introns and evidence for a homing-endonuclease gene in the mtDNA rnl gene in Ophiostoma ulmi s. lat.

inferredcites →https://doi.org/10.1017/s1355838201010251openalex-snapshot

Coevolution of group II intron RNA structures with their intron-encoded reverse transcriptases

inferredcites →https://doi.org/10.1017/s1355838201010500openalex-snapshot

A new nomenclature of group I introns in ribosomal DNA

inferredcites →https://doi.org/10.1017/s1355838202023087openalex-snapshot

Identification of a family of group II introns encoding LAGLIDADG ORFs typical of group I introns

inferredcites →https://doi.org/10.1017/s1355838298971758openalex-snapshot

Group I-like ribozymes with a novel core organization perform obligate sequential hydrolytic cleavages at two processing sites

inferredcites →https://doi.org/10.1038/316641a0openalex-snapshot

Mitochondrial class II introns encode proteins related to the reverse transcriptases of retroviruses

inferredcites →https://doi.org/10.1038/332654a0openalex-snapshot

Independent evolution of structural and coding regions in a Neurospora mitochondrial intron

inferredcites →https://doi.org/10.1038/nature10947openalex-snapshot

Emerging fungal threats to animal, plant and ecosystem health

inferredcites →https://doi.org/10.1038/nsb0594-273openalex-snapshot

Representation of the secondary and tertiary structure of group I introns

inferredcites →https://doi.org/10.1073/pnas.1107719108openalex-snapshot

Tapping natural reservoirs of homing endonucleases for targeted gene modification

inferredcites →https://doi.org/10.1073/pnas.96.24.13880openalex-snapshot

Recurrent invasion and extinction of a selfish gene

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New insights into classification and evolution of the Lecanoromycetes (Pezizomycotina, Ascomycota) from phylogenetic analyses of three ribosomal RNA- and two protein-coding genes

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Tree View: An application to display phylogenetic trees on personal computers

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MrBayes 3: Bayesian phylogenetic inference under mixed models

inferredcites →https://doi.org/10.1093/emboj/20.24.7259openalex-snapshot

Mechanism of maturase‐promoted group II intron splicing

inferredcites →https://doi.org/10.1093/molbev/msp145openalex-snapshot

Genes within Genes: Multiple LAGLIDADG Homing Endonucleases Target the Ribosomal Protein S3 Gene Encoded within an rnl Group I Intron of Ophiostoma and Related Taxa

inferredcites →https://doi.org/10.1093/nar/15.18.7217openalex-snapshot

Structural conventions for group I introns

inferredcites →https://doi.org/10.1093/nar/18.20.6097openalex-snapshot

Sequence logos: a new way to display consensus sequences

inferredcites →https://doi.org/10.1093/nar/19.23.6491openalex-snapshot

A mixed group II/group III twintron in theEuglena gracilischloroplast ribosomal protein S3 gene: evidence for intron insertion during gene evolution

inferredcites →https://doi.org/10.1093/nar/22.6.1029openalex-snapshot

A group III twintron encoding a maturase-like gene excises through lariat intermediates

inferredcites →https://doi.org/10.1093/nar/25.17.3389openalex-snapshot

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

inferredcites →https://doi.org/10.1093/nar/25.24.4876openalex-snapshot

The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools

inferredcites →https://doi.org/10.1093/nar/29.18.3757openalex-snapshot

Homing endonucleases: structural and functional insight into the catalysts of intron/intein mobility

inferredcites →https://doi.org/10.1093/nar/9.21.5689openalex-snapshot

Nucleotide sequence of the Aspergillus nidulans mitochondria! gene coding for the small ribosomal subunit RNA: homology to E. coli 16S rRNA

inferredcites →https://doi.org/10.1093/nar/gkg153openalex-snapshot

Putative proteins related to group II intron reverse transcriptase/maturases are encoded by nuclear genes in higher plants

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Mfold web server for nucleic acid folding and hybridization prediction

inferredcites →https://doi.org/10.1093/nar/gkh520openalex-snapshot

The spread of LAGLIDADG homing endonuclease genes in rDNA

inferredcites →https://doi.org/10.1093/nar/gki517openalex-snapshot

Predicting the secondary structures and tertiary interactions of 211 group I introns in IE subgroup

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Lateral transfer of introns in the cryptophyte plastid genome

inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a003952openalex-snapshot

Evolutionary Dynamics of Multiple Group I Introns in Nuclear Ribosomal RNA Genes of Endoparasitic Fungi of the Genus Cordyceps

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New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

inferredcites →https://doi.org/10.1094/mpmi.2000.13.1.88openalex-snapshot

Transmissible Mitochondrial Hypovirulence in a Natural Population of Cryphonectria parasitica

inferredcites →https://doi.org/10.1101/087969589.37.451openalex-snapshot

18 Group I and Group II Ribozymes as RNPs: Clues to the Past and Guides to the Future

inferredcites →https://doi.org/10.1101/cshperspect.a003616openalex-snapshot

Group II Introns: Mobile Ribozymes that Invade DNA

inferredcites →https://doi.org/10.1101/gad.1162503openalex-snapshot

Two for the price of one: a bifunctional intron-encoded DNA endonuclease-RNA maturase

inferredcites →https://doi.org/10.1101/gr.849004openalex-snapshot

WebLogo: A Sequence Logo Generator: Figure 1

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Better late than early: delayed translation of intron‐encoded endonuclease I‐TevI is required for efficient splicing of its host group I intron

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CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP

inferredcites →https://doi.org/10.1126/science.6163215openalex-snapshot

Secondary Structure of 16 S Ribosomal RNA

inferredcites →https://doi.org/10.1128/9781555817954.ch31openalex-snapshot

Mobile Introns: Pathways and Proteins

inferredcites →https://doi.org/10.1139/b05-095openalex-snapshot

Fungi vectored by the introduced bark beetle Tomicus piniperda in Ontario, Canada, and comments on the taxonomy of Leptographium lundbergii, Leptographium terebrantis, Leptographium truncatum, and Leptographium wingfieldii

inferredcites →https://doi.org/10.1139/b74-222openalex-snapshot

Taxonomy of the genus Ceratocystis in Manitoba

inferredcites →https://doi.org/10.1139/g2012-049openalex-snapshot

Homing endonucleases: DNA scissors on a mission

inferredcites →https://doi.org/10.1146/annurev.bi.64.070195.002251openalex-snapshot

STRUCTURE AND ACTIVITIES OF GROUP II INTRONS

inferredcites →https://doi.org/10.1146/annurev.ge.26.120192.002031openalex-snapshot

FUNGAL SENESCENCE

inferredcites →https://doi.org/10.1159/000084992openalex-snapshot

Group II intron retroelements: function and diversity

inferredcites →https://doi.org/10.1186/1471-2105-3-2openalex-snapshot

The Comparative RNA Web (CRW) Site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs

inferredcites →https://doi.org/10.1186/1471-2148-5-68openalex-snapshot

Phylogenetic analyses suggest reverse splicing spread of group I introns in fungal ribosomal DNA

inferredcites →https://doi.org/10.1186/1471-2148-6-94openalex-snapshot

Inteins, introns, and homing endonucleases: recent revelations about the life cycle of parasitic genetic elements.

inferredcites →https://doi.org/10.1186/1741-7007-11-9openalex-snapshot

Open questions: Chromosome condensation - Why does a chromosome look like a chromosome?

inferredcites →https://doi.org/10.1186/1741-7007-9-22openalex-snapshot

Learning to live together: mutualism between self-splicing introns and their hosts

inferredcites →https://doi.org/10.1261/rna.2184010openalex-snapshot

A group II intron encodes a functional LAGLIDADG homing endonuclease and self-splices under moderate temperature and ionic conditions

inferredcites →https://doi.org/10.1261/rna.2655911openalex-snapshot

Recurrent insertion of 5′-terminal nucleotides and loss of the branchpoint motif in lineages of group II introns inserted in mitochondrial preribosomal RNAs

inferredcites →https://doi.org/10.1371/journal.pone.0049551openalex-snapshot

The Mitochondrial LSU rRNA Group II Intron of Ustilago maydis Encodes an Active Homing Endonuclease Likely Involved in Intron Mobility

inferredcites →https://doi.org/10.1515/bc.2007.090openalex-snapshot

Group II introns: structure, folding and splicing mechanism

inferredcites →https://doi.org/10.2174/1566524043360410openalex-snapshot

Ribozymes in the Age of Molecular Therapeutics

inferredcites →https://doi.org/10.2307/3759682openalex-snapshot

Cycloheximide Sensitivity as a Taxonomic Character in Ceratocystis

inferredcites →https://doi.org/10.3114/sim.55.1.75openalex-snapshot

Multi-gene phylogenies define Ceratocystiopsis and Grosmannia distinct from Ophiostoma

inferredcites →https://doi.org/10.3852/08-132openalex-snapshot

Resolving taxonomic and phylogenetic incongruence within speciesCeratocystiopsis minuta

inferredcites →https://doi.org/10.5281/zenodo.1060797openalex-snapshot

Characterization Of The O.Ul-Ms952 Intron:A Potential Molecular Marker To Distinguish Between Ophiostoma Ulmi And Ophiostoma Novo-Ulmi Subsp. Americana

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Characterization of the mitochondrial genomes for Ophiostoma ips and related taxa from various geographic origins and related species: large intron-rich genomes and complex intron arrangements

inferred← citeshttps://doi.org/10.1007/978-1-4939-6472-7_9openalex-snapshot

Insertion of Group II Intron-Based Ribozyme Switches into Homing Endonuclease Genes

inferred← citeshttps://doi.org/10.1007/s10482-015-0547-7openalex-snapshot

New species of Ophiostomatales from Scolytinae and Platypodinae beetles in the Cape Floristic Region, including the discovery of the sexual state of Raffaelea

inferred← citeshttps://doi.org/10.1016/j.fgb.2013.06.003openalex-snapshot

Spliceosome twin introns in fungal nuclear transcripts

inferred← citeshttps://doi.org/10.1016/j.fgb.2014.01.004openalex-snapshot

A homing endonuclease with a switch: Characterization of a twintron encoded homing endonuclease

inferred← citeshttps://doi.org/10.1016/j.funbio.2013.10.002openalex-snapshot

Evolutionary dynamics of introns and their open reading frames in the U7 region of the mitochondrial rnl gene in species of Ceratocystis

inferred← citeshttps://doi.org/10.1016/j.funbio.2014.05.002openalex-snapshot

I-OmiI and I-OmiII: Two intron-encoded homing endonucleases within the Ophiostoma minus rns gene

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The ribosome as a missing link in prebiotic evolution II: Ribosomes encode ribosomal proteins that bind to common regions of their own mRNAs and rRNAs

inferred← citeshttps://doi.org/10.1038/s41598-018-35926-yopenalex-snapshot

The mitochondrial genome of Endoconidiophora resinifera is intron rich

inferred← citeshttps://doi.org/10.1073/pnas.1322248111openalex-snapshot

Speciation of a group I intron into a lariat capping ribozyme

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Convergent evolution of twintron-like configurations: One is never enough

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The intron landscape of the mtDNA cytb gene among the Ascomycota: introns and intron-encoded open reading frames

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The fungal mitochondrial Nad5 pan-genic intron landscape

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A functional twintron, ‘zombie’ twintrons and a hypermobile group II intron invading itself in plant mitochondria

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Intraspecific Mitochondrial DNA Comparison of Mycopathogen Mycogone perniciosa Provides Insight Into Mitochondrial Transfer RNA Introns

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Three new active members of the I-OnuI family of homing endonucleases

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Homing endonucleases: DNA scissors on a mission

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Intra-specific comparison of mitochondrial genomes reveals host gene fragment exchange via intron mobility in Tremella fuciformis

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Evolution of group II introns

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The diversity of mtDNA rns introns among strains of Ophiostoma piliferum, Ophiostoma pluriannulatum and related species

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Using Group II Introns for Attenuating the In Vitro and In Vivo Expression of a Homing Endonuclease

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Comparison of the Mitochondrial Genome Sequences of Six Annulohypoxylon stygium Isolates Suggests Short Fragment Insertions as a Potential Factor Leading to Larger Genomic Size

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The Mitogenomes of Ophiostoma minus and Ophiostoma piliferum and Comparisons With Other Members of the Ophiostomatales

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Organellar Introns in Fungi, Algae, and Plants

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Contributions to the study of the architecture and evolution of ribozymes

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