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Convergent Evolution of Fern-Specific Mitochondrial Group II Intron atp1i361g2 and Its Ancient Source Paralogue rps3i249g2 and Independent Losses of Intron and RNA Editing among Pteridaceae

https://doi.org/10.1093/gbe/evw173
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What this work says

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

inferredcites →https://doi.org/10.1002/j.1460-2075.1983.tb01376.xopenalex-snapshot
Conservation of RNA secondary structures in two intron families including mitochondrial‐, chloroplast‐ and nuclear‐encoded members.
inferredcites →https://doi.org/10.1002/wrna.1339openalex-snapshot
Group II introns: versatile ribozymes and retroelements
inferredcites →https://doi.org/10.1002/wrna.72openalex-snapshot
Organellar RNA editing
inferredcites →https://doi.org/10.1007/b97636openalex-snapshot
Model Selection and Multimodel Inference
inferredcites →https://doi.org/10.1007/bf00280188openalex-snapshot
RNA editing of tRNAPhe and tRNACys in mitochondria of Oenothera berteriana is initiated in precursor molecules
inferredcites →https://doi.org/10.1007/bf00283874openalex-snapshot
Differential RNA editing in closely related introns in Oenothera mitochondria
inferredcites →https://doi.org/10.1007/bf00283881openalex-snapshot
Intron loss from the NADH dehydrogenase subunit 4 gene of lettuce mitochondrial DNA: evidence for homologous recombination of a cDNA intermediate
inferredcites →https://doi.org/10.1007/s00018-010-0538-9openalex-snapshot
When you can’t trust the DNA: RNA editing changes transcript sequences
inferredcites →https://doi.org/10.1007/s001220100744openalex-snapshot
The sugar beet mitochondrial nad4 gene: an intron loss and its phylogenetic implication in the Caryophyllales
inferredcites →https://doi.org/10.1007/s00294-009-0283-5openalex-snapshot
Introducing the plant RNA editing prediction and analysis computer tool PREPACT and an update on RNA editing site nomenclature
inferredcites →https://doi.org/10.1007/s00294-011-0349-zopenalex-snapshot
RNA editing restores critical domains of a group I intron in fern mitochondria
inferredcites →https://doi.org/10.1007/s00294-015-0512-zopenalex-snapshot
The evolutionary conservation of rps3 introns and rps19-rps3-rpl16 gene cluster in Adiantum capillus-veneris mitochondria
inferredcites →https://doi.org/10.1007/s00438-002-0657-6openalex-snapshot
Loss of the mitochondrial cox2 intron 1 in a family of monocotyledonous plants and utilization of mitochondrial intron sequences for the construction of a nuclear intron
inferredcites →https://doi.org/10.1007/s00438-009-0424-zopenalex-snapshot
RNA editing: only eleven sites are present in the Physcomitrella patens mitochondrial transcriptome and a universal nomenclature proposal
inferredcites →https://doi.org/10.1007/s004380000345openalex-snapshot
Variation in sequence and RNA editing within core domains of mitochondrial group II introns among plants
inferredcites →https://doi.org/10.1016/0014-5793(90)81282-sopenalex-snapshot
The role of introns in evolution
inferredcites →https://doi.org/10.1016/0092-8674(79)90353-2openalex-snapshot
Structure analysis at the ends of the intervening DNA sequences in the chloroplast 23S ribosomal genes of C. reinhardii
inferredcites →https://doi.org/10.1016/0092-8674(80)90246-9openalex-snapshot
Sequence of the intron and flanking exons of the mitochondrial 21S rRNA gene of yeast strains having different alleles at the ω and rib-1 loci
inferredcites →https://doi.org/10.1016/0092-8674(86)90751-8openalex-snapshot
The generality of self-splicing RNA: Relationship to nuclear mRNA splicing
inferredcites →https://doi.org/10.1016/0092-8674(93)90166-nopenalex-snapshot
Reverse transcriptase activity associated with maturase-encoding group II introns in yeast mitochondria
inferredcites →https://doi.org/10.1016/0168-9525(91)90102-vopenalex-snapshot
Intron phylogeny: a new hypothesis
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/10.1016/0960-9822(91)90214-hopenalex-snapshot
The origins of introns
inferredcites →https://doi.org/10.1016/j.biochi.2006.09.011openalex-snapshot
RNA editing has been lost in the mitochondrial cox3 and rps13 mRNAs in Asparagales
inferredcites →https://doi.org/10.1016/j.mito.2007.09.005openalex-snapshot
Cis- and trans-splicing of group II introns in plant mitochondria
inferredcites →https://doi.org/10.1016/j.plaphy.2010.05.003openalex-snapshot
Lineage-specific group II intron gains and losses of the mitochondrial rps3 gene in gymnosperms
inferredcites →https://doi.org/10.1016/j.ympev.2003.12.013openalex-snapshot
Distribution of introns in the mitochondrial gene nad1 in land plants: phylogenetic and molecular evolutionary implications
inferredcites →https://doi.org/10.1016/j.ympev.2005.04.008openalex-snapshot
Incongruence between primary sequence data and the distribution of a mitochondrial atp1 group II intron among ferns and horsetails
inferredcites →https://doi.org/10.1016/j.ympev.2007.04.011openalex-snapshot
A molecular phylogeny of the fern family Pteridaceae: Assessing overall relationships and the affinities of previously unsampled genera
inferredcites →https://doi.org/10.1016/j.ympev.2009.09.011openalex-snapshot
Fast evolution of the retroprocessed mitochondrial rps3 gene in Conifer II and further evidence for the phylogeny of gymnosperms
inferredcites →https://doi.org/10.1016/j.ympev.2011.03.010openalex-snapshot
First insights into fern matK phylogeny
inferredcites →https://doi.org/10.1016/j.ympev.2015.05.008openalex-snapshot
Horsetails are the sister group to all other monilophytes and Marattiales are sister to leptosporangiate ferns
inferredcites →https://doi.org/10.1016/s0022-5193(05)80104-3openalex-snapshot
The general stochastic model of nucleotide substitution
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/s0959-437x(05)80194-7openalex-snapshot
The recent origins of introns
inferredcites →https://doi.org/10.1016/s0959-437x(98)80031-2openalex-snapshot
The recent origins of spliceosomal introns revisited
inferredcites →https://doi.org/10.1016/s0959-440x(98)80062-6openalex-snapshot
The architectural organization and mechanistic function of group II intron structural elements
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/10.1038/29286openalex-snapshot
The gain of three mitochondrial introns identifies liverworts as the earliest land plants
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/10.1038/35010029openalex-snapshot
Retrotransposition of a bacterial group II intron
inferredcites →https://doi.org/10.1038/364289a0openalex-snapshot
Why introns-in-pieces?
inferredcites →https://doi.org/10.1038/ng0197-57openalex-snapshot
The mitochondrial genome of Arabidopsis thaliana contains 57 genes in 366,924 nucleotides
inferredcites →https://doi.org/10.1038/sj.emboj.7600852openalex-snapshot
Linking the group II intron catalytic domains: tertiary contacts and structural features of domain 3
inferredcites →https://doi.org/10.1038/sj.hdy.6800791openalex-snapshot
The rise and falls of introns
inferredcites →https://doi.org/10.1074/jbc.271.4.1898openalex-snapshot
RNA Editing Is Required for Efficient Excision of tRNAPhe from Precursors in Plant Mitochondria
inferredcites →https://doi.org/10.1093/aob/mcu086openalex-snapshot
Molecular phylogeny and biogeography of the fern genus Pteris (Pteridaceae)
inferredcites →https://doi.org/10.1093/bioinformatics/btp250openalex-snapshot
VARNA: Interactive drawing and editing of the RNA secondary structure
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/gbe/evr027openalex-snapshot
Extreme RNA Editing in Coding Islands and Abundant Microsatellites in Repeat Sequences of Selaginella moellendorffii Mitochondria: The Root of Frequent Plant mtDNA Recombination in Early Tracheophytes
inferredcites →https://doi.org/10.1093/molbev/msh259openalex-snapshot
Ancestors of Trans-Splicing Mitochondrial Introns Support Serial Sister Group Relationships of Hornworts and Mosses with Vascular Plants
inferredcites →https://doi.org/10.1093/molbev/msr121openalex-snapshot
MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods
inferredcites →https://doi.org/10.1093/molbev/mss130openalex-snapshot
Loss of Two Introns from the Magnolia tripetala Mitochondrial cox2 Gene Implicates Horizontal Gene Transfer and Gene Conversion as a Novel Mechanism of Intron Loss
inferredcites →https://doi.org/10.1093/molbev/mst024openalex-snapshot
Ultrafast Approximation for Phylogenetic Bootstrap
inferredcites →https://doi.org/10.1093/molbev/msu300openalex-snapshot
IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
inferredcites →https://doi.org/10.1093/molbev/msw024openalex-snapshot
GinkgoandWelwitschiaMitogenomes Reveal Extreme Contrasts in Gymnosperm Mitochondrial Evolution
inferredcites →https://doi.org/10.1093/nar/22.22.4673openalex-snapshot
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
inferredcites →https://doi.org/10.1093/nar/24.16.3229openalex-snapshot
RNA editing of larch mitochondrial tRNA(His) precursors is a prerequisite for processing
inferredcites →https://doi.org/10.1093/nar/25.2.403openalex-snapshot
RNA editing status of nad7 intron domains in wheat mitochondria
inferredcites →https://doi.org/10.1093/nar/28.13.2571openalex-snapshot
The complete nucleotide sequence of the mitochondrial genome of sugar beet (Beta vulgaris L.) reveals a novel gene for tRNACys(GCA)
inferredcites →https://doi.org/10.1093/nar/7.6.1513openalex-snapshot
A rapid alkaline extraction procedure for screening recombinant plasmid DNA
inferredcites →https://doi.org/10.1093/nar/gkp532openalex-snapshot
A trans -splicing group I intron and tRNA-hyperediting in the mitochondrial genome of the lycophyte Isoetes engelmannii
inferredcites →https://doi.org/10.1093/nar/gkq1227openalex-snapshot
A unique transcriptome: 1782 positions of RNA editing alter 1406 codon identities in mitochondrial mRNAs of the lycophyte Isoetes engelmannii
inferredcites →https://doi.org/10.1093/nar/gkq591openalex-snapshot
Intron RNA editing is essential for splicing in plant mitochondria
inferredcites →https://doi.org/10.1093/sysbio/sys001openalex-snapshot
Overcoming Deep Roots, Fast Rates, and Short Internodes to Resolve the Ancient Rapid Radiation of Eupolypod II Ferns
inferredcites →https://doi.org/10.1093/sysbio/syt058openalex-snapshot
Accelerated Rate of Molecular Evolution for Vittarioid Ferns is Strong and Not Driven by Selection
inferredcites →https://doi.org/10.1101/cshperspect.a003616openalex-snapshot
Group II Introns: Mobile Ribozymes that Invade DNA
inferredcites →https://doi.org/10.1105/tpc.104.027516openalex-snapshot
CRS1, a Chloroplast Group II Intron Splicing Factor, Promotes Intron Folding through Specific Interactions with Two Intron Domains
inferredcites →https://doi.org/10.1111/cla.12094openalex-snapshot
A global plastid phylogeny of the brake fern genus Pteris (Pteridaceae) and related genera in the Pteridoideae
inferredcites →https://doi.org/10.1111/j.1365-313x.2012.04998.xopenalex-snapshot
nMAT1, a nuclear‐encoded maturase involved in the trans‐splicing of nad1 intron 1, is essential for mitochondrial complex I assembly and function
inferredcites →https://doi.org/10.1111/j.1438-8677.1999.tb00249.xopenalex-snapshot
Phylogenetic Information in the Mitochondrial nad5 Gene of Pteridophytes: RNA Editing and Intron Sequences
inferredcites →https://doi.org/10.1111/j.1759-6831.2012.00228.xopenalex-snapshot
Plant mitochondrial genome peculiarities evolving in the earliest vascular plant lineages
inferredcites →https://doi.org/10.1111/tpj.12466openalex-snapshot
n MAT 4, a maturase factor required for nad1 pre‐m RNA processing and maturation, is essential for holocomplex I biogenesis in A rabidopsis mitochondria
inferredcites →https://doi.org/10.1146/annurev.bi.62.070193.003103openalex-snapshot
INTRONS AS MOBILE GENETIC ELEMENTS
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.genet.38.072902.091600openalex-snapshot
Mobile Group II Introns
inferredcites →https://doi.org/10.11646/bde.31.1.10openalex-snapshot
Looking for sense in the nonsense: a short review of non-coding organellar DNA elucidatingn the phylogeny of bryophytes
inferredcites →https://doi.org/10.1186/1471-2148-13-8openalex-snapshot
Complete plastid genomes from Ophioglossum californicum, Psilotum nudum, and Equisetum hyemale reveal an ancestral land plant genome structure and resolve the position of Equisetales among monilophytes
inferredcites →https://doi.org/10.1186/s12862-016-0589-0openalex-snapshot
Frequent chloroplast RNA editing in early-branching flowering plants: pilot studies on angiosperm-wide coexistence of editing sites and their nuclear specificity factors
inferredcites →https://doi.org/10.1198/tech.2003.s146openalex-snapshot
Model Selection and Multimodel Inference
inferredcites →https://doi.org/10.1214/aos/1176344136openalex-snapshot
Estimating the Dimension of a Model
inferredcites →https://doi.org/10.1261/rna.045575.114openalex-snapshot
Chloroplast RNA editing going extreme: more than 3400 events of C-to-U editing in the chloroplast transcriptome of the lycophyte Selaginella uncinata
inferredcites →https://doi.org/10.1261/rna.1056108openalex-snapshot
Group II introns in Eubacteria and Archaea: ORF-less introns and new varieties
inferredcites →https://doi.org/10.1261/rna.1776409openalex-snapshot
AtnMat2, a nuclear-encoded maturase required for splicing of group-II introns in Arabidopsis mitochondria
inferredcites →https://doi.org/10.1371/journal.pone.0035168openalex-snapshot
The Mitochondrial Genome of the Lycophyte Huperzia squarrosa: The Most Archaic Form in Vascular Plants
inferredcites →https://doi.org/10.1371/journal.pone.0052644openalex-snapshot
RNA Editing in Mitochondrial Trans-Introns Is Required for Splicing
inferredcites →https://doi.org/10.1534/genetics.110.118000openalex-snapshot
Extensive Loss of RNA Editing Sites in Rapidly Evolving Silene Mitochondrial Genomes: Selectionvs. Retroprocessing as the Driving Force
inferredcites →https://doi.org/10.3389/fpls.2014.00035openalex-snapshot
Group II intron splicing factors in plant mitochondria
inferredcites →https://doi.org/10.3732/ajb.1500089openalex-snapshot
The evolutionary history of ferns inferred from 25 low‐copy nuclear genes
inferredcites →https://doi.org/10.4137/bbi.s11059openalex-snapshot
PREPACT 2.0: Predicting C-to-U and U-to-C RNA Editing in Organelle Genome Sequences with Multiple References and Curated RNA Editing Annotation

What points at this work

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

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Comprehensive analysis of Actiniopteris Link and Onychium Kaulf. (Pteridophyta) relationships according to their phylogeography, phylogeny and spore morphology
inferred← citeshttps://doi.org/10.1002/jemt.23921openalex-snapshot
Phylogenetic comparative morphological analysis of fern spores in subfamily Pteridoideae (Pteridaceae, Pteridophyta)
inferred← citeshttps://doi.org/10.1002/tax.13314openalex-snapshot
A phylogenetically informed generic reclassification of the hemionitid ferns (Pteridaceae: Cheilanthoideae)
inferred← citeshttps://doi.org/10.1007/s11103-019-00940-9openalex-snapshot
The dual-targeted RNA editing factor AEF1 is universally conserved among angiosperms and reveals only minor adaptations upon loss of its chloroplast or its mitochondrial target
inferred← citeshttps://doi.org/10.1016/j.mito.2020.06.002openalex-snapshot
Variation in protein gene and intron content among land plant mitogenomes
inferred← citeshttps://doi.org/10.1038/s41598-017-10388-wopenalex-snapshot
Multiple origins of endosymbionts in Chlorellaceae with no reductive effects on the plastid or mitochondrial genomes
inferred← citeshttps://doi.org/10.1038/s42003-023-04659-8openalex-snapshot
Rickettsial DNA and a trans-splicing rRNA group I intron in the unorthodox mitogenome of the fern Haplopteris ensiformis
inferred← citeshttps://doi.org/10.1093/nar/gkz1194openalex-snapshot
A functional twintron, ‘zombie’ twintrons and a hypermobile group II intron invading itself in plant mitochondria
inferred← citeshttps://doi.org/10.1111/nph.16297openalex-snapshot
Towards a plant model for enigmatic U‐to‐C RNA editing: the organelle genomes, transcriptomes, editomes and candidate RNA editing factors in the hornwort Anthoceros agrestis
inferred← citeshttps://doi.org/10.1111/tpj.14578openalex-snapshot
Plant organellar RNA editing: what 30 years of research has revealed
inferred← citeshttps://doi.org/10.1186/s12862-020-1582-1openalex-snapshot
The complete mitochondrial genome of Taxus cuspidata (Taxaceae): eight protein-coding genes have transferred to the nuclear genome
inferred← citeshttps://doi.org/10.1186/s12862-023-02108-yopenalex-snapshot
Categorizing 161 plant (streptophyte) mitochondrial group II introns into 29 families of related paralogues finds only limited links between intron mobility and intron-borne maturases
inferred← citeshttps://doi.org/10.1186/s12915-025-02449-8openalex-snapshot
A record-setting mitogenome in the holoparasitic plant Balanophora yakushimensis accompanied by exceptional loss of organellar DNA repair and recombination genes
inferred← citeshttps://doi.org/10.18475/cjos.v51i2.a13openalex-snapshot
DNA Barcoding of Adiantum (Pteridaceae: Vittarioideae) in Puerto Rico
inferred← citeshttps://doi.org/10.3390/genes8120395openalex-snapshot
Comparative Analysis of Four Calypogeia Species Revealed Unexpected Change in Evolutionarily-Stable Liverwort Mitogenomes
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