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31 results for “group I intron”
Fig. 5 in Loss and Gain of Group I Introns in the Mitochondrial Gene of the Scleractinia (Cnidaria; Anthozoa).
Fig. 5. Bayesian estimates of divergence times in scleractinians. The basal axis is a geologic time scale in units of million years ago (mya). Different time intervals are labeled with abbreviations (Cam, Cambrian; Ord, Ordovician; Sil, Silurian; Dev, Devonian; Car, Carboniferous; Per, Permian; Tri, Triassic; Jur, Jurassic; Cre, Cretaceous; Pal, Paleogene; Neo, Neogene). The chart below the phylogenetic tree gives the extinction rate (solid line) and origination rate (dashed line) in different geological periods, which were modified from Kiessling (2004) with major extinction events labeled with abbreviations (Rhae, Rhaetian; Plie, Pliensbachian; Kimm, Kimmeridgian; Ceno, Cenomanian; Maa, Maastrichtian, KT-extinction). Species with different types of intron are labeled with symbols: ●, Intron-729 (I729); ▲, Intron-893 (I893); ■, Intron-876 (I876).
Fig. 4 in Loss and Gain of Group I Introns in the Mitochondrial Gene of the Scleractinia (Cnidaria; Anthozoa).
Fig. 4. Comparison of phylogenetic trees between the cox1 exon (left side) and intron (right side) in complex corals and corallimorpharians (A) and in sponges and robust corals (B). Tree topologies presenting the phylogenetic relationships of exons and introns were consensus trees between the maximum-likelihood analysis and Bayesian algorism. Numbers on branches are Shimedaira- Hasegawa-like/posterior probabilities. Dashed lines are potential changes in phylogenetic positions between the exon and intron trees.
Fig. 3 in Loss and Gain of Group I Introns in the Mitochondrial Gene of the Scleractinia (Cnidaria; Anthozoa).
Fig. 3. Phylogeny and characteristics of cox1 intron traits in hexacorals. The tree topology was constructed with Mrbayes. Numbers labeled on branches are Shimodaira-Hasegawa-like support/posterior probabilities. Species with different types of introns are labeled with symbols: ●, Intron-729 (I729); ▲, Intron-893 (I893); ■, Intron-876 (I876).
Fig. 1 in Loss and Gain of Group I Introns in the Mitochondrial Gene of the Scleractinia (Cnidaria; Anthozoa).
Fig. 1. Secondary structures of representative cox1 introns in anthozoans. A: Corallimorpharian (Rhodactis howesii); B: basal and complex corals (Gardeneris hawaiinesis); C: robust corals (Diploastrea heliopora); D: actiniarian (Metridinium senile); E: poriferian (Plakortis angulospiculatus); F: zoantharian (Savalia savaglia). Features of the secondary structure indicate the characteristics of group I introns: 10 helical elements P1~P10; consensus primary structures P, Q, R, and S in hollow letters; internal guide sequence, IGS. Initial and terminal sites of the predicted open reading frame are labeled "ORF start" and "ORF stop", respectively.
Figure 6 in An unprecedented new genus and family of Tetractinellida (Porifera, Demospongiae) from New Zealand's Colville Ridge, with a new type of mitochondrial group I intron
Figure 6. Megascleres and microscleres of Stupenda singularis gen. et sp. nov., holotype NIWA 86177, Colville Ridge, Kermadec Volcanic Arc, 387–422 m: A, oxea, one end showing strong attenuation, scale bar = 1000 μm; B, orthotriaene I megascleres with clubbed clads, scale bar = 1000 μm; C, orthotriaene I megascleres with clubbed bulbous clads, scanning electron microscopy (left), light microscopy (LM) (right), scale bar = 200 μm; D, orthotriaene I megasclere with reduced irregular clads, scale bar = 200 μm; E, orthotriaene I megascleres with diaene modifications, scale bar = 200 μm; F, orthotriaene I megasclere with monaene modification, LM, scale bar = 200 μm; G, orthotriaene II megasclere with normal clads, scale bar = 200 μm; H, orthotriaene II megasclere with irregular reduced clads, entirely smooth, scale bar = 200 μm; I, sigmaspires, scale bar = 5 μm.
Figure 2. Tetractinellida 18S in An unprecedented new genus and family of Tetractinellida (Porifera, Demospongiae) from New Zealand's Colville Ridge, with a new type of mitochondrial group I intron
Figure 2. Tetractinellida 18S rDNA maximum likelihood (ML) tree reconstructed with RAxML under the generalized time-reversible Gamma (GTRGAMMA) model: 89 sequences. At each key node, ML bootstrap supports (100 bootstrap replicates) and Bayesian posterior probabilities are given (only bootstrap supports above 50 are shown). GenBank accession numbers are given after each taxon name; when sequences have been merged, two accession numbers are given. 'K94' indicates that this is a short 18S sequence (V4–V5 region) from Kelly-Borges & Pomponi (1994) (accession numbers KT356876–KT356885).
Figure 3. Tetractinellida cytochrome c oxidase subunit I in An unprecedented new genus and family of Tetractinellida (Porifera, Demospongiae) from New Zealand's Colville Ridge, with a new type of mitochondrial group I intron
Figure 3. Tetractinellida cytochrome c oxidase subunit I (COI) maximum likelihood (ML) trees reconstructed with RAxML under the generalized time-reversible Gamma – GTRGAMMA – model: 140 sequences At each key node, ML bootstrap supports (100 bootstrap replicates) and Bayesian posterior probabilities are given. There are two bootstrap supports: nucleotide analyses/amino-acid analyses (only bootstrap supports above 50 are shown). GenBank accession numbers are given after each taxon name. Presence of mitochondrial introns are given in the COI tree (the number given to each intron indicates its position with respect to the Amphimedon queenslandica complete COI as reference).
Figure 5 in An unprecedented new genus and family of Tetractinellida (Porifera, Demospongiae) from New Zealand's Colville Ridge, with a new type of mitochondrial group I intron
Figure 5. Morphology and skeletal architecture of Stupenda singularis gen. et sp. nov., holotype NIWA 86177, Colville Ridge, Kermadec Volcanic Arc, 387–422 m: A, preserved specimen, scale bar = 10 mm; B, preserved specimen showing thick cortex and strictly radiating skeleton, emanating from a centrum, scale bar = 10 mm; C, D, histological thick section showing strictly radiating megascleres in cortex, scale bars = 200 μm.
Figure 4 in An unprecedented new genus and family of Tetractinellida (Porifera, Demospongiae) from New Zealand's Colville Ridge, with a new type of mitochondrial group I intron
Figure 4. Mitochondrial intron of Stupenda singularis gen. et sp. nov. COI, cytochrome c oxidase subunit I gene; COB, cytochrome b gene; nt, nucleotide; ORF, open reading frame.
Figure 1 in An unprecedented new genus and family of Tetractinellida (Porifera, Demospongiae) from New Zealand's Colville Ridge, with a new type of mitochondrial group I intron
Figure 1. Study area showing the collection locality for Stupenda singularis gen. et sp. nov. (●), Colville Ridge volcano, Colville Ridge, New Zealand Exclusive Economic Zone.
Fig. 1 in Sex or no sex? Group I introns and independent marker genes reveal the existence of three sexual but reproductively isolated biospecies in Trichia varia (Myxomycetes)
Fig. 1 Three-gene phylogeny of Trichia varia. a Associations between partial SSU and partial COI genotypes within the three groups (1, 2a, 2b). Dotted lines indicate associations found in one specimen, dashed lines in two to five specimens, and solid lines more than five specimens. b Bayesian majority-rule consensus tree of combined partial sequences of
First unravelling of the hidden and intricate evolutionary history of a bacterial group II intron family
<p>Bacterial group II introns are large RNA enzymes that self-splice from primary transcripts. Following excision, they can invade various DNA target sites using RNA-based mobility pathways. <span>As fast-evolving retromobile elements that move between genetic loci within and across species, their evolutionary history was proved difficult to study and infer. Here we identified several homologs of Ll.LtrB, the model group II intron from <em>Lactococcus lactis</em>, and traced back</span> their evolutionary relationship through phylogenetic analyses. Our data demonstrate that the Ll.LtrB homologs in Lactococci originate from a single and recent lateral transfer event of Ef.PcfG from <em>Enterococcus faecalis</em>. We also show that these <span>introns disseminated in </span>Lactococci <span>following recurrent episodes of independent mobility events in conjunction with occurences of lateral transfer. Our phylogenies identified additional lateral transfer events from the environmental clade of the more diverged Lactococci introns to a series of low GC gram-positive bacterial species including <em>E. faecalis</em>. We also determined that functional intron adaptation occurred early in Lactococci following Ef.PcfG acquisition from <em>E. faecalis </em>and that two of the more diverged Ll.LtrB homologs remain proficient mobile elements despite the significant number of mutations acquired.</span><span> This study describes the first comprehensive </span>evolutionary history of a bacterial group II intron family.</p>
First unravelling of the hidden and intricate evolutionary history of a bacterial group II intron family
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Template switching by a group II intron reverse transcriptase: biochemical analysis and implications for RNA-seq
GEO Series GSE138200. synthetic construct. 11 samples. Type: Other.
Arabidopsis Mitochondrial Transcription Termination Factor mTERF2 Promotes Splicing of Group IIB Introns
GEO Series GSE163618. Arabidopsis thaliana. 6 samples. Type: Expression profiling by high throughput sequencing.
NicOPURE: Nickless RNA Circularization and One-Step Purification with Engineered Group II Introns and Cyclizing UTRs
GEO Series GSE246246. Gaussia princeps (in: crustaceans). 6 samples. Type: Other.
Characterization of group I introns in generating circular RNAs as vaccines [SPLASH]
GEO Series GSE277434. synthetic construct. 7 samples. Type: Other.
Characterization of group I introns in generating circular RNAs as vaccines
GEO Series GSE239954. synthetic construct. 39 samples. Type: Expression profiling by high throughput sequencing; Other.
Fig. 4 in Sex or no sex? Group I introns and independent marker genes reveal the existence of three sexual but reproductively isolated biospecies in Trichia varia (Myxomycetes)
Fig. 4 Simplified SSU phylogeny showing distribution of IC1 and IE class introns at position S956 in myxomycetes. Tree topology was derived from published SSU phylogenies (Fiore-Donno et al. 2010, 2012, 2013) and the tree presented in Supplementary Fig. S1 of this study. Trichia varia group 1 is represented by a specimen with an intron lacking an HEG; group 2a is represented by a specimen with a HEG-containing intron. Taxa printed in red and marked with "IC1" carry IC1 introns; those printed in blue and marked with "IE" carry IE introns. Nodes marked by dots received support of both Bayesian posterior probability>0.70 and bootstrap replicates>50 (Color figure online)
Fig. 3 in Sex or no sex? Group I introns and independent marker genes reveal the existence of three sexual but reproductively isolated biospecies in Trichia varia (Myxomycetes)
Fig. 3 Intron types found in 66 specimens of Trichia varia at six insertion positions. For each of the phylogroups 1 and 2a, introns are drawn to scale as horizontal bars. White sections denote intron sequences and gray sections homing endonuclease genes. Red/solid and
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