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416 results for “introns”
Brief exposure to warm temperatures reduces intron retention in Kdm6b in a species with temperature-dependent sex determination
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Data from: An intronic transposon insertion associates with a trans-species color polymorphism in Midas cichlid fishes
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Data from: where the minor things are: a pan-eukaryotic survey suggests neutral processes may dominate minor spliceosomal intron evolution
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Analysis of fungal genomes reveals commonalities of intron gain or loss and functions in intron-poor species
<p>Datasets for DOI: <a href="https://doi.org/10.1101/2020.08.11.247098">10.1101/2020.08.11.247098</a>. Jupyter notebooks to reproduce the analysis of this study is available at <a href="https://github.com/Brookesloci/fungi_intron_paper_2020">GitHub</a></p> <ul> <li>annotations.total.txt.gz - gene annotation file of 350 fungi species and outgroups <em>Homo sapiens</em> and <em>Fonticula alba</em></li> <li>site_histories_41490_51_2L_1G.txt.gz - intron site histories of 263 fungi species and outgroups <em>Homo sapiens</em> and <em>Fonticula alba.</em></li> </ul>
The evolution of hemocyanin genes in Tectipleura - a multitude of conserved introns in highly diverse gastropods
<p><strong>Background</strong>: Hemocyanin is the oxygen transporter of most molluscs. Thus, it is an essential protein of these animals which needs to be adapted perfectly to their environments. In Tectipleura, which is a very large and diverse gastropod group with >27,000 species living in all kinds of habitats, several hemocyanin genes have already been identified. They evolved independently from each other within different lineages due to multiple gene duplications and represent potential adaptations to different environments or lifestyles. The aim of this study is to explore the evolution of these genes by analyzing their exon-intron architectures for characteristic features indicating adaptations.</p> <p><strong>Results</strong>: We reconstructed gene architectures of ten hemocyanin genes of four species of Tectipleura: (i) Aplysia californica (ii) Lymnaea stagnalis (iii) Cornu aspersum and (iv) Helix pomatia . Their hemocyanin genes comprise 53 introns each, which is conspicuously more than in known hemocyanin genes of Cephalopoda (9-11), Vetigastropoda (15) and Caenogastropoda (28-33). The gene structures of Tectipleura hemocyanins are identical in terms of number and locations of the introns with exception of only one hemocyanin of Lymnaea stagnalis that comprises one additional intron. Deeper analyses reveal that introns which vary between gene structures of different molluscan lineages most probably evolved more recently through independent intron gains.</p> <p><strong>Conclusions</strong>: The strong conservation of the large number of introns in hemocyanin genes in Tectipleura for over 200 million years suggests a selective pressure on the gene structure. While we have not found characteristic positions or sequence motifs of introns that are conserved, it may be simply the great number of introns that offers increased possibilities of gene regulation and thus may facilitate habitat shifts, adaptive radiation and speciation. This hypothesis is supported by the increased number of introns within hemocyanin genes of Pomacea canaliculata which evolved independently from those of Tectipleura. This species belongs to Caenogastropoda, the sister group of Heterobranchia (where Tectipleura belong to) which is also very diverse and comprises species living in different habitats. Thus, our study provides first evidence that a multitude of introns may contribute to adaptive gene diversity of animals.</p>
Data from: Nuclear introns outperform mitochondrial DNA in inter-specific phylogenetic reconstruction: Lessons from horseshoe bats (Rhinolophidae: Chiroptera)
Despite many studies illustrating the perils of utilising mitochondrial DNA in phylogenetic studies, it remains one of the most widely used genetic markers for this purpose. Over the last decade, nuclear introns have been proposed as alternative markers for phylogenetic reconstruction. However, the resolution capabilities of mtDNA and nuclear introns have rarely been quantified and compared. In the current study we generated a novel ∼5 kb dataset comprising six nuclear introns and a mtDNA fragment. We assessed the relative resolution capabilities of the six intronic fragments with respect to each other, when used in various combinations together, and when compared to the traditionally used mtDNA. We focused on a major clade in the horseshoe bat family (Afro-Palaearctic clade; Rhinolophidae) as our case study. This old, widely distributed and speciose group contains a high level of conserved morphology. This morphological stasis renders the reconstruction of the phylogeny of this group with traditional morphological characters complex. We sampled multiple individuals per species to represent their geographic distributions as best as possible (122 individuals, 24 species, 68 localities). We reconstructed the species phylogeny using several complementary methods (partitioned Maximum Likelihood and Bayesian and Bayesian multispecies-coalescent) and made inferences based on consensus across these methods. We computed pairwise comparisons based on Robinson–Foulds tree distance metric between all Bayesian topologies generated (27,000) for every gene(s) and visualised the tree space using multidimensional scaling (MDS) plots. Using our supported species phylogeny we estimated the ancestral state of key traits of interest within this group, e.g. echolocation peak frequency which has been implicated in speciation. Our results revealed many potential cryptic species within this group, even in taxa where this was not suspected a priori and also found evidence for mtDNA introgression. We demonstrated that by using just two introns one can recover a better supported species tree than when using the mtDNA alone, despite the shorter overall length of the combined introns. Additionally, when combining any single intron with mtDNA, we showed that the result is highly similar to the mtDNA gene tree and far from the true species tree and therefore this approach should be avoided. We caution against the indiscriminate use of mtDNA in phylogenetic studies and advocate for pilot studies to select nuclear introns. The selection of marker type and number is a crucial step that is best based on critical examination of preliminary or previously published data. Based on our findings and previous publications, we recommend the following markers to recover phylogenetic relationships between recently diverged taxa (<20 My) in bats and other mammals: ACOX2, COPS7A, BGN, ROGDI and STAT5A.
Development of novel, Exon-Primed Intron-Crossing (EPIC) markers from EST databases and evaluation of their phylogenetic utility in Commiphora (Burseraceae)
Premise of the study: Novel nuclear exon-primed intron-crossing (EPIC) markers were developed to increase phylogenetic resolution among recently diverged lineages in the frankincense and myrrh family, Burseraceae, using Citrus, Arabidopsis, and Oryza genome resources. Methods and Results: Primer pairs for 48 nuclear introns were developed using the genome resource IntrEST and were screened using species of Commiphora and other Burseraceae taxa. Four putative intron regions (RPT6A, BXL2, mtATP Synthase D, and Rab6) sequenced successfully for multiple taxa and recovered phylogenies consistent with those of existing studies. In some cases, these regions yielded informative sequence variation on par with that of the nrDNA internal transcribed spacer. Conclusions: The combination of freely available genome resources and our design criteria have uncovered four, single-copy nuclear intron regions that are useful for phylogenetic reconstruction of Burseraceae taxa. Because our EPIC primers also amplify Arabidopsis, we recommend their trial in other rosid and eudicot lineages.
Data from: New DNA data from a Transthyretin nuclear intron suggest an Oligocene to Miocene diversification of living South America opossums (Marsupialia: Didelphidae).
Phylogenetic relationships of 19 species of didelphid marsupials were studied using two nuclear markers, the non-coding transthyretin intron 1 (TTR) and the coding interphotoreceptor retinoid binding protein exon 1 (IRBP), and two mitochondrial genes, the protein-coding cytochrome b (cyt-b) and the structural 12S ribosomal DNA (12S rDNA). Evolutionary dynamics of these four markers were compared to each other, revealing the appropriate properties presented by TTR intron 1 together with its well supported and resolved phylogenetic signal. Nuclear markers supported the monophyly of medium and large-sized opossums Metachirus+(Chironectes, Lutreolina, Didelphis, Philander), and the paraphyly of mouse-sized opossums, with the genera Gracilinanus, Thylamys, and Marmosops as a sister group to medium and large-sized didelphids. Conflicting branching patterns between mitochondrial and nuclear data involved the phylogenetic position of Marmosa-Micoureus-Monodelphis relative to other mouse-sized opossums. Nuclear phylogenetic inferences among genera were confirmed by the presence of synapomorphic indels observed in TTR intron 1. A Bayesian relaxed molecular clock dating of didelphid evolution using nuclear markers estimated their origin in the Middle Eocene (39.8 million years ago), with subsequent diversification during the Oligocene (Deseadan) and Miocene.
Hoarding and horizontal transfer led to an expanded gene and intron repertoire in the plastid genome of the diatom, Toxarium undulatum (Bacillariophyta)
<p>Multiple sequence alignments used to produce Figure 2</p>
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.
The 3'-RACE data (InPACT: A computational method for accurate characterization of intronic polyadenylation from RNA sequencing data)
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A single intronic SNP in splicing site of steroidogenic enzyme hsd17b1 is associated with phenotypic sex in oyster pompano, Trachinotus anak
<p>Teleosts show varied master sex determining (MSD) genes and sex determination (SD) mechanisms, with frequent turnovers of sex chromosomes. Tracing the origins of MSD genes and turnovers of sex chromosomes in a taxonomic group is of particular interest in evolutionary biology. Oyster pompano (<em>Trachinotus anak</em>), a marine fish, belongs to the family Carangidae, in which <em>17b-hydroxysteroid dehydrogenase 1</em> (<em>hsd17b1</em>) has repeatedly evolved to a MSD gene. Using whole genome resequencing, a single SNP at Chromosome 24 was identified to be strictly associated with phenotypic sex, with females being the heterozygous sex. This SNP is located in a splicing site at the first exon/intron boundary of <em>hsd17b1</em>. The Z-linked SNP results in malfunction of all spliced isoforms, whereas the W-linked isoforms were predicted to have open reading frames (ORF) that are conserved among vertebrates, suggesting that <em>hsd17b1</em> is a female determining gene. The differential alternative splicing patterns of ZZ and ZW genotypes were consistently observed both in undifferentiated stages and differentiated gonads. We observed elevated recombination around the SD locus and no differentiation between Z and W chromosomes. The extreme diversity of mutational mechanisms that <em>hsd17b1</em> evolves to a MSD gene highlights frequent <em>in situ</em> turnovers between sex chromosomes in the Carangidae.</p>
FIGURE 2. Bayesian tree for S7 intron 1 in Molecular systematics of the North American chub genus Macrhybopsis (Teleostei: Cyprinidae)
FIGURE 2. Bayesian tree for S7 intron 1 in the Platygobio-Macrhybopsis clade and two representatives of the shiner clade (L. umbratilis and H. winchelli). Outgroups excluded. Labels at terminal nodes = haplotype designation followed by locality numbers in Fig. 1; those beginning with GU or JX are accession numbers for sequences obtained from GenBank. Terminal nodes identified only by river system are Eisenhour's (2004) M. hyostoma. Numbers above internal nodes = Bayesian support ±0.90 (asterisks,>0.95); below nodes = maximum parsimony bootstrap support>50%.
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
Fig. 4 in ELAV Intron 8: a single-copy sequence marker for shallow to deep phylogeny in Eupulmonata Hasprunar & Huber, 1990 and Hygrophila Férussac, 1822 (Gastropoda: Mollusca)
Fig. 4 Comparison of ML phylogenetic reconstructions based on ELAVI8 and concatentated ITS1 +2 sequence from 21 California, USA, Haplotrema specimens representing 9 described and 3 undescribed species. The ELAVI8 Haplotrema tree was rooted on a Discidae, a chondrinid, two Orthurethra and two Limacoidea species. This was not possible in
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Allen Brain Atlas
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