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48 results for “gene alignments”
Aligned gene sequences
<p>Aligned gene sequences used for the phylogenetic analysis</p>
Data from 'Disparate inventories of hypoxia gene sets across corals align with inferred environmental resilience'
<p>Aquatic deoxygenation has been flagged as an overlooked but key factor driving mass bleaching-induced coral mortality as oxygen supplies lower to concentrations that can elicit an aerobic metabolic crisis i.e., hypoxia. Surprisingly little is known of the fundamental hypoxia responsive gene set inventory corals possess to respond to deoxygenation. It is unclear whether variation in gene copy number across species exist that potentially affect gene expression with subsequent differences in the effectiveness of a given stress response. Here, we used an ortholog-based meta-analysis to investigate how hypoxia gene inventories differed amongst coral species to assess putative copy number variation (CNV) across 24 coral protein sets from species with a sequenced genome that span corals from the robust and complex clade. We found approximately a third of the investigated genes exhibited copy number differences, and these differences were species-specific rather than the robust-complex split.</p> <p>Zipped folders of OrthoFinder results:</p> <p>'Results_Feb16' contains results including all 24 coral species from 7 genera (<em>Acropora, Pocillopora, Stylophora, Montastrea, Montipora, Obricella, Porites</em>).</p> <p>'gene_sets_acropora_acuminata_only' contains results including just one species per genera with <em>Acropora acuminata</em>.</p> <p>'gene_sets_acropora_cytherea_only' contains results including just one species per genera with <em>Acropora cytherea</em>.</p> <p>'gene_sets_acropora_digitifera_only' contains results including just one species per genera with <em>Acropora digitifera</em>.</p> <p> </p> <p>Results and Interpretations from these analyses are published open access here: <a href="https://doi.org/10.3389/fmars.2022.834332">https://doi.org/10.3389/fmars.2022.834332</a></p> <p>Full citation: Alderdice R, Hume BCC, Kühl M, Pernice M, Suggett DJ, Voolstra CR. Disparate inventories of hypoxia gene sets across corals align with inferred environmental resilience. Front Mar Sci. 2022;9. doi:10.3389/fmars.2022.834332</p> <p>Scripts are available here: <a href="https://zenodo.org/record/6396671#.YoYpoS8RoZg">https://github.com/didillysquat/alderdice_2021</a></p>
The primate Major Histocompatibility Complex: Sets of posterior trees from BEAST2 for the whole-class multi-gene alignments
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Gene trees and corresponding nucleotide/protein alignments across 17 species (including 13 fishes)
<p>This archive contains gene trees and corresponding nucleotide/protein alignments across 17 species (including 13 fishes).</p>
Alignments used for the phylogenies in "Caryophylliids (Anthozoa, Scleractinia) have a mitochondrial gene rearrangement: lesson learned from mitochondrial and nuclear phylogenomics"
<p>"mitochondrial_caryotree.phy": concatenated alignment of mitochondrial data in phylip format; "mitochondrial_caryotree.partitions.txt": indication of start/stop positions of each partition in the mitochondrial data alignment; "nuclear_caryotree_55taxa-50p.phylip": alignment of nuclear exons and ultraconserved elements in phylip format.</p>
Olfactory receptor alignments for: Ecological constraints on highly evolvable olfactory receptor genes and morphology in neotropical bats
<p>While evolvability of genes and traits may promote specialization during species diversification, how ecology subsequently restricts such variation remains unclear. Chemosensation requires animals to decipher a complex chemical background to locate fitness-related resources, and thus the underlying genomic architecture and morphology must cope with constant exposure to a changing odorant landscape; detecting adaptation amidst extensive chemosensory diversity is an open challenge. In phyllostomid bats, an ecologically diverse clade that evolved plant-visiting from an insectivorous ancestor, the evolution of novel food detection mechanisms is suggested to be a key innovation, as plant-visiting species rely strongly on olfaction, supplementarily using echolocation. If this is true, exceptional variation in underlying olfactory genes and phenotypes may have preceded dietary diversification. We compared olfactory receptor (OR) genes sequenced from olfactory epithelium transcriptomes and olfactory epithelium surface area of bats with differing diets. Surprisingly, although OR evolution rates were quite variable and generally high, they are largely independent of diet. Olfactory epithelial surface area, however, is relatively larger in plant-visiting bats and there is an inverse relationship between OR evolution rates and surface area. Relatively larger surface areas suggest greater reliance on olfactory detection and stronger constraint on maintaining an already diverse OR repertoire. Instead of the typical case in which specialization and elaboration are coupled with rapid diversification of associated genes, here the relevant genes are already evolving so quickly that increased reliance on smell has led to stabilizing selection, presumably to maintain the ability to consistently discriminate among specific odorants — a potential ecological constraint on sensory evolution.</p>
Olfactory receptor alignments for: Ecological constraints on highly evolvable olfactory receptor genes and morphology in neotropical bats
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Alignments of ITS1 gene sequences from Harpacticella inopinata
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Supplementary tables S5, S7, S9, S10, original protein models fasta files used for alignments, aligned and manually curated protein modes files used for phylogenies (PHYLIP format), and phylogenetic trees of plant cell wall decomposition gene families from 44 basidiomycete genomes (.tre files)
<p><span><span><span><span><span><span><span><span><span><span><span>Litter-decomposing Agaricales play key role in terrestrial carbon cycling, but little is known about their decomposition mechanisms. We assembled datasets of 42 gene families involved in plant-cell-wall decomposition from seven newly sequenced litter decomposers and 35 other Agaricomycotina members, mostly white-rot and brown-rot species. Using sequence similarity and phylogenetics, we split the families into phylogroups and compared their gene composition across nutritional strategies. Subsequently, we used Raman spectroscopy to examine the ability of litter decomposers, white-rot fungi, and brown-rot fungi to decompose crystalline cellulose. Both litter decomposers and white-rot fungi share the enzymatic cellulose decomposition, whereas brown-rot fungi possess a distinct mechanism that disrupts cellulose crystallinity. However, litter decomposers and white-rot fungi differ with respect to hemicellulose and lignin degradation phylogroups, suggesting adaptation of the former group to the litter environment. Litter decomposers show high phylogroup diversity, which is indicative of high functional versatility within the group, whereas a set of white-rot species shows adaptation to bulk-wood decomposition. In both groups, we detected species that have unique characteristics associated with hitherto unknown adaptations to diverse wood and litter substrates. Our results suggest that the terms white-rot fungi and litter decomposers mask a much larger functional diversity.</span></span></span></span></span></span></span></span></span></span></span></p>
Nucleotide alignments of eight meiosis genes under extreme selection following whole genome duplication in Arabidopsis lyrata/A.arenosa.
<p>In this study we performed a genotype-phenotype association analysis of meiotic stability in 10 autotetraploid <em>Arabidopsis lyrata</em> and <em>A</em>. <em>lyrata/A</em>. <em>arenosa</em> hybrid populations collected from the Wachau region and East Austrian Forealps. The aim was to determine the effect of eight meiosis genes under extreme selection upon adaptation to whole genome duplication. Individual plants were genotyped by high-throughput sequencing of the eight meiosis genes (<em>ASY1</em>, <em>ASY3</em>, <em>PDS5b</em>, <em>PRD3</em>, <em>REC8</em>, <em>SMC3</em>, <em>ZYP1a/b</em>) implicated in synaptonemal complex formation and phenotyped by assessing meiotic metaphase I chromosome configurations. Our results reveal that meiotic stability varied greatly (20–100%) between individual tetraploid plants and associated with segregation of a novel <em>ASYNAPSIS3</em> (<em>ASY3</em>) allele derived from <em>A</em>. <em>lyrata</em>. The <em>ASY3</em> allele that associates with meiotic stability possesses a putative in-frame tandem duplication (TD) of a serine-rich region upstream of the coiled-coil domain that appears to have arisen at sites of DNA microhomology. The frequency of multivalents observed in plants homozygous for the <em>ASY3 TD</em> haplotype was significantly lower than in plants heterozygous for <em>ASY3 TD/ND</em> (non-duplicated) haplotypes. The chiasma distribution was significantly altered in the stable plants compared to the unstable plants with a shift from proximal and interstitial to predominantly distal locations. The number of HEI10 foci at pachytene that mark class I crossovers was significantly reduced in a plant homozygous for <em>ASY3 TD</em> compared to a plant heterozygous for <em>ASY3 ND/TD</em>. Fifty-eight alleles of the 8 meiosis genes were identified from the 10 populations analysed, demonstrating dynamic population variability at these loci. Widespread chimerism between alleles originating from <em>A</em>. <em>lyrata/A</em>. <em>arenosa</em> and diploid/tetraploids indicates that this group of rapidly evolving genes may provide precise adaptive control over meiotic recombination in the tetraploids, the very process that gave rise to them.</p>
Genome reduction is associated with bacterial pathogenicity across different scales of temporal and ecological divergence - between species core gene alignments
<p><span>Emerging bacterial pathogens threaten global health and food security, and so it is important to ask whether these transitions to pathogenicity have any common features. We present a systematic study of the claim that pathogenicity is associated with genome reduction and gene loss. We compare broad-scale patterns across all bacteria, with detailed analyses of <i>Streptococcus suis</i>, an emerging zoonotic pathogen of pigs, which has undergone multiple transitions between disease and carriage forms. We find that pathogenicity is consistently associated with reduced genome size across three scales of divergence (between species within genera, and between and within genetic clusters of <i>S. suis</i>). While genome reduction is also found in mutualist and commensal bacterial endosymbionts, genome reduction in pathogens cannot be solely attributed to the features of their ecology that they share with these species, i.e. host restriction or intracellularity. Moreover, other typical correlates of genome reduction in endosymbionts (reduced metabolic capacity, reduced GC content, and the transient expansion of non-functional elements) are not consistently observed in pathogens. Together, our results indicate that genome reduction is a predictive marker of pathogenicity in bacteria.</span></p>
Alignments from: Gene count from target sequence capture places three whole genome duplication events in Hibiscus L. (Malvaceae)
<p class="BodyA"><span><b>Background:</b> The great diversity in plant genome size and chromosome number is partly due to polyploidization (i.e., genome doubling events). The differences in genome size and chromosome number among diploid plant species can be a window into the intriguing phenomenon of past genome doubling that may be obscured through time by the process of diploidization. The genus <i>Hibiscus </i>L. (Malvaceae) has a wide diversity of chromosome numbers and a complex genomic history. <i>Hibiscus </i>is ideal for exploring past genomic events because although two ancient genome duplication events have been identified, more are likely to be found due to its diversity of chromosome numbers. To reappraise the history of whole genome duplication events, we tested three alternative scenarios describing different polyploidization events.</span></p> <p class="BodyA"><span><b>Results:</b> Using target sequence capture, we designed a new probe set for <i>Hibiscus </i>and generated 87 orthologous genes from four diploid species. We detected paralogues in >54% putative single-copy genes. 34 of these genes were selected for testing three different genome duplication scenarios using gene counting. All species of <i>Hibiscus</i> sampled shared one genome duplication with <i>H. syriacus</i> and one whole genome duplication occurred along the branch leading to <i>H. syriacus</i>.</span></p> <p class="BodyA"><span><b>Conclusions:</b> Here, we corroborated the independent genome doubling previously found in the lineage leading to <i>H. syriacus </i>and a shared genome doubling of this lineage and the remainder of <i>Hibiscus</i>. Additionally, we found a previously undiscovered genome duplication shared by the /Pavonia and /Malvaviscus clades (both nested within <i>Hibiscus</i>) with the occurrences of two copies in what were otherwise single-copy genes. Our results highlight the complexity of genomic diversity in some plant groups, which makes orthology assessment and accurate phylogenomic inference difficult.</span></p>
Data from: Nearly complete rRNA genes from 371 Animalia: updated structure-based alignment and phylogenetic analysis
This study presents a manually constructed alignment of nearly complete rRNA genes from most animal clades (371 taxa from ∼33 of the ∼36 metazoan phyla), expanded from the 197 sequences in a previous study. This thorough, taxon-rich alignment, available at http://www.wsu.edu/≃jmallatt/research/rRNAalignment.html and in the Dryad Repository (doi: http://dx.doi.org/10.5061/dryad.1v62kr3q), is based rigidly on the secondary structure of the SSU and LSU rRNA molecules, and is annotated in detail, including labeling of the erroneous sequences (contaminants). The alignment can be used for future studies of the molecular evolution of rRNA. Here, we use it to explore if the larger number of sequences produces an improved phylogenetic tree of animal relationships. Disappointingly, the resolution did not improve, neither when the standard maximum-likelihood method was used, nor with more sophisticated methods that partitioned the rRNA into paired and unpaired sites (stem, loop, bulge, junction), or accounted for the evolution of the paired sites. For example, no doublet model of paired-site substitutions (16-state, 16A and 16B, 7A–F, or 6A–C models) corrected the placement of any rogue taxa or increased resolution. The following findings are from the simplest, standard, ML analysis. The 371-taxon tree only imperfectly supported the bilaterian clades of Lophotrochozoa and Ecdysozoa, and this problem remained after 17 taxa with unstably positioned sequences were omitted from the analysis. The problem seems to stem from base-compositional heterogeneity across taxa and from an overrepresentation of highly divergent sequences among the newly added taxa (e.g., sequences from Cephalopoda, Rotifera, Acoela, and Myxozoa). The rogue taxa continue to concentrate in two locations in the rRNA tree: near the base of Arthropoda and of Bilateria. The approximately uncertain (AU) test refuted the monophyly of Mollusca and of Chordata, probably due to long-branch attraction of the highly divergent cephalopod and urochordate sequences out of those clades. Unlikely to be correct, these refutations show for the first time that rRNA phylogeny can support some 'wrong' clades. Along with its weaknesses, the rRNA tree has strengths: It recovers many clades that are supported by independent evidence (e.g., Metazoa, Bilateria, Hexapoda, Nonoculata, Ambulacraria, Syndermata, and Thecostraca with Malacostraca) and shows good resolution within certain groups (e.g., in Platyhelminthes, Insecta, Cnidaria). As another strength, the newly added rRNA sequences yielded the first rRNA-based support for Carnivora and Cetartiodactyla (dolphin + llama) in Mammalia, for basic subdivisions of Bryozoa ('Gymnolaemata + Stenolaemata' versus Phylactolaemata), and for Oligostraca (ostracods + branchiurans + pentastomids + mystacocarids). Future improvement could come from better sequence-evolution models that account for base-compositional heterogeneity, and from combining rRNA with protein-coding genes in phylogenetic reconstruction.
6255 gene alignments of Asellidae CDS
<p>Families of orthologous genes used in "<strong>No evidence that nitrogen limitation influences the elemental composition of isopod transcriptomes and proteomes"</strong></p> <p>The 6,255 alignments used in this publication are archived here. Each alignment corresponds to one "pattern" (~ gene family, except when one family X is composed of several patterns = e.g. multigenic family). Each alignment includes between 2 and 26 species. These alignments have been created with:</p> <ul> <li>prank -codon -F</li> <li>GBlocks -b5=h (to allow some gaps)</li> </ul> <p>Alignment are named according to the corresponding family_pattern, e.g. "FAM003424_1.fas.prank_codon.best.fas-gb.bis" corresponds to the family "003424" and the pattern "1". They are composed of several fasta sequences, each sequence corresponding to one species. The name of each fasta sequence starts with the species code (e: BMOV, PCANC) in upper letters. Gaps are present ("----"). ATTENTION: species order differs in each alignment!</p> <p> </p> <p>Table of the correspondance species - code:</p> <p>Species Code couple eco<br /> P. beticus PBTS c1 epi<br /> P. jaloniacus PJJ c1 hypo<br /> P. aragonensis PARE c2 epi<br /> P. spelaeus PSSE c2 hypo<br /> B. peltatus BPM c3 epi<br /> B. molinai BMOV c3 hypo<br /> P. ibericus PIBB c4 epi<br /> P. arthrodilus PATL c4 hypo<br /> P. meridianus PMLL c5 epi<br /> P. margalefi PMAF c5 hypo<br /> P. granandensis PGRP c6 epi<br /> P. solanasi PSOG c6 hypo<br /> P. coxalis PCOB c7 epi<br /> P. parvulus PPRS c7 hypo<br /> P. assaforensis PASA c8 epi<br /> P. rectus PRUE c8 hypo<br /> P. karamani PKK c9 epi<br /> P. hercegovinensis PHEZ c9 hypo<br /> P. coiffaiti PCOIP c10 epi<br /> P. cavaticus PCBF c10 hypo<br /> P. racovitzai PRBE c11 epi<br /> P. escolai PECD c11 hypo<br /> P. ortizi POJ c12 epi<br /> P. grafi PGC c12 hypo<br /> P. ebrensis PEF c13 epi<br /> P. cantabricus PCANC c13 hypo</p> <p>Remark: out of these 6,255 alignments, 8 alignments are empty (when Gblock has removed ALL aligned positions): [1] "FAM000157_5.fas" "FAM000587_3.fas" "FAM000615_1.fas" "FAM008836_1.fas" [5] "FAM013862_1.fas" "FAM015586_1.fas" "FAM017544_1.fas" "FAM022381_1.fas"</p> <p> </p>
Evolutionary "crowdsourcing": alignment of fitness landscapes allows for cross-species adaptation of a horizontally transferred gene
<p>This repository accompanies the publication of <i><strong>Evolutionary "crowdsourcing": alignment of fitness landscapes allows for cross-species adaptation of a horizontally transferred gene</strong></i> by Kosterlitz et. al. This research project explores the cross-species adaptation of a horizontally transferred gene through evolutionary "crowdsourcing." The repository provides all relevant data, code, and figures associated with the publication, enabling users to replicate the results and explore the findings in-depth.</p>
Confocal images from: Cell density, alignment, and orientation correlate with C-signal-dependent gene expression during Myxococcus xanthus development
<p>Starving <em>Myxococcus xanthus</em> bacteria use short-range C-signaling to coordinate their movements and construct multicellular mounds, which mature into fruiting bodies as rods differentiate into spherical spores. Differentiation requires efficient C-signaling to drive the expression of developmental genes, but how the arrangement of cells within nascent fruiting bodies (NFBs) affects C-signaling is not fully understood. Here, we used confocal microscopy and cell segmentation to visualize and quantify the arrangement, morphology, and gene expression of cells near the bottom of NFBs at much higher resolution than previously achieved. We discovered that "transitioning cells" (TCs), intermediate in morphology between rods and spores, comprised 10 to 15% of the total population. Spores appeared midway between the center and the edge of NFBs early in their development and near the center as maturation progressed. The developmental pattern as well as C-signal-dependent gene expression in TCs and spores were correlated with cell density, the alignment of neighboring rods, and the tangential orientation of rods early in the development of NFBs. These dynamic radial patterns support a model in which the arrangement of cells within the NFBs affects C-signaling efficiency to regulate precisely the expression of developmental genes and cellular differentiation in space and time. Developmental patterns in other bacterial biofilms may likewise rely on short-range signaling to communicate multiple aspects of cellular arrangement, analogous to juxtacrine and paracrine signaling during animal development.</p>
Aminoacyl-tRNA synthetase gene alignments from multiple Sileneae species generated from full-length transcripts using Iso-Seq and raw microscopy image files
<p>Trimmed and untrimmed alignments for the final aminoacyl-tRNA synthetases in <em>Sileneae </em>species and <em>Arabidopsis thaliana. W</em>e investigated the evolution of subcellular localization of aaRS enzymes in five different species from the plant lineage <em>Sileneae</em> that has experienced extensive and rapid mitochondrial tRNA loss. By analyzing full-length mRNA transcripts with single-molecule sequencing technology (PacBio Iso-Seq) and searching genome sequences, we found instances of predicted retargeting of an ancestrally cytosolic aaRS to the mitochondrion as well as scenarios where enzyme localization does not appear to change despite functional tRNA replacement.</p> <p>Nikon .nd2 raw microscopy files for the transient expression and imaging of predicted transit peptides and colocalization assays in <em>N. benthamiana</em> epithelial cells. The amino acid sequence plus 10 upstream amino acids of the protein body were fused to GFP and co-transfected with an eqFP611-tagged transit peptide from a known mitochondrially localized protein (isovaleryl-CoA dehydrogenase).</p>
Sergestidae shrimp family single- and multi-gene alignments and tree files
<p>Deep-sea shrimp belonging to the family Sergestidae provide a unique system for studying the evolution of bioluminescence. Most species within the family possess autogenic bioluminescent photophores in one of three distinct forms: lensed photophores, non-lensed photophores, or internal organs of Pesta. This morphological diversity across Sergestidae has resulted in recent major taxonomic revisions, dividing the two major genera (<em>Sergia </em>and<em> Sergestes</em>) into 15. Here, we capitalize on molecular data to construct an updated genus-level phylogeny of sergestid shrimp. DNA was successfully extracted from approximately 87 individuals belonging to 13 of the 15 newly proposed genera. We implemented a "genome skimming" approach, allowing us to capture mitochondrial genomic data across 19 Sergestidae species. Additional individuals have been incorporated into the phylogeny through Sanger sequencing of both nuclear (H3, NAK) and mitochondrial (16S and COI) genes. The resulting molecular phylogeny is compared with previous morphological trees with specific attention to genus-level relationships. The -<em>sergestes</em> group was rendered non-monophyletic, and the -<em>sergia</em> group was recovered as monophyletic. Ancestral state reconstructions of light organ type indicate the organs of Pesta is the ancestral state for the family. Non-lensed photophores evolved once across the -<em>sergia</em> group, but were later lost in the deepest living genus, <em>Sergia</em>. Lensed photophores also evolved once within the genera <em>Prehensilosergia</em>, <em>Lucensosersgia</em>, and <em>Challengerosergia</em>. Our findings identify preliminary patterns across light organ type and species' depth distributions, however future research that incorporates finer-scale depth data and more species is needed to confirm our findings. </p>
Supplementary collection of preprocessed and analysed data objects for the paper: "Gene-level alignment of single cell trajectories"
<p>Supplementary collection of h5ad data files containing preprocessed and analysed single-cell reference and query datasets discussed in the case studies of the paper:<em><strong>"Gene-level alignment of single cell trajectories"</strong></em> (<a href="https://doi.org/10.1101/2023.03.08.531713" rel="nofollow">https://doi.org/10.1101/2023.03.08.531713</a>).</p> <p>Our artificial thymic organoid raw sequencing data are available from ArrayExpress (E-MTAB-12720).</p> <p>Below lists the original sources of the literature datasets we downloaded prior to our own preprocessing and trajectory analysis.</p> <ul> <li> <p>Original pan fetal reference data from: Suo, C. et al. (2022) "Mapping the developing human immune system across organs" (<a href="https://doi.org/10.1126/science.abo0510">https://doi.org/10.1126/science.abo0510</a><a href="http://paperpile.com/b/XTpgLG/TQtQ3">), </a>downloaded from <a href="https://developmental.cellatlas.io/fetal-immune">https://developmental.cellatlas.io/fetal-immune</a>.</p> </li> </ul> <ul> <li> <p>Original healthy/IPF data from: Adams, T. S. et al. (2020), "Single-cell RNA-seq reveals ectopic and aberrant lung-resident cell populations in idiopathic pulmonary fibrosis" (<a href="https://doi.org/10.1126/sciadv.aba1983">https://doi.org/10.1126/sciadv.aba1983</a>), downloaded from GEO (GSE136831).</p> </li> </ul> <p>We have run our scripts in <a href="https://github.com/Teichlab/G2G_notebooks">https://github.com/Teichlab/G2G_notebooks</a> to generate new latent embeddings and infer pseudotime trajectories for the above datasets, and used them to model trajectory alignments with our newly developed framework: ‘Genes2Genes’ <a href="https://github.com/Teichlab/Genes2Genes">https://github.com/Teichlab/Genes2Genes</a>. </p>
61 taxa and 2399 loci alignment of phylodiverse Klebsormidiophyceae trimmed gene-wise with clipkit
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
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