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175 results for “sequence alignments”
Multiple sequence alignment of DNA-A sequences from ACMBFV, ACMV, CMMGV, EACMCV, EACMKV, EACMMV, EACMV, EACMZV, SACMV, ICMV, SLCMV (11 species)
<p>All full-length DNA-A sequences available in GenBank as of July 2019 were downloaded via the Taxonomy Browser interface. Sequence names were normalized/simplified and orientations of these circular sequences were standardized to begin at the replication origin nick site. Sequences were aligned with MUSCLE and alignments were manually adjusted with SeAl (A. Rambaut) and AliView (A. Larsson).</p>
Coregonus spp. opsin amplicon sequence alignments
<p>Local adaptation can drive diversification of closely related species across environmental gradients and promote convergence of distantly related taxa that experience similar conditions. We examined a potential case of adaptation to novel visual environments in a species flock (Great Lakes salmonids, genus <i>Coregonus</i>) using a new amplicon genotyping protocol on the Oxford Nanopore Flongle. Five visual opsin genes were sequenced for individuals of <i>C. artedi</i>,<i> C. hoyi</i>,<i> C. kiyi</i>, and <i>C. zenithicus.</i> Comparisons revealed species-specific differences in a key spectral tuning amino acid in <i>rhodopsin</i> (Tyr261Phe substitution), suggesting local adaptation of <i>C. kiyi </i>to the blue-shifted depths of Lake Superior. Ancestral state reconstruction demonstrates that parallel evolution and "toggling" at this amino acid residue has occurred several times across the fish tree of life, resulting in identical changes to the visual systems of distantly related taxa across replicated environmental gradients. Our results suggest that ecological differences and local adaptation to distinct visual environments are strong drivers of both evolutionary parallelism and diversification.</p>
Prosopis laevigata microsatellite and sequence alignment data
<p>Patterns of genetic and phylogeographic structure and recent population history of plant species in the Mexican arid zones has been scarcely investigated. <i>Prosopis laevigata</i> is the most widely spread species of mesquite in Mexico, with extensive populations in the arid and semi-arid zones of the central and northern plateaus and scattered presence in southern Mexico. We evaluated the genetic and phylogeographic structure of this species to infer its recent demographic history. We genotyped six nuclear microsatellite loci and sequenced the psbA3´-trnH chloroplast DNA (cpDNA) region in individuals from 21 populations covering the whole distribution of the species. Nuclear genetic diversity was moderately high (H<sub>E</sub>=0.527) and genetic differentiation was moderate (F<sub>ST</sub>=0.16). A positive correlation between genetic diversity and latitude was observed. The cpDNA analyses indicated a lack of phylogeographic structure in <i>P. laevigata</i> (G<sub>ST</sub>=0.090, N<sub>ST</sub>=0.101; P=0.497). Historical demography statistics indicated a population expansion supported by a skyline plot analysis, the star-like shape of the haplotype network, and the unimodal shape of the mismatch distribution. Ecological niche modeling suggested a contracted distribution into west-central Mexico during the Last Interglacial (~140 Ka), followed by an expansion in both northwards and southwards directions in the Last Glacial Maximum (~22 Ka), which continued in the mid-Holocene (~6 Ka) and the present. Results are congruent with a recent population growth and colonization of newly opened arid zones by <i>P. laevigata</i> populations. This pattern is consistent with the high capacity of colonization of nutrient-poor areas, high germination rates and resistance to drought reported for <i>Prosopis</i> species</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>
Sequence alignments of Corallicolids, apicomplexan symbionts of coral
<p class="BodyA">Corals (Metazoa; Cnidaria; Anthozoa) have recently been shown to play host to a widespread and diverse group of intracellular symbionts of the phylum Apicomplexa. These symbionts, colloquially called 'corallicolids', are mostly known through molecular analyses, and no formal taxonomy has been proposed. Another apicomplexan, <i>Gemmocystis cylindrus</i> (described from the coral <i>Dendrogyra cylindrus</i>), may be related to corallicolids, but lacks molecular data. Here, we isolate and describe motile trophozoite (feeding) corallicolids cells using microscopic (light, SEM, and TEM) and molecular phylogenetic analysis to provide the basis for a formal description. Phylogenetic analyses using nuclear and plastid rRNA operons, and three mitochondrial protein sequences derived from single-cell transcriptomes, all confirm that these organisms fall into a discrete deep-branching clade within the Apicomplexa not closely related to any known species or major subgroup. As a result, we assign this clade to a new order, Corallicolida ord. nov., and family, Corallicolidae fam. nov. We describe a type species, <i>Corallicola aquarius</i> gen. nov. sp. nov. from its <i>Rhodactis </i>sp.<i> </i>host, and also describe a second species, <i>Anthozoaphila gnarlus</i> gen. nov. sp. nov., from the coral host <i>Madracis mirabilis</i>. Finally, we propose reassigning the incertae sedis taxon <i>G. cylindrus</i> from the order Agamococcidiorida to the Corallicolida, based on similarities in morphology and host localization to that of the corallicolids.</p>
Two new species of Aphyllon from northeastern Mexico: Sequence alignments and phylogenetic trees
<p>Plants originally identified as <em>Aphyllon ludovicianum</em> that occur near Monterrey, Nuevo Leon, and Cuatro Ciénegas Bolson, Coahuila, Mexico, were found to not align with the protologue of that species, the close relative <em>A. multiflorum,</em> or any other species of <em>Aphyllon</em>. Following a detailed study of floral morphology, geographic range, host species, and phylogenetic position using dry herbarium specimens, field study and georeferenced color photographs, we propose the new binomials <em>Aphyllon spectabile </em>for the plants from Nuevo Leon and <em>Aphyllon gypsophilum</em> for the plants from Coahuila, Mexico. This increases the taxonomic diversity of <em>Aphyllon</em> to 27 species plus ten additional subspecies. <em>Gymnosperma glutinosum</em> and two species of <em>Xanthisma</em> were reported for the first time as a host species for the genus <em>Aphyllon</em>. We also provide an updated key to <em>Aphyllon</em> in Mexico. </p>
Aligned DNA sequence matrix for phylogenetic analyses in the article "Systematics of the Dendropsophus leucophyllatus species group (Anura, Hylidae) from the Chocó region of Ecuador, with description of a new species"
<p>Aligned DNA sequence matrix for phylogenetic analyses of the article "Systematics of the <em>Dendropsophus leucophyllatus</em> species group (Anura, Hylidae) from the Chocó region of Ecuador, with description of a new species"</p> <p>The matrix is in NEXUS format and has 7691 bp and 203 terminals.</p> <p>Partitions are as follows:</p> <div> <div>charset 12S = 1-996;</div> <div> </div> <div>charset CO1codonPos1 = 997-1639\3;</div> <div>charset CO1codonPos2 = 998-1640\3;</div> <div>charset CO1codonPos3 = 999-1638\3;</div> <div> </div> <div>charset ND1nonCoding = 1641- 1713 2675- 2796 ;</div> <div>charset ND1codonPos1 = 1714-2674\3;</div> <div>charset ND1codonPos2 = 1715-2672\3;</div> <div>charset ND1codonPos3 = 1716-2673\3;</div> <div> </div> <div>charset CytbcodonPos1 = 2798-3686\3;</div> <div>charset CytbcodonPos2 = 2799-3687\3;</div> <div>charset CytbcodonPos3 = 2797-3685\3;</div> <div> </div> <div>charset RhodcodonPos1 = 3689-4001\3;</div> <div>charset RhodcodonPos2 = 3690-4002\3;</div> <div>charset RhodcodonPos3 = 3688-4003\3;</div> <div> </div> <div>charset TYRcodonPos1 = 4005-4539\3;</div> <div>charset TYRcodonPos2 = 4006-4537\3;</div> <div>charset TYRcodonPos3 = 4004-4538\3;</div> <div> </div> <div>charset RAG1codonPos1 = 4542-4965\3;</div> <div>charset RAG1codonPos2 = 4540-4966\3;</div> <div>charset RAG1codonPos3 = 4541-4964\3;</div> <div> </div> <div>charset POMCcodonPos1 = 4967-5441\3;</div> <div>charset POMCcodonPos2 = 4968-5439\3;</div> <div>charset POMCcodonPos3 = 4969-5440\3;</div> <div> </div> <div>charset SIAH1codonPos1 = 5443-5836\3;</div> <div>charset SIAH1codonPos2 = 5444-5837\3;</div> <div>charset SIAH1codonPos3 = 5442-5838\3;</div> <div> </div> <div>charset 16S_rec = 5839-7695;</div> </div>
Aligned DNA sequences of Vanilla
<p><strong><span>Premise</span></strong></p> <p><span>Although vanilla is one of the best-known spices, there is a limited understanding of its biology and genetics within Mexico, where its cultivation originated and where phenotypic variability is high. This study aims to augment our understanding of vanilla's genetic resources by assessing species delimitation and genetic, geographic, and climatic variability within Mexican cultivated vanilla. </span></p> <p><strong><span>Methods</span></strong></p> <p><span>Nuclear and plastid DNA sequence data from 58 Mexican samples collected from three regions and 133 <em>ex-situ</em> accessions were used to assess species monophyly using phylogenetic analyses and genetic distances. Intra-specific genetic variation was summarized through the identification of haplotypes. Within the primarily cultivated species, <em>V. planifolia</em>, haplotype relationships were further verified using plastome and rRNA gene sequences. Climatic niche and haplotype composition were assessed across the landscape.</span></p> <p><strong><span>Key Results</span></strong></p> <p><span>Three species (<em>Vanilla planifolia</em>, <em>V. pompona</em>, and <em>V. insignis</em>) and 13 haplotypes were identified among Mexican vanilla. Within <em>V. planifolia</em> haplotypes, hard phylogenetic incongruences between plastid and nuclear sequences suggest past hybridization events. Eight haplotypes exclusively consisted of Mexican samples. The dominant <em>V. planifolia</em> haplotype occurred throughout all three regions as well as outside of its country of origin. Haplotype richness was found to be highest in regions around Papantla and La Chinantla.</span></p> <p><strong><span>Conclusions</span></strong></p> <p><span>Long histories of regional cultivation support the consideration of endemic haplotypes as landraces shaped by adaptation to local conditions and/or hybridization. Results may aid further genomic investigations of vanilla's genetic resources and ultimately support the preservation of genetic diversity within the economically important crop.</span></p>
Sample graphs and sequences for testing sequence-to-graph alignment
<p>File descriptions:</p> <ul> <li>MHC-61.agc: 61 complete MHC sequences, including GRCh38, CHM13 and 59 haplotypes extracted from <a href="https://github.com/human-pangenomics/HPP_Year1_Assemblies">HPRC year-1 assemblies</a>. Use <a href="https://github.com/refresh-bio/agc">AGC</a> to extract individual haplotype sequences.</li> <li>MHC-57.gfa.gz: sequence graph constructed by <a href="https://github.com/lh3/minigraph">minigraph</a>-0.18, excluding sample HG002 and HG005</li> <li>C4-96.agc: 96 complete C4 sequences obtained from HPRC</li> <li>C4-90.gfa.gz: sequence graph extracted from the <a href="https://doi.org/10.5281/zenodo.6499594">full HPRC year-1 minigraph graph (v0.17)</a> around the C4A/C4B genes. The graph takes GRCh38 as the reference and excludes sample HG002, HG005 and NA19240.</li> </ul>
Queries and graphs for sequence to graph alignment method evaluation
<p>The tar contains two directories for queries and graphs used to evaluate the sequence to graph alignment methods. </p>
Highly significant improvement of protein sequence alignments with AlphaFold2
<p>Data, figures and tables from the manuscript "Highly significant improvement of protein sequence alignments with AlphaFold2" (https://doi.org/10.1093/bioinformatics/btac625).</p> <p>The repository containing all the steps to replicate the analysis is available at GitHub (https://github.com/cbcrg/msa-af2-nf).</p> <p>*The authors Athanasios Baltzis and Leila Mansouri contributed equally.</p>
Aligned and curated mtDNA sequences from: Ancient DNA reveals interstadials as a driver of common vole population dynamics during the last glacial period
<p><strong><span>Aim: </span></strong><span>Many species experienced population turnover and local extinction during the Late Pleistocene. In the case of megafauna, it remains challenging to disentangle climate change and the activities of Palaeolithic hunter-gatherers as the main cause. In contrast, the impact of humans on rodent populations </span><span>is likely to be negligible. This study investigated which climatic and/or environmental factors affect the population dynamics of the common vole. </span><span>This temperate rodent is widespread across Europe and was one of the most abundant small mammal species throughout the Late Pleistocene.</span></p> <p><span><strong>Location:</strong> </span><span>Europe</span></p> <p><strong><span>Taxon: </span></strong><span>Common vole (<em>Microtus arvalis</em>)</span></p> <p><strong><span>Methods: </span></strong><span>We generated a dataset comprised of a 4.2-kb-long fragment of mitochondrial DNA (mtDNA) from 148 ancient and 51 modern specimens sampled from multiple localities across Europe and covering the last 60 thousand years (ka). We used Bayesian inference to reconstruct their phylogenetic relationships and to estimate the age of the specimens that were not directly dated.</span></p> <p><span><strong>Results:</strong> </span><span>We estimated the time to the most recent common ancestor of all last glacial and extant common vole lineages to be 90 ka ago and the divergence of the main mtDNA lineages present in extant populations to between 55 and 40 ka ago, which is earlier than previous estimates. </span><span>We detected several lineage turnovers in Europe during the period of high climate variability at the end of Marine Isotope Stage 3 (MIS 3; 57–29 ka ago) in addition to those found previously around the Pleistocene/Holocene transition.</span><span> </span><span>In contrast, data from the Western Carpathians suggest continuity throughout the Last Glacial Maximum (LGM), even at high latitudes.</span></p> <p><strong><span>Main conclusions: </span></strong><span>The main factor affecting the common vole populations during the last glacial period was the decrease in open habitat during the interstadials, whereas </span><span>climate </span><span>deterioration </span><span>during</span><span> the LGM had little impact on population dynamics. This suggests that the rapid environmental change rather than other factors was the major force shaping the histories of the Late Pleistocene faunas.</span></p>
Alignment of ITS sequences of Erysiphe specimens from Koelreuteria hosts, with Golovinomyces spp. as outgroup. The scientific names are followed by the respective GenBank accession number.
Open the record for dataset details and reuse information.
Data from: Evaluating statistical multiple sequence alignment in comparison to other alignment methods on protein data sets
The estimation of multiple sequence alignments of protein sequences is a basic step in many bioinformatics pipelines, including protein structure prediction, protein family identification, and phylogeny estimation. Statistical co-estimation of alignments and trees under stochastic models of sequence evolution has long been considered the most rigorous technique for estimating alignments and trees, but little is known about the accuracy of such methods on biological benchmarks. We report the results of an extensive study evaluating the most popular protein alignment methods as well as the statistical co-estimation method BAli-Phy on 1192 protein data sets from established benchmarks as well as on 120 simulated data sets. Our study (which used more than 230 CPU years for the BAli-Phy analyses alone) shows that BAli-Phy has better precision and recall (with respect to the true alignments) than the other alignment methods on the simulated data sets, but has consistently lower recall on the biological benchmarks (with respect to the reference alignments) than many of the other methods. In other words, we find that BAli-Phy systematically under-aligns when operating on biological sequence data, but shows no sign of this on simulated data. There are several potential causes for this change in performance, including model misspecification, errors in the reference alignments, and conflicts between structural alignment and evolutionary alignments, and future research is needed to determine the most likely explanation. We conclude with a discussion of the potential ramifications for each of these possibilities.
Sample data for sequencing reads alignment
<p>These data are used for learning sequencing reads alignment and cluster usage</p>
FIGURE 59. ITS2 sequence alignment for putative species sequenced here. Where identical ITS2 in Cardicola Short, 1953 and Braya n. gen. Digenea: Sanguinicolidae) from five families of tropical Indo-Pacific fishes (
FIGURE 59. ITS2 sequence alignment for putative species sequenced here. Where identical ITS2 sequences were obtained from sanguinicolids of different host/location combinations (not differentiated by morphological comparisons) only one representative sequence has been included here. Gaps of five spaces delineate the 5' and 3' ends of ITS2 (and subsequent 3' end of 5.8S and the 5' end of 28S).
FIGURE 1. ITS2 sequence alignment for threadlike sanguinicolids. Where identical ITS2 in An exceptionally rich complex of Sanguinicolidae von Graff, 1907 (Platyhelminthes: Trematoda) from Siganidae, Labridae and Mullidae (Teleostei: Perciformes) from the Indo-west Pacific Region
FIGURE 1. ITS2 sequence alignment for threadlike sanguinicolids. Where identical ITS2 sequences were obtained for sanguinicolids from different host/location combinations only one sequence has been included here. Gaps of five spaces delineate the 5' and 3' ends of ITS2 (and subsequent 3' end of 5.8S and the 5' end of 28S).
TAPER: Pinpointing errors in multiple sequence alignments despite varying rates of evolution
<p>Datasets related to "TAPER: Pinpointing errors in multiple sequence alignments despite varying rates of evolution."</p>
Sequence alignment for 7 gene regions for new Phytophthora species in clade 2a
<p>Five new taxa from <i>Phytophthora</i> ITS Clade 2a are described from <i>Cinnamomum cassia</i> plantations and adjacent waterways in Van Yen, Vietnam, and disturbed rainforest in the Hela Province of Papua New Guinea and from disturbed forest on Christmas Island. Phylogenetic analyses were performed using data from nuclear regions (ITS, β-tubulin; Heat shock protein 90) and mitochondrial regions (cytochrome c oxidase subunit 1; cytochrome c oxidase subunit2; NADH dehydrogenase subunit 1; ribosomal protein L10). The molecular data supported recognition of three species: <i>Phytophthora insulinativitatica, P. multibullata </i>and <i>P. </i>x<i> vanyenensis</i> and two informal taxa, <i>P.</i> sp. germisporangia and <i>P.</i> sp. awatangi. <i>P. </i>x<i> vanyenensis</i> appears to be a hybrid between <i>P. </i>sp<i>. mekongensis</i> and an unknown species. <i>P. multibullata </i>and<i> P</i>. sp. germisporangia are phylogenetically close to <i>P. citrophthora,</i> but morphologically distinct. <i>P. insulinativitatica</i> is most closely related to <i>P. botryosa </i>but has different morphology.<b> </b><i>P.</i> sp. germisporangia and <i>P.</i> sp. awatangi were morphologically distinct and separated in the phylogeny based on mitochondrial sequences, but their nuclear sequences were identical. When comparing the sequences of these new species to that available on GenBank, it became evident that some of these species shared similarity with isolates submitted to GenBank under other species names and a re-evaluation of all P<i>. meadii</i> and <i>P. colocasiae</i> ITS sequence data identified an additional 7 putatively new species all isolated from Asia. The results support the view that many more <i>Phytophthora</i> species remain to be discovered in the Asia-Pacific region.</p>
Multiple sequence alignments and phylogenetic trees from: Co-option of the limb patterning program in cephalopod eye development
<p>Background</p> <p><span>Across the Metazoa, similar genetic programs are found in the development of analogous, independently evolved, morphological features. The functional significance of this reuse and the underlying mechanisms of co-option remain unclear. Cephalopods have evolved a highly acute visual system with a cup shaped retina and a novel refractive lens in the anterior, important for a number of sophisticated behaviors including predation, mating and camouflage. Almost nothing is known about the molecular-genetics of lens development in the cephalopod.</span></p> <p><span>Results</span></p> <p><span>Here we identify the co-option of the canonical bilaterian limb pattering program during cephalopod lens development, a functionally unrelated structure. We show radial expression of transcription factors <i>SP6-9/sp1, Dlx/dll, </i><i>Pbx/exd, Meis/hth, </i>and a <i>Prdl</i> homolog in the squid <i>Doryteuthis pealeii</i>, similar to expression required in <i>Drosophila</i> limb development.<i> </i>We assess the role of Wnt signaling in the cephalopod lens, a positive regulator in the developing <i>Drosophila </i>limb, and find the regulatory relationship reversed, with ectopic Wnt signaling leading to lens loss. </span></p> <p><span>Conclusion</span></p> <p><span>This regulatory divergence suggests that duplication of SP6-9 in cephalopods may mediate the co-option of the limb patterning program. Thus our study suggests that the limb network could perform a more universal developmental function in radial pattering and highlights how canonical genetic programs are repurposed in novel structures.</span></p>
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