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90 results for “sequence divergence”
Figure 4. Approximate distributions and associated divergence times for A in Mitochondrial Dna Sequence Data Indicate Evidence For Multiple Species Within Peromyscus Maniculatus
Figure 4. Approximate distributions and associated divergence times for A) Peromyscus maniculatus-like ancestor; B) P. melanotis-like ancestor; C) P. gambelii/keeni/sejugis/sp.-like ancestor; D) P. polionotus-like ancestor; E) P. sonoriensis-like ancestor; F) P. labecula and P. maniculatus - like ancestor; G) P. keeni/sp.-like ancestor; and H) P. keeni-like, P. gambelii-like, P. sejugis-like, and P. sp.-like ancestors. Divergence times were estimated from the BEAST analysis (Version 2.4, Bouckaert et al. 2014) of the mitochondrial cytochrome-b gene dataset (see Fig. 3). Shading schemes that correspond to species distributions are shown in the inset.
Data from: Coding-sequence evolution does not explain divergence in petal anthocyanin pigmentation between Mimulus luteus var. luteus and M. l. variegatus
<p><span>Biologists have long been interested in understanding genetic constraints on the evolution of development. For example, noncoding changes in a gene might be favored relative to coding changes due to being less constrained by pleiotropic effects. Here we evaluate the importance of coding-sequence changes to the recent evolution of a novel anthocyanin pigmentation trait in the monkeyflower genus <em>Mimulus</em>. The magenta-flowered <em>Mimulus</em> <em>luteus</em> var. <em>variegatus</em> recently gained petal lobe anthocyanin pigmentation via a single-locus Mendelian difference from its sister taxon, the yellow-flowered <em>M. l. luteus</em>. Previous work showed that the differentially expressed transcription factor gene <em>MYB5a</em>/<em>NEGAN</em> is the single causal gene. However, it was not clear whether <em>MYB5a</em> coding-sequence evolution (in addition to the observed patterns of differential expression) might also have contributed to increased anthocyanin production in <em>M. l. variegatus</em>. Quantitative image analysis of tobacco leaves, transfected with <em>MYB5a</em> coding sequence from each taxon, revealed robust anthocyanin production driven by both alleles. Counter to expectations, significantly higher anthocyanin production was driven by the allele from the low-anthocyanin <em>M. l. luteus.</em> Together with previously-published expression studies, this supports the hypothesis that petal pigment in <em>M. l. variegatus</em> was not gained by protein-coding changes, but instead solely via non-coding cis-regulatory evolution. Finally, while constructing the transgenes needed for this experiment, we unexpectedly discovered two sites in <em>MYB5a</em> that appear to be post-transcriptionally edited – a phenomenon that has been rarely reported, and even less often explored, for nuclear-encoded plant mRNAs.</span></p>
Data from: Coding-sequence evolution does not explain divergence in petal anthocyanin pigmentation between Mimulus luteus var. luteus and M. l. variegatus
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Data from: Genotyping by sequencing and genome–environment associations in wild common bean predict widespread divergent adaptation to drought
Drought will reduce global crop production by >10% in 2050 substantially worsening global malnutrition. Breeding for resistance to drought will require accessing crop genetic diversity found in the wild accessions from the driest high stress ecosystems. Genome–environment associations in crop wild relatives reveal natural adaptation, and therefore can be used to identify adaptive variation. We explored this approach in the food crop Phaseolus vulgaris L., characterizing 86 geo-referenced wild accessions using Genotyping by Sequencing (GBS) to discover single-nucleotide-polymorphisms (SNPs). The wild beans represented Mesoamerica, Guatemala, Colombia, Ecuador/Northern Peru and Andean groupings. We found high polymorphism with a total of 22,845 SNPs across the 86 accessions loci that confirmed genetic relationships for the groups. As a second objective, we quantified allelic associations with a bioclimatic-based drought index using 10 different statistical models that accounted for population structure. Based on the optimum model, 115 SNPs in 90 regions, widespread in all 11 common bean chromosomes, were associated with the bioclimatic-based drought index. A gene coding for an Ankyrin repeat-containing protein and a phototropic-responsive NPH3 gene were identified as potential candidates. Genomic windows of 1Mb containing associated SNPs had more positive Tajima's D scores than windows without associated markers. This indicates that adaptation to drought, as estimated by bioclimatic variables, has been under natural divergent selection, suggesting that drought tolerance may be favorable under dry conditions but harmful in humid conditions. Our work exemplifies that genomic signatures of adaptation are useful for germplasm characterization, potentially enhancing future marker-assisted selection and crop improvement.
Resolution, validation and divergence of heterozygous haplotypes from pooled long read sequencing of the diamondback moth (Lepidoptera: Plutellidae)
<p>This data sets includes the full set of intermediate genome assemblies produced during our analyses. We make these available for researchers who may be interested in the variation between assembly results and variation within the study organism (<em>Plutella xylostella</em>) prior to removal during subsequent genome processing.</p>
Raw Data for the article: A retrospective molecular epidemiological scenario of carbapenemase-producing Klebsiella pneumoniae clinical isolates in a Sicilian transplantation hospital shows a swift polyclonal divergence among sequence types, resistome and virulome
<p>In this work, we assessed and characterized the epidemiological scenario of carbapenem-resistant Klebsiella pneumoniae strains (CR-Kp) at IRCCS-ISMETT, a transplantation hospital in Palermo, Italy, from 2008 to 2017. A total of 288 K. pneumoniae clinical isolates were selected based on their resistance to carbapenems. Molecular characterization was also done in terms of the presence of virulence and resistance genes. All patients were inpatients from our facility and clinical isolates were collected from several sources, either from infection or colonization cases. We observed that, in agreement with the Italian epidemiological scenario, initially only ST258 and ST512 clade II (but not from clade I) were identified from 2008 to 2011. From 2012 onwards, other STs have been observed, including the clinically relevant ST101 and ST307, but also others not previously observed in other Italian health settings, such as ST220 and ST753. The presence of genes involved in resistance and virulence was confirmed, and a heterogeneous genetic resistance profile throughout the years was observed. Our work highlights that resistance genes are rapidly disseminating between different and novel K. pneumoniae clones which, combined with resistance to multiple antibiotics, can derive into more aggressive and pathogenic multidrug-resistant strains of clinical importance. Our results stress the importance of continuous surveillance of CR Enterobacterales in health facilities so that novel STs carrying resistance and virulence genes that may become increasingly pathogenic can be identified and adequate therapies to adopted to avoid their dissemination and derived pathologies.</p>
Aligned DNA sequence matrixes for the study of the divergent times of phytoplasmas
<p>Sequence alignments of 16S rRNA and methionine aminopeptidase (map) are provided in FASTA files “Cao_et_al_16S.fas” and “Cao_et_al_map.fas”, respectively. Detailed information of the data matrixes is as follows:</p> <p> </p> <p>File name: Cao_et_al_16S.fas</p> <p>Number of taxa: 220</p> <p>Number of characters: 1655</p> <p>Gap: -</p> <p> </p> <p>File name: Cao_et_al_map.fas</p> <p>Number of taxa: 83</p> <p>Number of characters: 564</p> <p>Gap: -</p>
Aligned DNA sequence matrixes for the study of the divergent times of phytoplasmas
<p>Sequence alignments of 16S rRNA and methionine aminopeptidase (map) are provided in FASTA files “Cao_et_al_16S.fas” and “Cao_et_al_map.fas”, respectively. Detailed information of the data matrixes is as follows:</p> <p> </p> <p>File name: Cao_et_al_16S.fas</p> <p>Number of taxa: 220</p> <p>Number of characters: 1655</p> <p>Gap: -</p> <p> </p> <p>File name: Cao_et_al_map.fas</p> <p>Number of taxa: 83</p> <p>Number of characters: 564</p> <p>Gap: -</p>
Sequencing data from: Divergent lineages in a young species: the case of Datilillo (Yucca valida), a broadly distributed plant from the Baja California Peninsula
<div> <div> <p><strong>Premise: </strong>Globally, barriers triggered by climatic changes have caused habitat fragmentation and population allopatric divergence. Across North America, oscillations during the Quaternary have played important roles in the distribution of wildlife. Notably, diverse plant species from the Baja California Peninsula in western North America, isolated during the Pleistocene glacial–interglacial cycles, exhibit strong genetic structure and highly concordant divergent lineages across their ranges. A representative plant genus of the peninsula is <em>Yucca</em>, with <em>Y. valida</em> having the widest range. Although a dominant species, it has an extensive distribution discontinuity between 26° N and 27° N, suggesting restricted gene flow. Moreover, historical distribution models indicate the absence of an area with suitable conditions for the species during the Last Interglacial, making it an interesting model for studying genetic divergence.<br>Methods: We assembled 4411 SNPs from 147 plants of <em>Y. valida</em> throughout its range to examine its phylogeography to identify the number of genetic lineages, quantify their genetic differentiation, reconstruct their demographic history and estimate the age of the species.<br>Results: Three allopatric lineages were identified based on the SNPs. Our analyses support that genetic drift is the driver of genetic differentiation among these lineages. We estimated an age of less than 1 million years for the common ancestor of <em>Y. valida</em> and its sister species.<br>Conclusions: Habitat fragmentation caused by climatic changes, low dispersal, and an extensive geographical range gap acted as cumulative mechanisms leading to allopatric divergence in <em>Y. valida</em>.</p> </div> </div>
Genome sequence and silkomics of the spindle ermine moth, Yponomeuta cagnagella, representing the early diverging lineage of the ditrysian Lepidoptera
<p>Many lepidopteran caterpillars produce silk, cocoons, feeding tubes, or nests for protection from predators and parasites. Yet, the number of lepidopteran species whose silk composition has been studied in detail is very small, because the genes encoding the major structural silk proteins tend to be large and repetitive, making their assembly and sequence analysis difficult. Here we have analyzed the silk of <em>Yponomeuta cagnagella</em>, which represents one of the early diverging lineages of the ditrysian Lepidoptera thus improving the coverage of the order. To obtain a comprehensive list of the <em>Y. cagnagella</em> silk genes, we sequenced, assembled, and annotated the draft genome using Oxford Nanopore and Illumina technologies. The 626 Mb assembly with N50 of 96.5 kb contained 96.9% insect orthologs recovered by BUSCO and 30,003 predicted gene models. We then used a silk-gland transcriptome and a silk proteome to identify major silk components and verified the tissue specificity of the expression of individual genes. </p>
Sequencing data for: Chronosequence of invasion reveals minimal losses of population genomic diversity, niche expansion, and trait divergence in the polyploid, leafy spurge
<p>Rapid evolution may play an important role in the range expansion of invasive species and modify forecasts of invasion, which are the backbone of land management strategies. However, losses of genetic variation associated with colonization bottlenecks may constrain trait and niche divergence at leading range edges, thereby impacting management decisions that anticipate future range expansion. The spatial and temporal scales over which adaptation contributes to invasion dynamics remain unresolved. We leveraged detailed records of the ~130-year invasion history of the invasive polyploid plant, leafy spurge (<em>Euphorbia</em> <em>virgata</em>), across ~500km in Minnesota, U.S.A. We examined the consequences of range expansion for population genomic diversity, niche breadth, and the evolution of germination behavior. Using genotyping-by-sequencing, we found some population structure in the range core, where introduction occurred, but panmixia among all other populations. Range expansion was accompanied by only modest losses in sequence diversity, with small, isolated populations at the leading edge harboring similar levels of diversity to those in the range core. The climatic niche expanded during most of the range expansion, and the niche of the range core was largely non-overlapping with the invasion front. Ecological niche models indicated that mean temperature of the warmest quarter was the strongest determinant of habitat suitability and that populations at the leading edge had the lowest habitat suitability. Guided by these findings, we tested for rapid evolution in germination behavior over the time course of range expansion using a common garden experiment and temperature manipulations. Germination behavior diverged from early to late phases of the invasion, with populations from later phases having higher dormancy at lower temperatures. Our results suggest that trait evolution may have contributed to niche expansion during invasion and that distribution models, which inform future management planning, may underestimate invasion potential without accounting for evolution.</p>
Single-cell and spatial RNA sequencing identify divergent microenvironments and progression signatures in early- versus late-onset prostate cancer
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Genome sequence and silkomics of the spindle ermine moth, Yponomeuta cagnagella, representing the early diverging lineage of the ditrysian Lepidoptera
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Data from: Genotyping by sequencing and genome–environment associations in wild common bean predict widespread divergent adaptation to drought
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Sequencing data for: Chronosequence of invasion reveals minimal losses of population genomic diversity, niche expansion, and trait divergence in the polyploid, leafy spurge
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Divergence in coding sequence and expression of different functional categories of immune genes between two wild rodent species
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Data from: Genetic incompatibilities in reciprocal hybrids between populations of Tigriopus californicus with low to moderate mitochondrial sequence divergence
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standard with together) corner left bottom (analysis genetic the in included species among bold gene in shown oxidase-I are SE cytochrome and species the within at) % (divergence divergence sequence average The . pairwise) corner showing right upper (Matrix) %;. SE 4 ABLE (T error in Description of a new species of the Rhinolophus trifoliatus-group (Chiroptera: Rhinolophidae) from Southeast Asia
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TA B L E 2 Estimates of pairwise sequence divergence (cyt-b gene) in pale-bellied Micronycteris, where M. minuta is divided in three clades. Below the diagonal: pairwise distance using the Kimura 2-parameter model (percentage). On the diagonal: within-clade distance using the Kimura 2-parameter model (percentage). Above the diagonal: pairwise p-distance values. Number of specimens sequenced in parenthesis. *Chimeric sequence obtained from two paratypes (Siles et al., 2013). in Revision of the pale-bellied Micronycteris Gray, 1866 (Chiroptera, Phyllostomidae) with descriptions of two new species
TA B L E 2 Estimates of pairwise sequence divergence (cyt-b gene) in pale-bellied Micronycteris, where M. minuta is divided in three clades. Below the diagonal: pairwise distance using the Kimura 2-parameter model (percentage). On the diagonal: within-clade distance using the Kimura 2-parameter model (percentage). Above the diagonal: pairwise p-distance values. Number of specimens sequenced in parenthesis. *Chimeric sequence obtained from two paratypes (Siles et al., 2013).
Data from: Genotyping by sequencing reveals contrasting patterns of population structure, ecologically mediated divergence and long-distance dispersal in North American palms
Comparative studies can provide powerful insights into processes that affect population divergence and thereby help to elucidate the mechanisms by which contemporary populations may respond to environmental change. Furthermore, approaches such as genotyping by sequencing (GBS) provide unprecedented power for resolving genetic differences among species and populations. We therefore used GBS to provide a genome-wide perspective on the comparative population structure of two palm genera, Washingtonia and Brahea, on the Baja California peninsula, a region of high landscape and ecological complexity. First, we used phylogenetic analysis to address taxonomic uncertainties among five currently recognised species. We resolved three main clades, the first corresponding to W. robusta and W. filifera, the second to B. brandegeei and B. armata, and the third to B. edulis from Guadalupe Island. Focusing on the first two clades, we then delved deeper by investigating the underlying population structure. Striking differences were found, with GBS uncovering four distinct Washingtonia populations and identifying a suite of loci associated with temperature, consistent with ecologically mediated divergence. By contrast, individual mountain ranges could be resolved in Brahea and few loci were associated with environmental variables, implying a more prominent role of neutral divergence. Finally, evidence was found for long-distance dispersal events in Washingtonia but not Brahea, in line with knowledge of the dispersal mechanisms of these palms including the possibility of human-mediated dispersal. Overall, our study demonstrates the power of GBS together with a comparative approach to elucidate markedly different patterns of genome-wide divergence mediated by multiple effectors.
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Allen Brain Atlas
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International Brain Laboratory public data
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OpenNeuro
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