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High genomic plasticity and unique features of Xanthomonas translucens pv. graminis revealed through comparative analysis of complete genome sequences
<p><strong>Background:</strong> <i>Xanthomonas</i> <i>translucens</i> pv. <i>graminis</i> (<i>Xtg</i>) is a major bacterial pathogen of economically important forage grasses, causing severe yield losses. So far, genomic resources for this pathovar consisted mostly of draft genome sequences, and only one complete genome sequence was available, preventing comprehensive comparative genomic analyses. Such comparative analyses are essential in understanding the mechanisms involved in the virulence of pathogens and to identify virulence factors involved in pathogenicity.</p><p><strong>Results:</strong> In this study, we produced high-quality, complete genome sequences of four strains of <i>Xtg</i>, complementing the recently obtained complete genome sequence of the <i>Xtg </i>pathotype strain. These genomic resources allowed for a comprehensive comparative analysis, which revealed a high genomic plasticity with many chromosomal rearrangements, although the strains were highly related, with 99.9 to 100% average nucleotide identity. A high number of transposases were exclusively found in <i>Xtg </i>and corresponded to 413 to 457 insertion/excision transposable elements per strain. These mobile genetic elements are likely to be involved in the observed genomic plasticity and may play an important role in the adaptation of <i>Xtg</i>. The pathovar was found to lack a type IV secretion system, and it possessed the smallest set of type III effectors in the species. However, three XopE and XopX family effectors were found, while in the other pathovars of the species two or less were present. Additional genes that were specific to the pathovar were identified, including a unique set of minor pilins of the type IV pilus, 17 TonB-dependent receptors (TBDRs), and 11 degradative enzymes. </p><p><strong>Conclusion:</strong> These results suggest a high adaptability of <i>Xtg</i>, conferred by the abundance of mobile genetic elements, which may have led to the loss of many features. Conserved features that were specific to <i>Xtg </i>were identified, and further investigation will help to determine genes that are essential to pathogenicity and host adaptation of <i>Xtg</i>.</p>
cDNA sequence of E2 gene family in Arabidopsis thaliana and data of statistical analysis
<p>E2 ubiquitin-conjugating enzymes act as a heart role in the ubiquitination process and are responsible for catalysis ubiquitin transfer. Although the function of ubiquitin-protein ligases (E3s) in plant response to diverse abiotic stress by targeting specific substrates has been well studied, the E2s' involvement in environmental responses and their downstream targets are not well understood. Here, we demonstrated that the E2 ubiquitin-conjugating enzyme 18 (UBC18) regulates the stability of FREE1 to modulate iron deficiency stress. UBC18 affects the ubiquitination of FREE1 and promotes its degradation, overexpression of<em> UBC18</em> in plants decreases their sensitivity to iron deficiency by reducing the level of FREE1, and high accumulation of FREE1 in<em> </em>the<em> ubc18</em> mutant resulted in sensitivity to iron deficiency. In addition, we demonstrated the lysine residues K227, K295, K315, and K540 are required for FREE1 ubiquitination and stability regulation, and mutation of these lysines of FREE1 residues resulted in sensitivity to iron starvation in plants. Taken together, our findings reveal a mechanism of UBC18 in response to iron deficiency stress by altering the abundance of FREE1, and further elucidate the role of ubiquitination sites in FREE1 stability regulation and the plant iron deficiency response.</p>
Source data of the MultiSTAAR manuscript "A statistical framework for multi-trait rare variant analysis in large-scale whole-genome sequencing studies".
<p>This dataset serves as the source data for Figures 2-3 and Extended Data Figures 1-2 of the MultiSTAAR manuscript titled "A statistical framework for multi-trait rare variant analysis in large-scale whole-genome sequencing studies". MultiSTAAR is a statistical framework and computationally-scalable analytical pipeline for functionally-informed multi-trait rare variant analysis in large-scale WGS studies.<br><br><strong>Figure 2.</strong> Manhattan plots and Q-Q plots for unconditional gene-centric coding, noncoding and ncRNA multi-trait analysis of low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C) and triglycerids (TG) using TOPMed data (<em>n</em> = 61,838).<br><br><strong>Figure 3.</strong> TOPMed genetic region (2-kb sliding window) unconditional multi-trait analysis results of low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C) and triglycerides (TG) using TOPMed data (<em>n</em> = 61,838).<br><br><strong>Extended Data Figure 1.</strong> Manhattan plots and Q-Q plots for unconditional gene-centric coding, noncoding and genetic region (2-kb sliding window) multi-trait analysis of fasting glucose (FG) and fasting insulin (FI) using TOPMed data (<em>n</em> = 21,731).<br><br><strong>Extended Data Figure 2.</strong> Manhattan plots and Q-Q plots for unconditional gene-centric coding, noncoding and genetic region (2-kb sliding window) multi-trait analysis of C-reactive protein (CRP), interleukin 6 (IL-6), lipoprotein-associated phospholipase A2 (Lp-PLA2) activity, and lipoprotein-associated phospholipase A2 (Lp-PLA2) mass using TOPMed data (<em>n</em> = 9,380).</p>
BactPrep: A user-friendly whole-genome sequencing analysis platform for the detection of homologous recombination and horizontal gene transfer in bacteria - Sample Dataset
<p>This is the dataset used as the sample dataset for the pipeline BactPrep. This dataset consists of 218 <em>Streptococcus pneumoniae</em> PMEN1 WGS assemblies collected from the year 1984 - 2008 from 22 unique countries globally. The raw sequencing data was originally published in the work: Rapid pneumococcal evolution in response to clinical interventions (doi: 10.1371/journal.ppat.1002745) under the bioproject PRJEB2085.</p> <p>We have assembled the raw sequences records with the following steps: 1) raw reads were first quality checked using fastQC 0.11.9; 2) adapters and low quality reads were removed using Trimmomatic 0.39 with parameter “ILLUMINACLIP:TruSeq2-PE.fa:2:30:10:2:keepBothReads LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36”; 3) trimmed reads were error-corrected and assembled into WGS assemblies using SPAdes 3.15.0 with parameters "--careful --mismatch-correction”.</p>
Integrative taxonomic analysis to reveal the species status of Bombus flavidus, combining COI and nuclear sequencing, wing morphometrics and secretions used for mate attraction as well as patterns of color polymorphism
<p>Bumble bees, due to their morphological monotony and color diversity, have presented difficulties with species delimitation. Recent bumble bee declines have made it ever more imperative to resolve the status of species to address conservation concerns. Some of the taxa found to be most threatened are the often-rare socially parasitic bumble bees, which have additional trophic requirements. Among the socially parasitic bumble bees,<i> Bombus flavidus</i> Eversmann has contentious species status. While multiple separate species allied with <i>Bombus flavidus</i> have been suggested, until recently, recognition of two species, a Nearctic <i>Bombus fernaldae</i> (Franklin) and Palearctic <i>B. flavidus,</i> was favoured. Limited genetic data, however, suggested that even these could be a single widespread species, <i>B. flavidus</i>. We addressed the species status of this lineage using an integrative taxonomic approach, combining <i>COI</i> and nuclear sequencing, wing morphometrics and secretions used for mate attraction. We also explore patterns of color polymorphism that have previously confounded taxonomy in this lineage. Our results support the conspecific status of <i>Bombus fernaldae</i> and <i>Bombus flavidus,</i> however, sampling specimens from across the range of these two taxa revealed a distinct population within this broader species confined to eastern North America. This makes the distribution of the social parasite <i>B. flavidus</i> the broadest of any bumble bee, broader than the known distribution of any non-parasitic bumble bee species. Analysis of color phenotypes revealed that color polymorphisms are retained across the range of the species, but may be influenced by local mimicry complexes. Following these results, <i>Bombus flavidus</i> Eversmann, 1852<i> </i>is synonymized with <i>Bombus fernaldae </i>(Franklin, 1911) <b>syn. nov.</b> and a subspecific status, <i>Bombus flavidus </i><i>appalachiensis</i> <b>ssp. nov.</b>, is assigned to the distinct lineage ranging from the Appalachians to the eastern boreal regions of the United States and far southeastern Canada.</p>
Fig. 1 in Emendation of the Genus Auritidibacter Yassin et al. 2011 and Auritidibacter ignavus Yassin et al. 2011 based on features observed from Canadian and Swiss clinical isolates and wholegenome sequencing analysis
Fig. 1. Phylogenetic consensus tree based on nearly full-length 16S rRNA gene sequences. Phylogeny reconstructed with neighbourjoining (NJ), maximum-likelihood (ML) and maximum parsimony algorithms with NJ/ML/MP data respectively shown at nodes for type strains of type species of genera assigned to the family Micrococcaceae. The tree was calculated using MEGA X based on 1000 resamplings (bootstrap analysis, with only values ≥70% shown). Bar, 0.01 (NJ) or 0.02 (ML) substitutions per nucleotide position. The type strain of Cellulomonas flavigena was included as an unrelated outlier.
Single cell Iso-Sequencing enables rapid genome annotation for scRNAseq analysis
<p>Single <span>cell RNA sequencing (scRNAseq) is a powerful technique that continues to expand across various biological applications. However, incomplete 3' UTR annotations can impede single cell analysis resulting in genes that are partially or completely uncounted. Performing scRNAseq with incomplete 3' UTR annotations can hinder the identification of cell identities and gene expression patterns and lead to erroneous biological inferences. We demonstrate that performing single cell isoform sequencing (ScISOr-Seq) in tandem with scRNAseq can rapidly improve 3' UTR annotations. Using threespine stickleback fish (</span><em>Gasterosteus aculeatus</em><span>), we show that gene models resulting from a minimal embryonic ScISOr-Seq dataset retained 26.1% greater scRNAseq reads than gene models from Ensembl alone. Furthermore, pooling our ScISOr-Seq isoforms with a previously published adult bulk Iso-Seq dataset from stickleback, and merging the annotation with the Ensembl gene models, resulted in a marginal improvement (+0.8%) over the ScISOr-Seq only dataset. In addition, isoforms identified by ScISOr-Seq included thousands of new splicing variants. The improved gene models obtained using ScISOr-Seq lead to successful identification of cell types and increased the reads identified of many genes in our scRNAseq stickleback dataset. Our work illuminates ScISOr-Seq as a cost-effective and efficient mechanism to rapidly annotate genomes for scRNAseq.</span></p>
Data for "Generative and interpretable machine learning for aptamer design and analysis of in vitro sequence selection"
<p>Once decompressed, the file contains a folder which contains:</p> <ul> <li>The files "s100_Nth.fasta" (where "N" is 5, 6, 7 or 8), which are the output of the SELEX experiment described in the paper with DOI: <a href="https://doi.org/10.1002/cbic.201900265">10.1002/cbic.201900265</a>. They are standard fasta files, and the descriptor of each sequence is of the form "seqX-Y", where "X" is an increasing label, and "Y" is the number of times "seqX" has been obtained (number of counts of "seqX").</li> <li>The file "Aptamer_Exp_Results.csv", which contains the sequences tested experimentally for the paper "Generative and interpretable machine learning for aptamer design and analysis of in vitro sequence selection" (preprint available at https://doi.org/10.1101/2022.03.12.484094), with the following experimental results for each sequence: (i) whether the sequence was able to bind thrombin ('B' for binders, 'NB' for non-binders); (ii) the thrombin exosite used for binding ('I' for exosite I, 'II' for exosite II, 'n/a' for sequences not tested).</li> </ul> <p>Examples of usage of the data are available at https://github.com/adigioacchino/RBMsForAptamers.</p>
FIGURE. Phylogenetic analysis of Chrysosporium spp. based on ITS sequences. Statistical support values (≥50 %) are shown at nodes, and presented as ML bootstrap support/Bayesian posterior probabilities. Names in black bold are the strains isolated in this study, the coloured names are the new species. in Morphological and phylogenetic characterisations reveal nine new species of Chrysosporium (Onygenaceae, Onygenales) in China
FIGURE. Phylogenetic analysis of Chrysosporium spp. based on ITS sequences. Statistical support values (≥50 %) are shown at nodes, and presented as ML bootstrap support/Bayesian posterior probabilities. Names in black bold are the strains isolated in this study, the coloured names are the new species.
Data from: Whole genome sequencing and phylogenomic analysis show support for the splitting of genus Pythium
<p>The genus <em>Pythium</em><span> (nom. cons.) sensu lato (s.l.) is composed of many important species of plant pathogens. Early molecular phylogenetic studies suggested paraphyly of </span><em>Pythium</em><span>, which led to a formal proposal by Uzuhashi and colleagues in 2010 to split the genus into </span><em>Pythium</em><span> sensu stricto (s.s.), </span><em>Elongisporangium, Globisporangium, Ovatisporangium</em><span> (= </span><em>Phytopythium</em><span>), and </span><em>Pilasporangium</em><span> using morphological characters and phylogenies of the mt cytochrome </span><em>c</em><span> oxidase subunit 2 (</span><em>cox2</em><span>) and D1–D2 domains of nuc 28S rDNA. Although the split was fairly justified by the delineating morphological characters, there were weaknesses in the molecular analyses, which created reluctance in the scientific community to adopt these new genera for the description of new species. In this study, this issue was addressed using phylogenomics. Whole genomes of 109 strains of </span><em>Pythium</em><span> and close relatives were sequenced, assembled, and annotated. These data were combined with 10 genomes sequenced in previous studies. Phylogenomic analyses were performed with 148 single-copy genes represented in at least 90% of the taxa in the data set. The results showed support for the division of </span><em>Pythium</em><span> s.l. The status of alternative generic names that have been used for species of </span><em>Pythium</em><span> in the past (e.g., </span><em>Artotrogus, Cystosiphon, Eupythium, Nematosporangium, Rheosporangium, Sphaerosporangium</em><span>) was investigated. Based on our molecular analyses and review of the </span><em>Pythium</em><span> generic concepts, we urge the scientific community to adopt the generic names </span><em>Pythium, Elongisporangium, Globisporangium</em><span>, and their concepts as proposed by Uzuhashi and colleagues in 2010 in their work going forward. In order to consolidate the taxonomy of these genera, some of the recently described </span><em>Pythium</em><span> spp. are transferred to </span><em>Elongisporangium</em><span> and </span><em>Globisporangium</em><span>.</span></p>
RNA sequencing analysis of CAF treated by colon cancer cell-derived exosomes
<p>In this study, we analyzed differentially expressed genes by obtaining gene expression values through transcriptome sequencing of Homo sapiens, and performed functional classification and gene annotation for significant genes based on gene ontology and pathway information. After the pre-processed trimmed reads were mapped to a known reference genome using the HISAT2 program, transcript assembly was performed through the StringTie program. As a result, expression profile values were obtained for each sample for the known transcript, and read count, based on transcript/gene Fragment per Kilobase of transcript per Million mapped reads (FPKM), Transcripts per Kilobase (TPM) Million) values have been summarized. This value was subjected to DEG (Differentially Expressed Genes) analysis using edgeR for comparison combinations (HT-29_Exo-CAF vs. CTL_PBS-CAF, LoVo_Exo-CAF vs. CTL_PBS-CAF, and SW480_Exo-CAF vs. CTL_PBS-CAF), and genes that satisfies the condition |fc|>=2 & exactTest raw p-value<0.05 in at least one comparison combination Dogs were extracted. Transcriptome resequencing data was used to compare expression profiles between comparable samples. Gene Ontology Enrichment analysis was performed using the g:Profiler tool (https://biit.cs.ut.ee/gprofiler/) for a list of genes with significant expression level differences. GO_stat is the result of organizing the associated gene and test stat based on term_id. GO_genes is the result of arranging the associated term_id and DEG analysis result stat based on the gene.</p>
FIGURE. Multilocus phylogenetic tree inferred from Bayesian analysis based on the combined TEF1-α and ACT sequences. Bayesian posterior probabilities are indicated next to the nodes. The tree was rooted with Cladosporium herbarum CBS 121621. The species in this study are indicated in bold. Types of species are indicated after the culture collection number (T = ex-type, ex-epitype, ex-neotype, or reference strain). in Six new species of Cladosporium associated with decayed leaves of native bamboo (Bambusoideae) in a fragment of Brazilian Atlantic Forest
FIGURE. Multilocus phylogenetic tree inferred from Bayesian analysis based on the combined TEF1-α and ACT sequences. Bayesian posterior probabilities are indicated next to the nodes. The tree was rooted with Cladosporium herbarum CBS 121621. The species in this study are indicated in bold. Types of species are indicated after the culture collection number (T = ex-type, ex-epitype, ex-neotype, or reference strain).
FIGURE. (Continued) Multilocus phylogenetic tree inferred from Bayesian analysis based on the combined TEF1-α and ACT sequences. Bayesian posterior probabilities are indicated next to the nodes. The tree was rooted with Cladosporium herbarum CBS 121621. The species in this study are indicated in bold. Types of species are indicated after the culture collection number (T = ex-type, ex-epitype, exneotype, or reference strain). in Six new species of Cladosporium associated with decayed leaves of native bamboo (Bambusoideae) in a fragment of Brazilian Atlantic Forest
FIGURE. (Continued) Multilocus phylogenetic tree inferred from Bayesian analysis based on the combined TEF1-α and ACT sequences. Bayesian posterior probabilities are indicated next to the nodes. The tree was rooted with Cladosporium herbarum CBS 121621. The species in this study are indicated in bold. Types of species are indicated after the culture collection number (T = ex-type, ex-epitype, exneotype, or reference strain).
Scalable mixed model approaches for set-based association studies on large-scale categorical data analysis and its application to 450k exome sequencing data in UK Biobank
<p>The ongoing release of large-scale sequencing data in the UK Biobank allows for identifying associations between rare variants and complex traits. SAIGE-GENE+ is a valid approach to conducting set-based association tests for quantitative and binary traits. However, for ordinal categorical phenotypes, applying SAIGE-GENE+ with treating the trait as quantitative or binarizing the trait can cause inflated type I error rates or power loss. In this study, we propose a novel method for rare-variant association tests, POLMM-GENE, in which a proportional odds logistic mixed model was used to characterize ordinal categorical phenotypes while adjusting for sample relatedness. POLMM-GENE fully utilizes the categorical nature of phenotypes and thus can well control type I error rates while remaining powerful. In the analyses of UK Biobank 450k whole exome-sequencing data for 5 ordinal categorical traits, POLMM-GENE identified 54 gene-phenotype associations.</p>
Supplementary material 1 from: Colihueque N, Gantz A, Rau JR, Parraguez M (2015) Genetic divergence analysis of the Common Barn Owl Tyto alba (Scopoli, 1769) and the Short-eared Owl Asio flammeus (Pontoppidan, 1763) from southern Chile using COI sequence. ZooKeys 534: 135-146. https://doi.org/10.3897/zookeys.534.5953
Pictures of external morphology of specimens of Tyto alba and Asio flammeus collected in southern Chile: Explanation note: Pictures of ventral and dorsal views of specimens showing plumage color and overall appearance. Data on body mass of these specimens are also provided.
Tutorial-Next-Generation-Sequence-Analysis
<p>This upload contains .fastq and reference genome files for learning and practicing NGS analysis.</p>
Sample data for analysis of FFPE sequencing data
Open the record for dataset details and reuse information.
APPENDIX. GenBank accession numbers of all DNA sequences of Cophyla used in this study. NA, not applicable. Asterisks mark cases where sequences from different samples were combined to chimeric terminals for analysis. in Description of the lucky Cophyla (Microhylidae, Cophylinae), a new arboreal frog from Marojejy National Park in north-eastern Madagascar
APPENDIX. GenBank accession numbers of all DNA sequences of Cophyla used in this study. NA, not applicable. Asterisks mark cases where sequences from different samples were combined to chimeric terminals for analysis.
Fig. 7 in Analysis of major sperm proteins in two nematode species from two classes, Enoplus brevis (Enoplea, Enoplida) and Panagrellus redivivus (Chromadorea, Rhabditida), reveals similar localization, but less homology of protein sequences than expected for Nematoda phylum
Fig. 7 Immunolocalization of MSP in E. brevis sperm. a Immature spermatozoon from male. MSP is diffusely distributed in cytoplasm and concentrated in large granules (scale bar 10 µm). b Spermatozoon recovered from male and partially activated by 10-min incubation in sea water. MSP undergoes transformation resulting in appearance of
Fig. 5 in Analysis of major sperm proteins in two nematode species from two classes, Enoplus brevis (Enoplea, Enoplida) and Panagrellus redivivus (Chromadorea, Rhabditida), reveals similar localization, but less homology of protein sequences than expected for Nematoda phylum
Fig. 5 Western blot analysis of MSP in E. brevis. a MSP has unusual mobility in gel and is found as protein with weight 36–38 kDa. Both male and female samples reveal MSP signal, because the latter include inseminated females. α-Tubulin was used as a loading control (approximate weight 55 kDa). b Peptide competition assay confirms reactivity of anti-MSP antibodies with protein band of 36–38 kDa
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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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