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507 results for “symbiont”
Demographic data from long-term symbiont removal experiments with grasses and Epichloë fungal endophytes
This project was designed to understand the demographic effects of vertically transmitted fungal endophytes (Epichloë spp.) on their grass hosts. The experiment includes seven host-symbiont taxonomic pairs: Agrostis perennans - E. amarillans, Elymus villosus - E. elymi, Elymus virginicus - E. elymi or EviTG-1, Festuca subverticillata - E. starrii, Poa alsodes - E. alsodes, Poa sylvestris - E. PsyTG-1, Schedonorus arundinaceus - E. coenophiala. Experimental plots were established at the Indiana University Lilly-Dickey Woods Research and Teaching Preserve in south-central Indiana, USA in 2007. For each species, 5-10 plots were planted with naturally symbiotic (S+) hosts, and 5-10 plots were plated with hosts that were disinfected of fungal endophytes by heat treatment (S-). Over 15 years (2007-2022) we collected demographic data on the survival, growth, reproduction, and recruitment of all plants in all plots. Beginning in 2018 we also collected data on the locations of all plants in every plot.
Cophylogeny and specificity between cryptic coral species (Pocillopora spp.) at Mo'orea and their symbionts (Symbiodiniaceae)
<p>GENERAL INFORMATION</p> <p>1. Title of Dataset: Cophylogeny and specificity between cryptic coral species (Pocillopora spp.) at Mo'orea and their symbionts (Symbiodiniaceae)</p> <p>2. Author Information<br> A. Principal Investigator Contact Information<br> Name: Scott Burgess<br> Institution: Florida State University<br> Address: 319 Stadium Drive, Tallahassee, FL, USA 32306<br> Email: sburgess@bio.fsu.edu</p> <p><br> 3. Date of data collection (single date, range, approximate date): 2019-08</p> <p>4. Geographic location of data collection: Moorea, French Polynesia</p> <p>5. Information about funding sources that supported the collection of the data: National Science Foundation (NSF; OCE-1829867)</p> <p> </p> <p><br> DATA & FILE OVERVIEW</p> <p>1. File List:<br> Figure 2 Make.R<br> Figure 4 Make.R<br> Figure 5b Make.R<br> Figure 6 Make.R</p> <p>Figure 1 SNAPP species tree.xml<br> Figure 2.txt<br> Figure 2.vcf<br> Figure 3b - Pocillopora mt genomes.nex<br> Figure 4 and 6 data.csv<br> Figure 4 colors.csv<br> Figure 5a - Cladocopium_psbA.nex<br> Figure 5b - Clad clades.csv<br> Figure 5b_Cladocopium.nex<br> Figure 5b_Pocillopora.nex<br> Figure 5b.csv</p> <p><br> 2. Relationship between files:<br> Figure 2 Make.R uses Figure 2.txt and Figure 2.vcf<br> Figure 4 Make.R uses Figure 4 and 6 data.csv and Figure 4 colors.csv<br> Figure 5b Make.R uses Figure 5b - Clad clades.csv, Figure 5b_Cladocopium.nex, Figure 5b_Pocillopora.nex, and Figure 5b.csv<br> Figure 6 Make.R Figure 4 and 6 data.csv</p> <p> </p> <p>3. Metadata</p> <p>Figure 2 Make.R:<br> R code to produce Figure 2, and the accompanying analyses presented in the text, in:<br> Johnston EC, Cunning, Burgess SC. Cophylogeny and specificity between cryptic coral species (Pocillopora spp.) at Mo’orea and their symbionts (Symbiodiniaceae).<br> Uses 'Figure 2.txt', 'Figure 2.vcf'</p> <p><br> Figure 4 Make.R:<br> R code to produce Figure 4, and the accompanying analyses presented in the text, in:<br> Johnston EC, Cunning, Burgess SC. Cophylogeny and specificity between cryptic coral species (Pocillopora spp.) at Mo’orea and their symbionts (Symbiodiniaceae).<br> Uses 'Figure 4 and 4 data.csv', 'Figure 4 colors'</p> <p><br> Figure 5b Make.R:<br> R code to produce Figure 5b, and the accompanying analyses presented in the text, in:<br> Johnston EC, Cunning, Burgess SC. Cophylogeny and specificity between cryptic coral species (Pocillopora spp.) at Mo’orea and their symbionts (Symbiodiniaceae).<br> Uses 'Figure 5b - Clad clades.csv', 'Figure 5b_Cladocopium.nex', 'Figure 5b_Pocillopora.nex', 'Figure 5b.csv'</p> <p><br> Figure 6 Make.R:<br> R code to produce Figure 6, and the accompanying analyses presented in the text, in:<br> Johnston EC, Cunning, Burgess SC. Cophylogeny and specificity between cryptic coral species (Pocillopora spp.) at Mo’orea and their symbionts (Symbiodiniaceae).<br> Uses 'Figure 4 and 6 data.csv'</p> <p><br> Figure 1 SNAPP species tree.xml:<br> Data for species tree used in Figure 1</p> <p>Figure 2.txt:<br> Metadata<br> Sample_ID: Sample ID<br> Hap_Spp: Pocillopora species or haplotype</p> <p>Figure 2.vcf:<br> Linked dataset of 7,887 SNPs</p> <p>Figure 3b - Pocillopora mt genomes.nex:<br> Nexus tree of Pocillopora mitochondrial genomes used in Figure 3b</p> <p><br> Figure 4 and 6 data.csv:<br> Metadata<br> Species.haplotype: Pocillopora species or haplotype<br> Depth.m: Sampling depth in meters<br> Site: Sampling site, label corresponds to the site used in the Moorea Coral Reef Long-Term Ecological Research (MCR-LTER) program.<br> Coral.ID: Coral colony identifier<br> Type_profile: ITS2 type profile generated by SymPortal<br> Type_profile_Prop: Proportion of that given ITS2 type profile in colony sampled<br> Remaining columns: Proportion of ITS2 sequences in colony sampled</p> <p>Figure 4 colors.csv:<br> Metadata<br> my_colors: Custom colors for each ITS2 sequence<br> Symbio.clade: ITS2 sequences</p> <p>Figure 5a - Cladocopium_psbA.nex:<br> Nexus tree of Cladocopium taxa in figure 5a</p> <p>Figure 5b - Clad clades.csv:<br> Metadata<br> UCI_links: Sample ID that contains Pocillopora species or haplotype, sample ID, and ITS2 type profile<br> Clad_clades: Clade assignment from figure 5a</p> <p>Figure 5b_Cladocopium.nex:<br> Nexus tree of Cladocopium taxa in Figure 5b</p> <p>Figure 5b_Pocillopora.nex:<br> Nexus tree of Pocillopora taxa used in PACo analysis, Figure 5b</p> <p>Figure 5b.csv:<br> Matrix of Pocillopora host and Cladocopium symbiont links</p>
Supplementary data for- Heat-evolved microalgae (Symbiodiniaceae) are stable symbionts and influence thermal tolerance of the sea anemone Exaiptasia diaphana
<p>Raw data and R codes for - Heat-evolved microalgae (Symbiodiniaceae) are stable symbionts and influence thermal tolerance of the sea anemone <em>Exaiptasia diaphana</em>. DOI: 10.1111/1462-2920.70011</p>
Genome sequence of the banana aphid, Pentalonia nigronervosa Coquerel (Hemiptera: Aphididae) and its symbionts
<p><strong><em>Pentalonia nigronervosa</em> v1 frozen release</strong></p> <p>Genome assembly: Pentalonia_nigronervosa.v1.scaffolds.fa.gz</p> <p>BRAKER2 gene models: Pentalonia_nigronervosa.v1.scaffolds.gff</p> <p>BRAKER2 protein sequences: Pentalonia_nigronervosa.v1.scaffolds.gff.aa.fa</p> <p>BRAKER2 protein sequences (longest transcript per gene only): Pentalonia_nigronervosa.v1.scaffolds.gff.aa.LTPG.fa</p> <p>BRAKER2 coding sequences: Pentalonia_nigronervosa.v1.scaffolds.gff.cds.fa</p> <p>InterProScan functional annotation: Pentalonia_nigronervosa.v1.scaffolds.gff.aa.LTPG.interproscan.tsv</p> <p><em>Pentalonia nigronervosa</em> v1 mitochondrial genome: Pentalonia_nigronervosa.v1.mt_genome.fa</p> <p><em>Buchnera aphidicola</em> (BPn) scaffolds: Buchnera_aphidicola_BPn.scaffolds.fa</p> <p><em>Wolbachia</em> (WolPenNig) scaffolds: Wolbachia_WolPenNig.scaffolds.fa</p> <p><strong><em>Myzus cerasi </em>v1.2 frozen release</strong></p> <p>Genome assembly: Myzus_cerasi.v1.2.scaffolds.fa</p> <p>BRAKER2 gene models: Myzus_cerasi.v1.2.scaffolds.gff</p> <p>BRAKER2 protein sequences: Myzus_cerasi.v1.2.scaffolds.gff.aa.fa</p> <p>BRAKER2 protein sequences (longest transcript per gene only): Myzus_cerasi.v1.2.scaffolds.gff.aa.LTPG.fa</p> <p>BRAKER2 coding sequences: Myzus_cerasi.v1.2.scaffolds.gff.cds.fa</p> <p><strong>Aphid orthogroups and species tree</strong></p> <p>Proteomes included in the analysis: proteomes.tar.gz</p> <p>Orthogroups: Orthogroups.txt</p> <p>Gene counts per orthogroup, per species: Orthogroups.GeneCount.csv</p> <p>Single copy conserved orthogroups used for species tree: Orthogroups_for_concatenated_alignment.txt</p> <p>Species tree alignment: SpeciesTreeAlignment.fa</p> <p>Rooted species tree: SpeciesTree_rooted.nwk</p> <p><strong>Bash script to run k-mer based assembly deduplication pipeline</strong></p> <p>File: disco_filter_dups.v1.1.sh</p> <p>This script will parse a discovar de novo assembly and remove scaffolds likely to be haplotigs based on their k-mer content and a self alignment of the assembly (see manuscript for details).</p> <p>The input discovar assembly needs to have white space in scaffold IDs replaced with "_" before running. Illumina reads should be unzipped before running.</p> <p>Usage:</p> <pre><code class="language-bash">sh disco_filter_dups.sh <./path_to_assembly> <./path_to_r1> <./path_to_r2> <homozyzgous_lower_cov> <homozyzgous_upper_cov> <nucmer_id_cutoff> <nucmer_cov_cutoff> <assembly_output_prefix> <threads> <./working_dir></code></pre> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p>
Data from: "Rapid molecular evolution of Spiroplasma symbionts of Drosophila"
<p>This repository contains data and information to reproduce the findings reported in the paper.</p> <p>File descriptions:</p> <ul> <li>OTU_sequences.fasta – all <em>Spiroplasma</em> sequences that contained an <a href="https://pfam.xfam.org/family/OTU">OTU domain</a> as predicted by <a href="https://www.ebi.ac.uk/Tools/pfa/pfamscan/">PfamScan</a></li> <li>OTU_alignments.fasta – alignment of OTU domains performed using <a href="https://mafft.cbrc.jp/alignment/software/">Mafft</a></li> <li>RIP_sequences.fasta – all <em>Spiroplasma</em> sequences that contained an <a href="https://pfam.xfam.org/family/RIP">RIP domain</a> as predicted by <a href="https://www.ebi.ac.uk/Tools/pfa/pfamscan/">PfamScan</a></li> <li>RIP_alignments.fasta – alignment of RIP domains performed using the <a href="http://hmmer.org/">HMMER package</a></li> <li>Spiroplasma_supermatrix.fasta – Fasta alignment of concatenated single copy <em>Spiroplasma</em> loci conserved across the investigated strains. Loci that showed signs of recombination were not included</li> <li>Spiroplasma_partitions.txt – Lists the loci that make up the <em>Spiroplasma</em> supermatrix</li> <li>Spiroplasma_partitioning.scheme.txt – Partitioning scheme employed in our Maximum Likelihood analysis of the supermatrix. This was the best fitting partitioning scheme as determined with <a href="http://www.iqtree.org/">IQ-TREE</a></li> <li>Protocol_1.pdf – Chloroform–Ethanol protocol used for extracting <em>Spiroplasma</em> DNA for <em>s</em>Hy-Tx</li> </ul>
Root symbionts alter the volatile profile of herbivore-infested tomato plants and aid the attraction of a predator
<p>Beneficial root microbes are among the most frequently used biocontrol agents in cropping systems, since they have been shown to promote plant growth and crop yield. Moreover, they are able to enhance protection against pathogens and insect herbivores by activating plant resistance mechanisms. Plant defense responses against herbivorous insects include the induction of metabolic pathways involved in the synthesis of defense-related metabolites. These metabolites include volatile organic compounds (VOCs), which attract natural enemies of the herbivores as a form of indirect resistance. Considering that beneficial root microbes may affect direct herbivore resistance, we hypothesized that also indirect resistance may be affected. We tested this hypothesis in a study system composed of tomato, the arbuscular mycorrhizal fungus <em>Rhizophagus irregularis</em>, the growth-promoting fungus <em>Trichoderma harzianum</em>, the generalist chewing herbivore <em>Spodoptera exigua </em>and the omnivorous predator<em> Macrolophus pygmaeus</em>. Using a Y-tube olfactometer we found that <em>M. pygmaeus</em> preferred plants with <em>S. exigua </em>herbivory, but microbe-inoculated plants more than non-inoculated ones. We used a targeted GC-MS approach to assess the impact of beneficial microbes on the emission of volatiles twenty-four hours after herbivory to explain the choice of <em>M. pygmaeus</em>. We observed that the volatile composition of the herbivore-infested plants differed from that of the non-infested plants, which was driven by the higher emission of green leaf volatile compounds, methyl salicylate, and several monoterpenes and sesquiterpenes. Inoculation with microbes had only a marginal effect on the emission of some terpenoids in our experiment. Gene expression analysis showed that the marker genes involved in the jasmonic and salicylic acid pathways were differentially expressed in the microbe-inoculated plants after herbivory. Our results pinpoint the role of root symbionts in determining plant-microbe-insect interactions up to the third trophic level, and elucidates their potential to be used in plant protection.</p>
Exploring mechanisms that affect coral cooperation: symbiont transmission mode, cell density and community composition
<p>This repository contains code to accompany the manuscript titled</p> <p><strong>Exploring mechanisms that affect coral cooperation: symbiont transmission mode, cell density and community composition</strong></p> <p>by <strong>Carly D. Kenkel and Line K. Bay</strong><br> </p> <p>In this study, we used a phylogenetically controlled design to investigate the role of vertical symbiont transmission, an evolutionary mechanism predicted to enhance cooperation and holobiont fitness of reef-building corals. Six species of coral, three vertical transmitters and their closest horizontally transmitting relatives, were fragmented and subjected to a two-week thermal stress experiment. Symbiont cell density, photosynthetic function and translocation of photosynthetically fixed carbon between symbionts and hosts were quantified to assess changes in physiological metrics of fitness and cooperation. Amplicon sequencing of the <em>Symbiodinium</em> ITS-2 locus was used to investigate differences in symbiont community composition among focal species. We did not observe universally higher levels of cooperation in vertically transmitting species. However, the reduction in cooperation at the onset of bleaching was marginally associated with symbiont community diversity. Analysis of ITS2 amplicon sequence data suggest that it may not be vertical transmission <em>per se</em> that influences host-symbiont cooperation, but genetic uniformity of the symbiont community.</p> <p>Repository contents:</p> <ul> <li> <p><strong>TraitDataAnalysis.R:</strong> Annotated R script for generating figures and re-creating statistical analyses</p> <ul> <li> <p><strong>RsquaredGLMM.R:</strong> Accessory R script for running RsquaredGLMM analyses, called by <strong>TraitDataAnalysis.R</strong></p> </li> <li> <p><strong>NSF_RunningPam.csv</strong>: Input file for statistical analysis. Contains photophysiological data. Column headers are as follows:</p> <ul> <li> <p>Tank: Number of experimental tank in which experimental coral fragment was held</p> </li> <li> <p>Treatment: short-hand notation for sample treatments (e.g. ctrl1-5 = control temperature, genotypes 1-5)</p> </li> <li> <p>Water: source sump for temperature controlled water jackets for each set of treatment tanks</p> </li> <li> <p>Position: numerical rack position of coral fragment within experimental treatment tank</p> </li> <li> <p>Species: Coral species (Amil=<em>A. millepora</em>, Maqe=<em>M. aequituberculata</em>, Gast=<em>G. astreata</em>, Gach=<em>G. acrhelia</em>, Plob=<em>P. lobata</em>, Gcol=<em>G. columna</em>)</p> </li> <li> <p>Genotype: source colony origin of individual coral fragments within species</p> </li> <li> <p>Temp: experimental temperature treatment (ctrl: 27°C ; heat: 31°C)</p> </li> <li> <p>Treat: whether experimental corals received C14-labeled bicarbonate (bicarb), artemia or were sampled separately for Gene Expression Analysis (not presented in this manuscript)</p> </li> <li> <p>EQY: Effective quantum yield of <em>Symbiodinium</em> photosystem II as measured using PAM fluorometry</p> </li> <li> <p>Date: Actual calendar date of measure</p> </li> <li> <p>Transmission: coral symbiont transmission mode</p> </li> <li> <p>Reef: reef site of original coral collection</p> </li> <li> <p>Date: experimental date of measure</p> </li> </ul> </li> <li> <p><strong>TraitData.csv:</strong> Input file for statistical analysis. Contains all physiological trait data.</p> <ul> <li> <p>Includes columns as described above for the Running_Pam file in addition to columns containing raw trait data as described in the manuscript.</p> </li> </ul> </li> <li> <p><strong>TraitData_DaysAsCols.csv:</strong> Reformatted input file with trait data split by sampling day across columns</p> </li> </ul> </li> <li> <p><strong>DADA2Analysis.R:</strong> Annotated R script for generating figures and running ITS2 amplicon analyses</p> <ul> <li> <p>GeoSymbio_ITS2_LocalDatabase_verForPhyloseq.fasta: FASTA file of the GeoSymbio ITS2 reference database <a href="https://sites.google.com/site/geosymbio/">https://sites.google.com/site/geosymbio/</a>, formatted for use with the R prograom Phyloseq</p> </li> <li> <p>SeqVars_6Feb.fasta: FASTA file of identified sequence variants resulting from DADA2 analysis</p> </li> <li> <p>OutputDADA_6Feb.csv: Counts of sequence variants by sample</p> </li> <li> <p>Raw FASTQ paired end read files can be downloaded from NCBI's SRA: PRJNA338365</p> </li> </ul> </li> </ul>
Data and code for: Genomic changes underlying host specialization in the bee gut symbiont Lactobacillus Firm5
<p>This dataset contains data and code underlying the comparative genomics, amplicon sequencing, and statistical analysis of the research article "Genomic changes underlying host specialization in the bee gut symbiont Lactobacillus Firm5”. Genome sequences and short read datasets are available under NCBI Bioproject accession PRJNA392822.</p> <p>The dataset contains tar-balls for the main workflows of the analysis. Dowload and unpack to view the contents (tar -zxvf filename.tar.gz). For each tar-ball, a README.txt file describes the contents of the directory. The analyses require certain open-source software packages to be installed. These are not provided here.</p>
Supplementary phylogenetic data for Manzano-Marín et. al. 2020 "Serial horizontal transfer of vitamin-biosynthetic genes enables the establishment of new nutritional symbionts in aphids' di-symbiotic systems"
<p>Supplementary data for Manzano-Marín et. al. 2019 "Serial horizontal transfer of vitamin-biosynthetic genes enables the establishment of new nutritional symbionts in aphids' di-symbiotic systems".</p> <p>The data set consists of four folders:</p> <p>1) "Buchnera_phylo”: PHYLIP-formatted file used for phylogenetic reconstruction of <em>Buchnera</em> and resulting tree in NEWICK format.</p> <p>2) "Erwinia_phylo”: PHYLIP-formatted file used for phylogenetic reconstruction of <em>Erwinia</em> and resulting tree in NEWICK format.</p> <p>3) "Hamiltonella_phylo”: FASTA-formatted nucleotide alignment files of each gene and NEXUS-formatted files used for Bayesian phylogenetic reconstruction of <em>Hamiltonella</em> symbionts.</p> <p>4) "HGT_genes": FASTA-formatted nucleotide alignment files of each horizontally transferred gene and non-horizontally transferred genes nupC, and <em>gpmA</em>. Also, NEXUS-formatted files used for Bayesian phylogenetic reconstruction and of resulting trees.</p> <p>5) "Tn3_pylo": FASTA-formatted amino acid alignment files of mobile elements related to the Tn3 family resolvase/invertase found in <em>Hamiltonella</em>-associated <em>Erwinia haradaeae</em> symbionts. Also, NEXUS-formatted files used for Bayesian phylogenetic reconstruction and of resulting trees.</p>
Dataset 'Yeast facilitates the multiplication of Drosophila bacterial symbionts but has no effect on the form or parameters of Taylor's law'
<p>Dataset from the manuscript 'Yeast facilitates the multiplication of <em>Drosophila </em>bacterial symbionts but has no effect on the form or parameters of Taylor’s law' (2020)</p> <p>Each line corresponds to a single experimental unit.</p>
Data and Code: Host-derived organic acids enable gut colonization of the honey bee symbiont Snodgrassella alvi
<p>Raw data and codes underlying the CFU count, qPCR, metabolomics, and NanoSIMS data for the paper "Host-derived organic acids enable gut colonization of the honey bee symbiont Snodgrassella alvi". Data is subdivided by main figure in the paper. Additionally, raw GC-MS datafiles (.cdf) are provided in separate folders. </p>
Data for "Host starvation and in hospite degradation of algal symbionts shape the heat stress response of the Cassiopea-Symbiodiniaceae symbiosis"
<p>Raw data associated with the publication "Host starvation and in hospite degradation of algal symbionts shape the heat stress response of the Cassiopea-Symbiodiniaceae symbiosis". Temperature profile, daily measurements, physiological measurements, elemental analysis, NanoSIMS data, and cell density data are included as individual tabs in the Excel file. </p>
Genbank annotation and sequence of the genome of a Rickettsiales symbiont of Reticulomyxa filosa
<p>The genome sequence of a Rickettsiales symbiont was selectively from the genome sequencing reads of its host, Reticulomyxa filosa. Those sequences were obtained from a previous third-party study (doi: 10.1016/j.cub.2013.11.027). The selective assembly procedure was based on GC content and coverage of contigs obtained from the total read sets with SPAdes. Full details are provided in the manuscript file.<br>The obtained symbiont sequence was then annotated with Prokka, and the gbk output file selected.</p><p>This genome was obtained and analysed in the context of a larger genome comparative studies on the Rickettsiales, aimed to investigate the evolutionary patterns within the whole lineage.</p>
lga BGC Domain alignment files for "Repeated horizontal acquisition of lagriamide-producing symbionts in Lagriinae beetles"
<p>Domains from all lga BGCs recovered from beetle metagenomes were aligned to identified conserved regions and determine if domains were potentially inactivated via mutation of deletion of conserved regions or residues. </p>
Should I stay or should I go? Coral bleaching from the symbionts' perspective
<p>Code to replicate figures in Should I Stay or Should I Go?</p>
Ecology and evolution of chlamydial symbionts of arthropods
<p><strong>The phylum Chlamydiae consists of obligate intracellular bacteria including major human pathogens and diverse environmental representatives. Here we investigated the Rhabdochlamydiaceae which is predicted to be the largest and most diverse chlamydial family, with the few known members infecting arthropod hosts. Using published 16S rRNA gene sequence data we identified at least 388 genus-level lineages containing about 14 051 putative species within this family. We show that rhabdochlamydiae are mainly found in freshwater and soil environments, suggesting the existence of diverse, yet unknown hosts. Next, we created a comprehensive genome dataset including metagenome assembled genomes classified as members of the family Rhabdochlamydiaceae, and we determined the genome sequences of two Rhabdochlamydia species, R. porcellionis infecting the woodlouse Porcellio scaber, and R. oedothoracis associated with the dwarf spider Oedothorax gibbosus. Comparative analysis of basic genome features and gene content with reference genomes of well-studied chlamydial families with known host ranges, namely Parachlamydiaceae (protist hosts) and Chlamydiaceae (human and other vertebrate hosts) suggested a distinct niche for members of the Rhabdochlamydiaceae. We propose that members of the family represent intermediate stages of adaptation of chlamydiae from protists to vertebrate hosts. Within the genus Rhabdochlamydia pronounced genome size reduction could be observed (1.49-1.93 Mb). The abundance and genomic distribution of transposases suggests transposable element expansion and subsequent gene inactivation as a mechanism of genome streamlining during adaptation to new hosts. Together, this study provides first insights into the molecular ecology, genomic diversity and evolution of representatives of one of the most successful chlamydial families.</strong></p>
Comparative genomics of eight aphid subfamilies reveals variable relationships between host horizontally-transferred genes and symbiont peptidoglycan metabolism.
<p>Genome assemblies, annotations, and orthologs of aphids (<em>Geopemphigus sp.</em>, <em>Stegophylla sp.</em>, <em>Chaitophorus viminalis</em>, and<em> Pemphigus obesinymphae</em>) and their symbionts. </p> <p>step1_final_assemblies_and_annotations.tar.gz: Aphid genomes and annotations</p> <p>step2_protein_evidence_used_for_genome_annotation.tar.gz: Protein evidence used for aphid genome annotation</p> <p>step3_amino_acid_inputs_for_aphid_orthologs: amino acid inputs for aphid ortholog assignmentt</p> <p>step5_buchnera_genomes_and_annotations.tar.gz: Buchnera genomes and annotations</p>
Host-symbiont stress response to lack-of-sulfide in the giant ciliate mutualism
<p>The mutualism between the thioautotrophic bacterial ectosymbiont <em>Candidatus</em> Thiobius zoothamnicola and the giant ciliate <em>Zoothamnium niveum</em> thrives in a variety of shallow-water marine environments with highly fluctuating sulfide emissions. To persist over time, both partners must reproduce and ensure the transmission of symbionts before the sulfide stops, which enables carbon fixation of the symbiont and nourishment of the host. We experimentally investigated the response of this mutualism to depletion of sulfide. We found that colonies released some initially present but also newly produced macrozooids until death, but in fewer numbers than when exposed to sulfide. The symbionts on the colonies proliferated less without sulfide, and became larger and more rod-shaped than symbionts from freshly collected colonies that were exposed to sulfide and oxygen. The symbiotic monolayer was severely disturbed by growth of other microbes and loss of symbionts. We conclude that the response of both partners to the termination of sulfide emission was remarkably quick. The development and the release of swarmers continued until host died and thus this behavior contributed to the continuation of the association.</p>
Fig. 2 in Symbiont Fauna Of Freshwater Zooplankton In Several Water Bodies Of The Dnipro River Basin
Fig. 2. Symbionts of fresh-water zooplankton: I — Haplocaulus kahlii; J — Haplocaulus epizoicus; K — Rhabdostyla cyclopis; L —Epistylis digitalis; M — Zoothamnium sp.; N — Vorticella lutea; O — Acineta nitocrae; P — Tokophrya actinostyla; Q — eggs of Thermocyclops oithonoides infected by parasitic flagellates Dinema undulaflagellatum; R — Bosmina longirostris filled by Coelosporidium chydoricola.
Data from: Plant host traits mediated by foliar fungal symbionts and secondary metabolites
<p>Fungal symbionts living inside plant leaves ("endophytes") can vary from beneficial to parasitic, but the mechanisms by which the fungi affect the plant host phenotype remain poorly understood. Chemical interactions are likely the proximal mechanism of interaction between foliar endophytes and the plant, as individual fungal strains are often exploited for their diverse secondary metabolite production. Here, we go beyond single strains to examine commonalities in how 16 fungal endophytes shift plant phenotypic traits such as growth and physiology, and how those relate to plant metabolomics profiles. We inoculated individual fungi on switchgrass, <em>Panicum virgatum</em> L. This created a limited range of plant growth and physiology (2–370% of fungus-free controls on average), but effects of most fungi overlapped, indicating functional similarities in unstressed conditions. Overall plant metabolomics profiles included almost 2000 metabolites, which were broadly correlated with plant traits across all the fungal treatments. Terpenoid-rich samples were associated with larger, more physiologically active plants and phenolic-rich samples were associated with smaller, less active plants. Only 47 metabolites were enriched in plants inoculated with fungi relative to fungus-free controls, and of these, LASSO regression identified 12 metabolites that explained from 14–43% of plant trait variation. Fungal long-chain fatty acids and sterol precursors were positively associated with plant photosynthesis, conductance, and shoot biomass, but negatively associated with survival. The phytohormone gibberellin, in contrast, was negatively associated with plant physiology and biomass. These results can inform ongoing efforts to develop metabolites as crop management tools, either by direct application or via breeding, by identifying how associations with more beneficial components of the microbiome may be affected.</p>
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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)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.