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10 results for “hologenomics”
Marine sponge Haliclona fulva hologenome sequences - total contigs assembled
<p>Dataset (multifasta) of DNA contig sequences assembled from Illumina metagenomic reads of Haliclona fulva hologenome. The sequences analyses are described in the peer-reviewed article at https://doi.org/10.3389/fmars.2021.736817 entitled: "The Hologenome of Haliclona fulva (Porifera, Demospongiae) Reveals an Abundant and Diverse Viral Community" by<br> Erika García-Bonilla1,2†, Diego Chaves-Moreno3†, Diego Riaño-Pachón4, Wilson Terán5, Alberto Acosta1 and Howard Junca2*<br> 1Laboratorio Ecosistemas Marinos Estratégicos, Unidad de Ecología y Sistemática - UNESIS, Facultad de Ciencias - Departamento de Biología, Pontificia Universidad Javeriana, Bogotá, Colombia<br> 2RG Microbial Ecology: Metabolism, Genomics & Evolution, Division of Ecogenomics & Holobionts, Microbiomas Foundation, Chía, Colombia<br> 3Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany<br> 4Laboratório de Biologia Computacional, Evolutiva e de Sistemas, Centro de Energía Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, Brazil<br> 5Biología de Plantas y Sistemas Productivos, Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia</p> <p>"Sample Collection</p> <p>Three specimens of <em>H. fulva</em> (HF1, HF2, and HF3) were collected by SCUBA diving in the Mediterranean Sea at the Grotte du Lido, in the bay of Villefranche-sur-Mer, France (latitude: 43° 41′ 31.49″ N; longitude: 7° 19′ 12.19″ E) at 35 m depth. After collection, all individual samples were placed in independent plastic bags. They were preserved in ethanol 70% (v/v) and stored at −20°C until further analysis. The samples were selected based on the findings of our previous study (<a href="https://www.frontiersin.org/articles/10.3389/fmars.2021.736817/full#B11">García-Bonilla et al., 2019</a>) and are coming from exactly the same spots and colonies/specimens analyzed regarding microbiome content by 16S amplicons, showing a stable and consistent microbial composition of low microbial abundance and diversity.</p> <p>DNA Extraction and Sequencing</p> <p>Metagenomic DNA was extracted from 15 g sponge wet weight using a MagAttract<sup>®</sup> HMW DNA kit (Qiagen, Germany) following the manufacturer’s instructions. Tissue lysis was made for 16 h according to protocol. Extracted DNA was eluted with 50 μl water, and its concentration determined by fluorescence using the Qubit<sup>®</sup> dsDNA BR assay kit (Thermo Fisher Scientific). Nucleic acid integrity was verified by 0.8% agarose gel electrophoresis. Sponge DNA extracts were used as template to perform isothermal multiple displacement hologenome amplification with a phi29 polymerase of high processivity and fidelity in order to increase total DNA concentrations (<a href="https://www.frontiersin.org/articles/10.3389/fmars.2021.736817/full#B36">Lasken, 2007</a>) and to avoid the effect of coextracted enzymatic inhibitors detected in <em>H. fulva</em>, improving further downstream processes (library construction and sequencing). The amplification process was made using REPLI-g Mini kit (Qiagen, Germany), according to manufacturer’s recommendations. Briefly, samples were incubated at 30°C for 11 h followed by 3 min at 65°C for polymerase inactivation. For all assays, a negative control was run to evaluate the presence of contaminants during amplification. Quantity and quality of DNA was measured as described previously.</p> <p>Genomic libraries were constructed using TruSeq DNA PCR free kit (Illumina, United States). Shotgun hologenome sequencing was performed using paired-end Illumina technology (Macrogen, South Korea). The complete raw sequencing data obtained is publicly accessible at NCBI GenBank SRA under Bioproject PRJNA741981.</p> <p>Raw Data Processing and Assembly</p> <p>An initial filtering of the sequencing reads was done after visual evaluation using FastQC (v.0.11.8) consisting of a quality and length-based filtering performed with Trimmomatic (v.0.31). Filtered and processed reads were assembled using Megahit (v.1.0) (<a href="https://www.frontiersin.org/articles/10.3389/fmars.2021.736817/full#B37">Li et al., 2014</a>) and IDBA-UD (<a href="https://www.frontiersin.org/articles/10.3389/fmars.2021.736817/full#B46">Peng et al., 2012</a>) with default parameters. To compare, identify and join overlaps between reads from each assembly, we used minimus2 from the AMOS suite with default parameters (<a href="https://www.frontiersin.org/articles/10.3389/fmars.2021.736817/full#B65">Treangen et al., 2011</a>). Obtained contigs were filtered and those <500 bp were removed."</p> <p> </p>
Data from: Hologenomic speciation: synergy between a male-killing bacterium and sex-linkage creates a ‘magic trait’ in a butterfly hybrid zone
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Data from: The hologenomic basis of speciation: gut bacteria cause hybrid lethality in the genus Nasonia
Although the gut microbiome influences numerous aspects of organismal fitness, its role in animal evolution and the origin of new species is largely unknown. Here we present evidence that beneficial bacterial communities in the guts of closely related species of the genus Nasonia form species-specific phylosymbiotic assemblages that cause lethality in interspecific hybrids. Bacterial constituents and abundance are irregular in hybrids relative to parental controls, and antibiotic curing of the gut bacteria significantly rescues hybrid survival. Moreover, feeding bacteria to germ-free hybrids reinstates lethality and recapitulates the expression of innate immune genes observed in conventionally reared hybrids. We conclude that in this animal complex, the gut microbiome and host genome represent a coadapted "hologenome" that breaks down during hybridization, promoting hybrid lethality and assisting speciation.
Data from: The hologenomic basis of speciation: gut bacteria cause hybrid lethality in the genus Nasonia
Although the gut microbiome influences numerous aspects of organismal fitness, its role in animal evolution and the origin of new species is largely unknown. Here we present evidence that beneficial bacterial communities in the guts of closely related species of the genus Nasonia form species-specific phylosymbiotic assemblages that cause lethality in interspecific hybrids. Bacterial constituents and abundance are irregular in hybrids relative to parental controls, and antibiotic curing of the gut bacteria significantly rescues hybrid survival. Moreover, feeding bacteria to germ-free hybrids reinstates lethality and recapitulates the expression of innate immune genes observed in conventionally reared hybrids. We conclude that in this animal complex, the gut microbiome and host genome represent a coadapted "hologenome" that breaks down during hybridization, promoting hybrid lethality and assisting speciation.
Data from: The hologenomic basis of speciation: gut bacteria cause hybrid lethality in the genus Nasonia
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Data from: The hologenomic basis of speciation: gut bacteria cause hybrid lethality in the genus Nasonia
Open the record for dataset details and reuse information.
The microbiome buffers tadpole hosts from heat stress: a hologenomic approach to understand host-microbe interactions under warming
GEO Series GSE208645. Lithobates clamitans. 20 samples. Type: Expression profiling by high throughput sequencing.
Supplementary Online Data for Characterizing the hologenome of L. pustulata and tracing genomic footprints of lichenization
<p>Processed data and scripts, as well as the the figures and tables for <em>Characterizing the hologenome of L. pustulata and tracing genomic footprints of lichenization</em>. The <em>zip</em> file contains three subfolders for <em>Chapter 3</em>, <em>Chapter 4</em>, <em>Chapter 5</em> of <em>Characterizing the hologenome of L. pustulata and tracing genomic footprints of lichenization</em>. Each subfolder comes with its own <em>README.md</em> further describing its contents.</p> <p>Furthermore the read mappings against <em>Lasallia pustulata</em> individually, as well as the ones used for the <em>anvi´o</em> visualization, which include <em>L. pustulata</em>, <em>Trebouxia sp.</em> as well as the 499 bacterial scaffolds are given. The <em>Trinity</em> RNAseq assemblies (guided and unguided) are given too.<br> </p>
Tracking the hologenome dynamics in aquatic invertebrates by the holo-2bRAD approach-1
<p>This is the raw data of "<em><strong>Tracking the hologenome dynamics in aquatic invertebrates by the holo-2bRAD approach</strong></em>", and these are only be provided to editors and reviewers.</p>
The microbiome buffers tadpole hosts from the deleterious effects of heat stress: a hologenomic approach to understand host-microbe interactions under warming conditions.
GEO Series GSE208646. Lithobates clamitans. 20 samples. Type: Expression profiling by high throughput sequencing.
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OpenNeuro
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