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339 results for “Host specificity”
Figure 1 in Cryptic genetic diversity and host specificity of Bothriocephalus acheilognathi Yamaguti, 1934 (Eucestoda: Bothriocephalidea)
Figure 1. Sample localities of Bothriocephalus acheilognathi studied in China. The code number is corresponding to the locality in Table 1.
Figiure 3 in Cryptic genetic diversity and host specificity of Bothriocephalus acheilognathi Yamaguti, 1934 (Eucestoda: Bothriocephalidea)
Figiure 3. Phylogenetic relationships of Bothriocephalus based on the ribosoml internal transcribed spacer sequences (ITS1+ITS2) using maximum likelihood (ML) method. Numbers near branch node are the bootstrap support value for ML, maximum parsimoy (MP), and posterior probability for Bayesian inference (BI).
Part 1: Dataset and script for a manuscript entitled 'Host-specific subtelomere: structural variation and horizontal transfer in asexual filamentous fungal pathogens'
<p>Datasets, scripts and instructions for reproducing some of the results in the manuscript. The file subtelomere.tar needs to be unpacked on a Linux system. After unpacking it, go to the directory subtelomere, which contains a number of subdirectories. One subdirectory is named data, which contains genome assemblies and is used to hold datasets of short reads; the datasets of short reads in the files Data.One.Focb.tar, Data.One.Focb-2.tar and reads.tar on the four-part depository need to be placed in the subdirectory subtelomere/data/reads/. The other subdirectories under the directory subtelomere contain instructions and scripts for reproducing some of the results in the manuscript. Please see the README and z.cmd files in each subdirectory.</p> <p>The file Data.One.Focb-2.tar contains 22 files of paired-end reads from F. oxysporum f.sp. cubense tropical race 1 isolate N2 (SRA accession: SRR550150, SRR550151), and F. oxysporum f.sp. cubense TR4 isolates Hainan.B2 (SRR550152), My-1 (SRR7226877), La-2 (SRR7226878), Vn-2 (SRR7226879), Leb1.2C (SRR7226880), JV11 (SRR7226881), Phi2.6C (SRR7226882), Pak1.1A (SRR7226883), UK0001 (SRR9733598).</p>
Part 2: Dataset and script for a manuscript entitled 'Host-specific subtelomere: structural variation and horizontal transfer in asexual filamentous fungal pathogens'
<p>Datasets, scripts and instructions for reproducing some of the results in the manuscript. The file subtelomere.tar needs to be unpacked on a Linux system. After unpacking it, go to the directory subtelomere, which contains a number of subdirectories. One subdirectory is named data, which contains genome assemblies and is used to hold datasets of short reads; the datasets of short reads in the files Data.One.Focb.tar, Data.One.Focb-2.tar and reads.tar on the four-part depository need to be placed in the subdirectory subtelomere/data/reads/. The other subdirectories under the directory subtelomere contain instructions and scripts for reproducing some of the results in the manuscript. Please see the README and z.cmd files in each subdirectory.</p> <p>The file Data.One.Focb.tar contains 16 files of paired-end reads from F. oxysporum f.sp. cubense TR4 isolates II-5 (SRA accession: SRR10054446), S1B8 (SRR10054447), JV14 (SRR10054448), FOC.TR4-5 (SRR10054449), FOC.TR4-1 (SRR10054450), Col2 (SRR10103605), Col4 (SRR10125423), Col17 (SRR10747097).</p> <p> </p>
Part 4: Dataset and script for a manuscript entitled 'Host-specific subtelomere: structural variation and horizontal transfer in asexual filamentous fungal pathogen
<p>Datasets, scripts and instructions for reproducing some of the results in the manuscript. The file subtelomere.tar needs to be unpacked on a Linux system. After unpacking it, go to the directory subtelomere, which contains a number of subdirectories. One subdirectory is named data, which contains genome assemblies and is used to hold datasets of short reads; the datasets of short reads in the files Data.One.Focb.tar, Data.One.Focb-2.tar and reads.tar on the four-part depository need to be placed in the subdirectory subtelomere/data/reads/. The other subdirectories under the directory subtelomere contain instructions and scripts for reproducing some of the results in the manuscript. Please see the README and z.cmd files in each subdirectory.</p> <p>The file reads.tar contains 44 files of paired-end reads from <em>F. oxysporum </em>f.sp. <em>lycopersici</em> isolate Fol069 (SRA accession: SRR307106, SRR307107, SRR307113, SRR307115, SRR307123, SRR307257, SRR307266), isolate Fol072 (SRR307122, SRR307092, SRR307091, SRR307090, SRR307086, SRR307281, SRR307250), isolate Fol4287 (SRR7690004, SRR3139043), and F. oxysporum f.sp. radicis-cucumerinum isolate Forc016 (SRR3139027, SRR3139028), isolate Forc024 (SRR3139029, SRR3139030), isolate Forc031 (SRR3139031, SRR3139032).</p>
MAG Collection - Rühlemann et al.: Comparative metagenomics reveals host-specific functional adaptation of intestinal microbiota across hominids
<p>This tar-Archives hold the complete collection of n=7,506 metagenome-assembled genomes presented in the preprint "Comparative metagenomics reveals host-specific functional adaptation of intestinal microbiota across hominids" by Rühlemann <em>et al., <a href="https://www.biorxiv.org/content/10.1101/2023.03.01.530589v1">bioRxiv</a>, </em>2023.</p> <p>Article Summary</p> <p>Characterizing trajectories of the composition and function of hominid gut microbiota across diverse environments and host species can help reveal specific properties of the human microbiota, with possible implications for host evolution and health. Using shotgun metagenomic sequencing, we investigated taxonomic and functional diversity in the gut microbiota of wild-living great apes, including two gorilla subspecies (<em>Gorilla gorilla gorilla, Gorilla beringei beringei</em>), three chimpanzee subspecies (<em>Pan troglodytes verus, P.t. troglodytes, P.t. schweinfurthii</em>), and bonobos (<em>Pan paniscus</em>), together with human samples from Africa and Europe. We identified microbial taxonomic and functional adaptations convergent with host phylogeny at both the community and microbial genomic levels. We could show that repeated horizontal gene transfer and gene loss are processes involved in these adaptations. We hypothesize, that these adaptation processes and changes in the microbiome predispose the host to chronic inflammatory disorders, such as type 2 diabetes via altered histidine metabolism and inflammatory bowel disease indicated by adaptation of microbes to aerobic conditions. Additionally, we find multiple lines of evidence suggesting a widespread loss of microbial diversity and evolutionary conserved clades in the human microbiota, especially in the European population. Lastly, we observed patterns consistent with codivergence of hosts and microbes, particularly for the bacterial family <em>Dialisteraceae</em>, though we find that overall, co-phylogeny patterns are frequently disrupted in humans.</p>
Dataset 1 for "Host-specificity and repeatability of haemosporidian infection parameters and potential consequences when testing host species-level hypotheses"
<p>Dataset with 9 host species (min. 5 study sites and min 45 sampled individuals sampled per site) for the first part of the analysis in "Host-specificity and repeatability of haemosporidian infection parameters and potential consequences when testing host species-level hypotheses". One file contains the data table. One file contains a table with descriptions of the columns in the data table.</p>
Host specificity of herbivorous insects promotes negative species–genetic diversity relationship
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Patterns of genotype-specific interactions in an obligate host-specific insect pathogenic fungus
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Energy input, habitat heterogeneity, and host specificity drive avian haemosporidian diversity at continental scales
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Data from: The polygenic strategies of host-specific and general virulence of Botrytis cinerea across diverse eudicot hosts
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Network specificity decreases community stability and competition among avian haemosporidian parasites and their hosts
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Data from: Multidimensional plasticity in the Glanville fritillary butterfly: larval performance is temperature, host and family specific
<p>Variation in environmental conditions during development can lead to changes in life-history traits with long-lasting effects. Here, we study how variation in temperature and host plant, i.e. the consequences of potential maternal oviposition choices, affects a suite of life-history traits in pre-diapause larvae of the Glanville fritillary butterfly. We focus on offspring survival, larval growth rates and relative fat reserves, and pay specific attention to intraspecific variation in the responses (GxExE). Globally, thermal performance and survival curves varied between diets of two host plants, suggesting that host modifies the temperature impact, or <i>vice versa</i>. Additionally, we show that the relative fat content has a host-dependent, discontinuous response to developmental temperature. This implies that a potential switch in resource allocation, from more investment in growth at lower temperatures to storage at higher temperatures, is dependent on the larval diet. Interestingly, a large proportion of the variance in larval performance is explained by differences among families, or interactions with this variable. Finally, we demonstrate that these family-specific responses to the host plant remain largely consistent across thermal environments. Altogether, the results of our study underscore the importance of paying attention to intraspecific trait variation in the field of evolutionary ecology.</p>
Fungal sporocarps house diverse and host-specific communities of fungicolous fungi
<p class="Corps"><span><span><span><span><span><span><span><span><span><span>Sporocarps (fruit bodies) are the sexual reproductive stage in the life cycle of many fungi. They are highly nutritious and consequently vulnerable to grazing by birds and small mammals, and invertebrates, and can be infected by microbial and fungal parasites and pathogens. The complexity of communities thriving inside sporocarps is largely unknown. In this study, we revealed the diversity, taxonomic composition and host-preference of fungicolous fungi (i.e fungi that feed on other fungi) in sporocarps. We carried out DNA metabarcoding of the ITS2 region from 176 sporocarps of 11 wood-decay fungal host species, all collected within a forest in northeast Finland. We assessed the influence of sporocarp traits, such as lifespan, morphology and size, on the fungicolous fungal community. The level of colonisation by fungicolous fungi, measured as the proportion of non-host ITS2 reads, varied between 2.8-39.8% across the 11 host species and was largely dominated by Ascomycota. Host species was the major determinant of the community composition and diversity of fungicolous fungi, suggesting that host adaptation is important for many fungicolous fungi. Furthermore, the alpha-diversity was consistently higher in short-lived and resupinate sporocarps compared to long-lived and pileate ones, perhaps due to a more hostile environment for fungal growth in the latter too. The fungicolous fungi represented numerous lineages in the fungal tree of life, among which a significant portion was poorly represented with reference sequences in databases. </span></span></span></span></span></span></span></span></span></span></p>
Data from: Molecular signatures of host specificity linked to habitat specialization in Exaiptasia sea anemones.
Rising ocean temperatures associated with global climate change induce breakdown of the symbiosis between coelenterates and photosynthetic microalgae of the genus Symbiodinium. Association with more thermotolerant partners could contribute to resilience, but the genetic mechanisms controlling specificity of hosts for particular Symbiodinium types are poorly known. Here we characterize wild populations of a sea anemone laboratory model system for anthozoan symbiosis, from contrasting environments in Caribbean Panama. Patterns of anemone abundance and symbiont diversity were consistent with specialization of holobionts for particular habitats, with Exaiptasia pallida/S. minutum (ITS2 type B1) abundant on vertical substrate in thermally stable, shaded environments but E. brasiliensis/Symbiodinium sp. (ITS2 clade A) more common in shallow areas subject to high temperature and irradiance. Population genomic sequencing revealed a novel E. pallida population from the Bocas del Toro Archipelago that only harbors S. minutum. Loci most strongly associated with divergence of the Bocas-specific population were enriched in genes with putative roles in cnidarian symbiosis, including activators of the complement pathway of the innate immune system, thrombospondin-type-1 repeat domain proteins, and coordinators of endocytic recycling. Our findings underscore the importance of unmasking cryptic diversity in natural populations and the role of long-term evolutionary history in mediating interactions with Symbiodinium.
Host-specificity in Scelionid parasitoids: Arrestment, competition, and egg electrophysiology results
<p>This archive contains the raw data from a series of experiments with Trissolcus basalis and Trissolcus oenone to better understand the chemical basis mediating differences in host-specificity between these parasitoids. First, we compared the searching behaviour of T. basalis and T. oenone in open arena arrestment bioassays contaminated with footprint compounds from Nezara viridula and Cuspicona simplex. Trissolcus basalis spent four times longer searching for N. viridula than C. simplex, while T. oenone spent four times longer searching for C. simplex than N. viridula. We then conducted competition experiments to assess factors important to determining the outcomes of extrinsic and intrinsic contests between these parasitoids when they are simultaneously exposed to C. simplex egg masses. Trissolcus oenone, was the superior competitor in extrinsic and intrinsic contests. Finally, we recorded the antennal responses of T. basalis to egg extracts of N. viridula to tentatively identify potential contact kairomones used by this parasitoid to recognise and accept hosts.</p>
Diversity and host specificity of Borrelia burgdorferi's outer surface protein C (ospC) alleles in synanthropic mammals, with a notable ospC allele U absence from mixed infections
<p>Interactions among pathogen genotypes that vary in host specificity may affect overall transmission dynamics in multi-host systems. <em>Borrelia burgdorferi</em>, a bacterium that causes Lyme disease, is typically transmitted among wildlife by <em>Ixodes</em> ticks. Despite the existence of many alleles of <em>B. burgdorferi</em>'s <em>sensu stricto</em> outer surface protein C (<em>ospC</em>) gene, most human infections are caused by a small number of <em>ospC</em> alleles ["human infectious alleles" (HIAs)], suggesting variation in host specificity associated with <em>ospC</em>. To characterize the wildlife host association of <em>B. burgdorferi</em>'s <em>ospC</em> alleles, we used metagenomics to sequence <em>ospC</em> alleles from 68 infected individuals belonging to eight mammalian species trapped at three sites in suburban New Brunswick, New Jersey (USA). We found that multiple allele ("mixed") infections were common. HIAs were most common in mice (<em>Peromyscus</em> spp.) and only one HIA was detected at a site where mice were rarely captured. <em>OspC </em>allele U was exclusively found in chipmunks (<em>Tamias striatus</em>), and although a significant number of different alleles were observed in chipmunks, including HIAs, allele U never co-occurred with other alleles in mixed infections. Our results suggest that allele U may be excluding other alleles, thereby reducing the capacity of chipmunks to act as reservoirs for HIAs.</p>
Data sets for Polyplax serrata article "Highly-resolved genomes of two closely related lineages of the rodent louse Polyplax serrata with different host specificities"
<p><strong>Supplementary data for Polyplax serrata article 2023</strong></p> <p>Data included in this repository were generated and used in various genomic and phylogenetic analysis presented by the publication "<strong>Highly-resolved genomes of two closely related lineages of the louse </strong><em><strong>Polyplax serrata</strong></em><strong> with different host specificities</strong>"</p> <p><strong>Description of the data and file structure</strong></p> <p>Data provided for each analyzed taxa include:</p> <p>- Annotation table.</p> <p>- fasta format files for transcripts (CDS and mRNA).</p> <p>- fasta format file for genome.</p> <p>- protein fasta file.</p> <p>- gbk format file that includes the genome with its corresponding annotations.</p> <p>Additionally,</p> <p>- repeat families in fasta format were included for <em>Polyplax serrata</em> S and N lineages.</p> <p>- rRNA in fasta format were included for <em>Polyplax serrata</em> S and N lineages, <em>Pediculus humanus, Columbicola columbae </em>and <em>Brueelia nebulsa</em>. </p> <p><strong>Sharing/Access information</strong></p> <p>GenBank accession number of analyzed taxa:</p> <p>· <em>Aedes Aegypti</em> (GenBank accession no. GCF_002204515.2).</p> <p>· <em>Brueelia nebulsa</em> ( GenBank accession no. GCA_028293925.1).</p> <p>· <em>Columbicola columbae</em> (GenBank accession no. GCA_016920875.1).</p> <p>· <em>Cimex lectularis</em> (GenBank accession no. GCF_000648675.2).</p> <p>· <em>Glossina morsitans</em> (GenBank accession no. GCA_001077435.1).</p> <p>· <em>Pediculus humanus</em> (GenBank accession no. GCA_000006295.1).</p> <p>· <em>Rhodnius prolixus</em> (GenBank accession no. GCA_000181055.3).</p> <p>· <em>Polyplax serrata S lineage</em> (GenBank accession no. JAWJWF000000000).</p> <p>· <em>Polyplax serrata N lineage</em> (GenBank accession no. JAWJWE000000000).</p> <p> </p> <p>Note: All the latter genomes except for the two genomes of <em>Polyplax serrata</em> S and N lineages, were acquired from GenBank database and were subjected to the same gene prediction and annotation workflow as <em>P. serrata</em> genomes to maintain methodological consistence in downstream analysis of the annotation results.</p> <p><strong>Software</strong></p> <p>- Gene prediction and annotation was performed using Funannotate v1.18.14 (<a href="https://github.com/nextgenusfs/funannotate">https://github.com/nextgenusfs/funannotate)</a>).</p> <p>- Repeat were identified in the genomes of P. serrata S and N lineages using RepeatModeler v2.0.3.</p>
Facultative symbiont virulence determines horizontal transmission rate without host specificity in Dictyostelium discoideum social amoebas
<p>In facultative symbioses, only a fraction of hosts are associated with symbionts. Specific host and symbiont pairings may be the result of host-symbiont coevolution driven by reciprocal selection, or priority effects pertaining to which potential symbiont became associated with a host first. Distinguishing between these possibilities is important for understanding the evolutionary forces that affect facultative symbioses. We used the social amoeba <em>Dictyostelium discoideum</em> and its symbiont <em>Paraburkholderia bonniea </em>to determine whether ongoing coevolution affects which host-symbiont strain pairs naturally co-occur within a facultative symbiosis. Relative to other <em>Paraburkholderia</em>,<em> </em>including another symbiont of <em>D. discoideum</em>, <em>P. bonniea</em> features a reduced genome size that indicates a significant history of coevolution with its host. We hypothesized that ongoing host-symbiont coevolution would lead to higher fitness for naturally co-occurring (native) host and symbiont pairings compared to novel pairings. We show for the first time that <em>P. bonniea</em> symbionts can horizontally transmit to new amoeba hosts when hosts aggregate together during the social stage of their life cycle. Here we find evidence for a virulence-transmission trade-off without host specificity. Although symbiont strains were significantly variable in virulence and horizontal transmission rate, hosts and symbionts responded similarly to associations in native and novel pairings. We go on to identify candidate virulence factors in the genomes of <em>P. bonniea </em>strains that may contribute to variation in virulence. We conclude that ongoing coevolution is unlikely for <em>D. discoideum </em>and <em>P. bonniea. </em>The system instead appears to represent a stable facultative symbiosis in which naturally co-occurring <em>P. bonniea </em>host and symbiont pairings are the result of priority effects.</p>
First insights into population structure and genetic diversity versus host specificity in trypanorhynch tapeworms using multiplexed shotgun genotyping
<p>Theory predicts relaxed host specificity and high host vagility should contribute to reduced genetic structure in parasites while strict host specificity and low host vagility should increase genetic structure. Though these predictions are intuitive, they have never been explicitly tested in a population genomic framework. Trypanorhynch tapeworms, which parasitize sharks and rays (elasmobranchs) as definitive hosts, are the only order of elasmobranch tapeworms that exhibit considerable variability in their definitive host specificity. This allows for unique combinations of host use and geographic range, making trypanorhynchs ideal candidates for studying how these traits influence population-level structure and genetic diversity. Multiplexed shotgun genotyping (MSG) datasets were generated to characterize component population structure and infrapopulation diversity for a representative of each trypanorhynch suborder: the ray-hosted <em>Rhinoptericola megacantha</em> (Trypanobatoida) and the shark-hosted Callitetrarhynchus gracilis (Trypanoselachoida). Adults of <em>R. megacantha</em> are more host-specific and less broadly distributed than adults of <em>C. gracilis</em>, allowing correlation between these factors and genetic structure. Replicate tapeworm specimens were sequenced from the same host individual, from multiple conspecific hosts within and across geographic regions, and from multiple definitive host species. For <em>R. megacantha</em>, population structure coincided with geography rather than host species. For <em>C. gracilis</em>, limited population structure was found, suggesting a potential link between degree of host specificity and structure. Conspecific trypanorhynchs from the same host individual were found to be as, or more, genetically divergent from one another as from conspecifics from different host individuals. For both species, high levels of homozygosity and positive FIS values were documented.</p>
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Allen Brain Atlas
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OpenNeuro
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