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15 results for “cryptic symbiont”
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>
Data from: Niche breadth and divergence in sympatric cryptic coral species (Pocillopora spp.) across habitats within reefs and among algal symbionts
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Droplet digital PCR (ddPCR) as a tool for investigating dynamics of cryptic symbionts
<p>Interactions among symbiotic organisms and their hosts are major drivers of ecological and evolutionary processes. Monitoring the infection patterns among natural populations and identifying factors affecting these interactions is critical for understanding symbiont-host relationships. However, many of these interactions remain understudied since the knowledge about the symbiont species is lacking and hinders the development of appropriate tools. In this study, we developed a digital droplet PCR (ddPCR) assay based on apicomplexan COX1 gene to detect an undescribed agamococcidian symbiont. We show that the method gives precise and reproducible results and enables detecting cryptic symbionts in low target concentration. We further exemplify the assay's use to survey seasonally sampled natural host (Pygospio elegans) populations for symbiont infection dynamics. We found that symbiont prevalence differs spatially but does not show seasonal changes. Infection load differed between populations and was low in spring and significantly increased towards fall in all populations. We also found that the symbiont prevalence is affected by host length and population density. Larger hosts were more likely to be infected and high host densities were found to have lower probability of infection. The observed variations could be due to characteristics of both symbiont and host biology, especially the seasonal variation in encounter rates. Our findings show that the developed ddPCR assay is a robust tool for detecting undescribed symbionts that are otherwise difficult to quantify, enabling further insight into the impact cryptic symbionts have on their hosts.</p>
Cryptic community structure and metabolic interactions among the heritable facultative symbionts of the pea aphid
<p>Most insects harbor influential, yet non-essential heritable microbes in their hemocoel. Communities of these symbionts exhibit low diversity. But their frequent multi-species nature raises intriguing questions on roles for symbiont-symbiont synergies in host adaptation, and on the stability of the symbiont communities, themselves. In this study, we build on knowledge of species-defined symbiont community structure across United States populations of the pea aphid, <em>Acyrthosiphon</em> <em>pisum</em>. Through extensive symbiont genotyping, we show that pea aphids' microbiomes can be more precisely defined at the symbiont strain level, with strain variability shaping ~5 out of 9 previously reported co-infection trends. Field data provide a mixture of evidence for symbiont-symbiont synergies, and symbiont hitchhiking, revealing causes and consequences of these co-infection trends. To test whether within-host metabolic interactions predict common versus rare strain-defined communities, we leveraged the high relatedness of our dominant, community-defined symbiont strains vs. twelve pea aphid-derived Gammaproteobacteria with sequenced genomes. Genomic inference, using metabolic complementarity indices, revealed high potential for cooperation among one pair of symbionts – <em>Serratia</em> <em>symbiotica</em> and <em>Rickettsiella</em> <em>viridis</em>. Applying the expansion network algorithm, through additional use of pea aphid and obligate <em>Buchnera</em> symbiont genomes, <em>Serratia</em> and <em>Rickettsiella</em> emerged as the only symbiont community requiring both parties to expand holobiont metabolism. Through their joint expansion of the biotin biosynthesis pathway, these symbionts may span missing gaps within a multi-party mutualism, within their nutrient-limited phloem-feeding hosts. Recent, complementary gene inactivation, within the biotin pathways of <em>Serratia</em> and <em>Rickettsiella</em>, raise further questions on the origins of mutualisms and host-symbiont interdependencies.</p>
Droplet digital PCR (ddPCR) as a tool for investigating dynamics of cryptic symbionts
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Cryptic community structure and metabolic interactions among the heritable facultative symbionts of the pea aphid
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Figure 4 from: Augustinos AA, Drosopoulou E, Gariou-Papalexiou A, Asimakis ED, Cáceres C, Tsiamis G, Bourtzis K, Mavragani-Tsipidou P, Zacharopoulou A (2015) Cytogenetic and symbiont analysis of five members of the B. dorsalis complex (Diptera, Tephritidae): no evidence of chromosomal or symbiont-based speciation events. In: De Meyer M, Clarke AR, Vera MT, Hendrichs J (Eds) Resolution of Cryptic Species Complexes of Tephritid Pests to Enhance SIT Application and Facilitate International Trade. ZooKeys 540: 273-298. https://doi.org/10.3897/zookeys.540.9857
Figure 4 - Comparison of the 3L polytene chromosome arm of a Bactrocera tryoni and b Bactrocera dorsalis s.s.. Dot lines connect characteristic landmarks of the two chromosomes.
Figure 1 from: Augustinos AA, Drosopoulou E, Gariou-Papalexiou A, Asimakis ED, Cáceres C, Tsiamis G, Bourtzis K, Mavragani-Tsipidou P, Zacharopoulou A (2015) Cytogenetic and symbiont analysis of five members of the B. dorsalis complex (Diptera, Tephritidae): no evidence of chromosomal or symbiont-based speciation events. In: De Meyer M, Clarke AR, Vera MT, Hendrichs J (Eds) Resolution of Cryptic Species Complexes of Tephritid Pests to Enhance SIT Application and Facilitate International Trade. ZooKeys 540: 273-298. https://doi.org/10.3897/zookeys.540.9857
Figure 1 - a, b Polytene nuclei of Bactrocera dorsalis s.s. from China. Chromosome arms are shown. Tips are marked with arrows and centromeres are indicated with 'C'.
Figure 5 from: Augustinos AA, Drosopoulou E, Gariou-Papalexiou A, Asimakis ED, Cáceres C, Tsiamis G, Bourtzis K, Mavragani-Tsipidou P, Zacharopoulou A (2015) Cytogenetic and symbiont analysis of five members of the B. dorsalis complex (Diptera, Tephritidae): no evidence of chromosomal or symbiont-based speciation events. In: De Meyer M, Clarke AR, Vera MT, Hendrichs J (Eds) Resolution of Cryptic Species Complexes of Tephritid Pests to Enhance SIT Application and Facilitate International Trade. ZooKeys 540: 273-298. https://doi.org/10.3897/zookeys.540.9857
Figure 5 - Comparison of the 4L polytene chromosome arms of a Bactrocera tryoni and b Bactrocera dorsalis s.s.. Dot lines connect characteristic landmarks of the two chromosomes.
Figure 3 from: Augustinos AA, Drosopoulou E, Gariou-Papalexiou A, Asimakis ED, Cáceres C, Tsiamis G, Bourtzis K, Mavragani-Tsipidou P, Zacharopoulou A (2015) Cytogenetic and symbiont analysis of five members of the B. dorsalis complex (Diptera, Tephritidae): no evidence of chromosomal or symbiont-based speciation events. In: De Meyer M, Clarke AR, Vera MT, Hendrichs J (Eds) Resolution of Cryptic Species Complexes of Tephritid Pests to Enhance SIT Application and Facilitate International Trade. ZooKeys 540: 273-298. https://doi.org/10.3897/zookeys.540.9857
Figure 3 - Characteristic asynapsis in the 3L, close to the tip region, observed in Bactrocera dorsalis colony derived from China. a almost completely synapsed region b–d asynapses of the same region; asterisks (*) indicate the specific region.
Figure 2 from: Augustinos AA, Drosopoulou E, Gariou-Papalexiou A, Asimakis ED, Cáceres C, Tsiamis G, Bourtzis K, Mavragani-Tsipidou P, Zacharopoulou A (2015) Cytogenetic and symbiont analysis of five members of the B. dorsalis complex (Diptera, Tephritidae): no evidence of chromosomal or symbiont-based speciation events. In: De Meyer M, Clarke AR, Vera MT, Hendrichs J (Eds) Resolution of Cryptic Species Complexes of Tephritid Pests to Enhance SIT Application and Facilitate International Trade. ZooKeys 540: 273-298. https://doi.org/10.3897/zookeys.540.9857
Figure 2 - a–e Characteristic asynapsis in 5R chromosome arm, close to the centromere (regions 73–74), observed in the Bactrocera dorsalis s.s. colony derived from China. Asterisks (*) mark the asynaptic region, while 'C' marks the 5R centromere.
Figure 8 from: Augustinos AA, Drosopoulou E, Gariou-Papalexiou A, Asimakis ED, Cáceres C, Tsiamis G, Bourtzis K, Mavragani-Tsipidou P, Zacharopoulou A (2015) Cytogenetic and symbiont analysis of five members of the B. dorsalis complex (Diptera, Tephritidae): no evidence of chromosomal or symbiont-based speciation events. In: De Meyer M, Clarke AR, Vera MT, Hendrichs J (Eds) Resolution of Cryptic Species Complexes of Tephritid Pests to Enhance SIT Application and Facilitate International Trade. ZooKeys 540: 273-298. https://doi.org/10.3897/zookeys.540.9857
Figure 8 - a, b Polytene nuclei derived from the F1 Bactrocera dorsalis s.s. × Bactrocera tryoni hybrids. Chromosome arms are indicated. Tips are marked with arrows and centromeres are indicated with 'C'. Note the overall banding pattern homosequentiallity and the presence of limited asynapses.
Figure 9 from: Augustinos AA, Drosopoulou E, Gariou-Papalexiou A, Asimakis ED, Cáceres C, Tsiamis G, Bourtzis K, Mavragani-Tsipidou P, Zacharopoulou A (2015) Cytogenetic and symbiont analysis of five members of the B. dorsalis complex (Diptera, Tephritidae): no evidence of chromosomal or symbiont-based speciation events. In: De Meyer M, Clarke AR, Vera MT, Hendrichs J (Eds) Resolution of Cryptic Species Complexes of Tephritid Pests to Enhance SIT Application and Facilitate International Trade. ZooKeys 540: 273-298. https://doi.org/10.3897/zookeys.540.9857
Figure 9 - a–e Part of the 2R chromosome arm including the fixed inversion. Photos derived from different polytene chromosome preparations. Asterisks (*) indicate the inversion breakpoints. 'C' indicates the 2R centromere.
Figure 7 from: Augustinos AA, Drosopoulou E, Gariou-Papalexiou A, Asimakis ED, Cáceres C, Tsiamis G, Bourtzis K, Mavragani-Tsipidou P, Zacharopoulou A (2015) Cytogenetic and symbiont analysis of five members of the B. dorsalis complex (Diptera, Tephritidae): no evidence of chromosomal or symbiont-based speciation events. In: De Meyer M, Clarke AR, Vera MT, Hendrichs J (Eds) Resolution of Cryptic Species Complexes of Tephritid Pests to Enhance SIT Application and Facilitate International Trade. ZooKeys 540: 273-298. https://doi.org/10.3897/zookeys.540.9857
Figure 7 - The inverted region on the 2R polytene arm that differentiates Bactrocera tryoni from the five members of the Bactrocera dorsalis complex: a Bactrocera tryoni b Bactrocera dorsalis s.s. Dotted lines mark the chromosomal region involved in the inversion while arrows indicate the orientation.
Figure 6 from: Augustinos AA, Drosopoulou E, Gariou-Papalexiou A, Asimakis ED, Cáceres C, Tsiamis G, Bourtzis K, Mavragani-Tsipidou P, Zacharopoulou A (2015) Cytogenetic and symbiont analysis of five members of the B. dorsalis complex (Diptera, Tephritidae): no evidence of chromosomal or symbiont-based speciation events. In: De Meyer M, Clarke AR, Vera MT, Hendrichs J (Eds) Resolution of Cryptic Species Complexes of Tephritid Pests to Enhance SIT Application and Facilitate International Trade. ZooKeys 540: 273-298. https://doi.org/10.3897/zookeys.540.9857
Figure 6 - Comparison of the 5L polytene chromosome arms of a Bactrocera tryoni and b Bactrocera dorsalis s.s.. Dot lines connect characteristic landmarks of the two chromosomes.
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