scholarly journals Next-generation sequencing reveals cryptic Symbiodinium diversity within Orbicella faveolata and Orbicella franksi at the Flower Garden Banks, Gulf of Mexico

2014 ◽  
Author(s):  
Elizabeth Green ◽  
Sarah W. Davies ◽  
Mikhail V. Matz ◽  
Mónica Medina
Keyword(s):  
Genetic Diversity ◽  
Local Community ◽  
Coral Species ◽  
Geographic Location ◽  
Amplicon Sequencing ◽  
Coral Host ◽  
Clade B ◽  
Orbicella Faveolata ◽  
Host Genetic ◽  
Physiological Variations

The genetic composition of the resident Symbiodinium endosymbionts appears to strongly modulate the physiological performance of reef-building corals. Here, we used deep amplicon sequencing to quantitatively assess Symbiodinium genetic diversity for the two mountainous star corals, Orbicella franksi and Orbicella faveolata, from two reefs separated by 19 kilometers of deep water. We aimed to determine if symbiont diversity is largely partitioned with respect to coral host species or geographic location. Our results demonstrate that across the two reefs both coral species contained only Symbiodinium identifiable as clade B type B1, represented by five distinct haplotypes. Three of these haplotypes have not been previously described and may be endemic to the Flower Garden Banks. No consistent differences in symbiont composition were detected between the two coral species. However, significant quantitative differences were observed between the east and west banks for two of the five haplotypes. These results highlight the need for consistent molecular genotyping techniques to assess local community assemblages of Symbiodinium-host relationships, which could be largely irrespective of host genetic background. This deep-sequencing approach used to sensitively characterize cryptic genetic diversity of Symbiodinium will potentially contribute to the understanding of physiological variations among coral populations.

scholarly journals Next-generation sequencing reveals cryptic Symbiodinium diversity within Orbicella faveolata and Orbicella franksi at the Flower Garden Banks, Gulf of Mexico

2014 ◽  
Author(s):  
Elizabeth Green ◽  
Sarah W. Davies ◽  
Mikhail V. Matz ◽  
Mónica Medina
Keyword(s):  
Genetic Diversity ◽  
Local Community ◽  
Coral Species ◽  
Geographic Location ◽  
Amplicon Sequencing ◽  
Coral Host ◽  
Clade B ◽  
Orbicella Faveolata ◽  
Host Genetic ◽  
Physiological Variations

The genetic composition of the resident Symbiodinium endosymbionts appears to strongly modulate the physiological performance of reef-building corals. Here, we used deep amplicon sequencing to quantitatively assess Symbiodinium genetic diversity for the two mountainous star corals, Orbicella franksi and Orbicella faveolata, from two reefs separated by 19 kilometers of deep water. We aimed to determine if symbiont diversity is largely partitioned with respect to coral host species or geographic location. Our results demonstrate that across the two reefs both coral species contained only Symbiodinium identifiable as clade B type B1, represented by five distinct haplotypes. Three of these haplotypes have not been previously described and may be endemic to the Flower Garden Banks. No consistent differences in symbiont composition were detected between the two coral species. However, significant quantitative differences were observed between the east and west banks for two of the five haplotypes. These results highlight the need for consistent molecular genotyping techniques to assess local community assemblages of Symbiodinium-host relationships, which could be largely irrespective of host genetic background. This deep-sequencing approach used to sensitively characterize cryptic genetic diversity of Symbiodinium will potentially contribute to the understanding of physiological variations among coral populations.

scholarly journals High throughput amplicon sequencing to assess within- and between-host genetic diversity in plant viruses

2017 ◽  
Author(s):  
Sylvain Piry ◽  
Catherine Wipf-Scheibel ◽  
Jean-François Martin ◽  
Maxime Galan ◽  
Karine Berthier
Keyword(s):  
Genetic Diversity ◽  
High Throughput ◽  
Variant Calling ◽  
Amplicon Sequencing ◽  
Plant Viruses ◽  
Sequencing Error ◽  
List Type ◽  
Data Generating Process ◽  
Host Genetic ◽  
Robust Variant

AbstractMolecular epidemiology approaches at the landscape scale require to study the genetic diversity of viral populations from numerous hosts and to characterize mixed infections. In such a context, high-throughput amplicon sequencing (HTAS) techniques create interesting opportunities as they allow identifying distinct variants within a same host while simultaneously genotyping a high number of samples. Validating variants produced by HTAS may, however, remain difficult due to biases occurring at different steps of the data-generating process (e.g. environmental contaminations and sequencing error). Here, we focused on Endive necrotic mosaic virus (ENMV), a member of family Potyviridae, genus Potyvirus to develop an HTAS approach and to characterize the genetic diversity at the intra- and inter-host levels from 430 samples collected over an area of 1660 km2 located in south-eastern France. We demonstrated how it is possible, by incorporating various controls in the experimental design and by performing independent sample replicates, to estimate potential biases in HTAS results and to implement an automated and robust variant calling procedure.HighlightsHigh-throughput amplicon sequencing to assess plant virus genetic diversityEstimating bias in high throughput amplicon sequencing resultsAutomated variant calling procedure for robust high throughput amplicon sequencing

Genetic diversity of the extremely rare Habenaria dentata and the rare Habenaria linearifolia (Orchidaceae) in South Korea: implications for population history and conservation

2018 ◽  
Vol 151 (1) ◽  
pp. 48-60
Author(s):  
Mi Yoon Chung ◽  
Hoa Thi Quynh Le ◽  
Sungwon Son ◽  
Huai Zhen Tian ◽  
Myong Gi Chung
Keyword(s):  
Genetic Diversity ◽  
Southern China ◽  
Geographic Location ◽  
Population History ◽  
Population Variation ◽  
Conservation Strategies ◽  
Ancestral Population ◽  
Allozyme Diversity ◽  
Glacial Origin

Background and aims – Since historical events often leave an indelible mark on levels of genetic diversity of plant populations, one may indirectly infer their evolutionary history with the help of current patterns of genetic diversity. The terrestrial orchid Habenaria dentata, an element of warm-temperate/subtropical vegetation, reaches its northernmost limits in the Korean Peninsula, and thus it is extremely rare there. As H. dentata was absent from the Peninsula during the Last Glacial Maximum (LGM), it is likely to be of post-glacial origin having arrived from either a single refugium or multiple refugia. However, its rare, temperate/boreal congener H. linearifolia might have persisted in situ in either macrorefugia or microrefugia on the Peninsula during the LGM.Methods – To test which hypothesis is most appropriate for each species, we investigated levels of allozyme-based (17 loci) genetic diversity and population genetic structure in the two only known populations of H. dentata and in 12 populations of H. linearifolia.Key results – No allozyme diversity was found in H. dentata (He = 0.000), whereas H. linearifolia exhibited low within-population variation (He = 0.060) and high among-population differentiation (FST = 0.237). We found little association between populations in relation to their geographic location; several populations presented individuals belonging to different clusters.Conclusions – Our results suggest that H. dentata likely originated from a single ancestral population (perhaps from southern Japan or southern China) through post-glacial dispersal, whereas H. linearifolia probably survived the LGM in situ in microrefugia situated at low to mid-elevated regions. We further suggest that separate conservation strategies for each species should be employed, given that the two taxa have different ecological and demographic traits and harbour different levels of genetic diversity.

scholarly journals Ocean acidification increases photosynthate translocation in a coral–dinoflagellates symbiosis

2013 ◽  
Vol 10 (1) ◽  
pp. 83-109 ◽  
Author(s):  
P. Tremblay ◽  
M. Fine ◽  
J. F. Maguer ◽  
R. Grover ◽  
C. Ferrier-Pagès
Keyword(s):  
Coral Species ◽  
Total Carbon ◽  
Coral Host ◽  
Climate Change Scenarios ◽  
Symbiotic Association ◽  
Stylophora Pistillata ◽  
Gross Photosynthesis ◽  
Total Percentage ◽  
Carbon Translocation ◽  
Tropical Coral

Abstract. This study has examined the effect of an increased seawater pCO2 on the rates of photosynthesis and carbon translocation in the scleractinian coral species Stylophora pistillata using a new model based on 13C-labelling of the photosynthetic products. Symbiont photosynthesis contributes for a large part of the carbon acquisition in tropical coral species and is therefore an important process that may determine their survival under climate change scenarios. Nubbins of S. pistillata were maintained for six months under two pHs (8.1 and 7.2). Rates of photosynthesis and respiration of the symbiotic association and of isolated symbionts were assessed at each pH. The fate of 13C-photosynthates was then followed in the symbionts and the coral host for 48 h. Nubbins maintained at pH 7.2 presented a lower areal symbiont concentration, lower areal rates of gross photosynthesis, and lower carbon incorporation rates compared to nubbins maintained at pH 8.1, therefore suggesting that the total carbon acquisition was lower in this first set of nubbins. However, the total percentage of carbon translocated to the host, as well as the amount of carbon translocated per symbiont cell was significantly higher under pH 7.2 than under pH 8.1 (70% at pH 7.2 versus 60% at pH 8.1), so that the total amount of photosynthetic carbon received by the coral host was equivalent under both pHs (5.5 to 6.1 μg C cm−2 h−1). Although the carbon budget of the host was unchanged, symbionts acquired less carbon for their own needs (0.6 against 1.8 μg C cm−2 h−1), explaining the overall decrease in symbiont concentration at low pH. In the long-term, this decrease might have important consequences for the survival of corals under an acidification stress.

scholarly journals ENSAMBLES DE MACROALGAS SOBRE SUPERFICIES MUERTAS DE CORALES ESCLERACTINIOS (ANTHOZOA: SCLERACTINIA) EN EL ARRECIFE ORO VERDE, VERACRUZ, MÉXICO

2017 ◽  
Vol 32 (1) ◽  
pp. 11
Author(s):  
IVONNE LUNA ORTEGA ◽  
VICENCIO DE LA CRUZ FRANCISCO
Keyword(s):  
Coral Species ◽  
Taxonomic Composition ◽  
Scleractinian Corals ◽  
Porites Astreoides ◽  
Orbicella Faveolata ◽  
Ordination Analysis ◽  
Species Similarity ◽  
Filamentous Macroalgae ◽  
Algal Assemblages ◽  
Montastraea Cavernosa

Las macroalgas son abundantes en el arrecife Oro Verde, Veracruz pero, hasta ahora, se desconocía su riqueza taxonómica, y se presume que presentan asentamientos en los corales escleractinios hermatípicos. Por ello el presente trabajo investigó qué especies de corales presentaron colonizaciones algales; además, se determinó la composición taxonómica y la similitud de los ensambles de macroalgas entre las especies de corales escleractinios. Se establecieron diez puntos de muestreo de manera sistemática en el arrecife; en cada lugar de estudio se colocó un transecto de banda de 50 x 2 m para localizar y recolectar macroalgas en superficies muertas de corales escleractinios. La frecuencia de aparición de las algas se estimó con base en el total de corales estudiados, así como para cada especie coral. Para explicar similitudes y diferencias significativas de la composición de ensamblajes macroalgales entre especies de corales se aplicaron análisis de similitud y ordenación. Los corales escleractinios con ensambles de algas fueron Siderastrea siderea, Montastraea cavernosa, Pseudodiploria strigosa, Colpophylia natans, Stephanocoenia intersepta, Porites astreoides, Orbicella annularis, Orbicella faveolata. De un total de 100 colonias coralinas revisadas se determinaron 32 especies de macroalgas, las cuales están representadas en tres divisiones, 10 órdenes y 15 familias. Las macroalgas corticadas, foliosas corticadas y filamentosas fueron las más representadas en especies. Las algas de mayor frecuencia sobre los corales masivos fueron Laurencia obtusa, Amphiroa rigida y Caulerpa chemnitzia. Los corales masivos con mayor número de registros de algas fueron S. siderea (9 especies), M. cavernosa (19) y P. strigosa (17). Los ensambles algales en los corales masivos presentaron baja similitud, sin embargo no se detectaron grupos significativamente disimiles. Solamente S. siderea y M. cavernosa son ligeramente parecidos en la composición ficológica. Los resultados sugieren que los corales masivos del arrecife Oro Verde son vulnerables a la colonización de algas, pero es necesario indagar qué condiciones preceden al asentamiento algal.Macroalgal assemblages on dead surfaces of scleractinian corals (Anthozoa: Scleractinia) in the Oro Verde reef, Veracruz, MexicoBenthic macroalgae are abundant in the Oro Verde reef but their taxonomic richness was hitherto unknown and it is presumed to present settlements on the massive corals. For this reason, the present work investigated which species of massive corals show algal colonization. Also, their taxonomic composition was determined, and the similarity of the algal assemblages between species of scleractinian corals was measured. Ten sampling points were systematically established in the reef, where a transect band of 50 x 2 m at each site was placed to locate and collect algae fron the dead surfaces of scleractinian corals. The frequency of occurrence of algae species was estimated based on the total number of coral species studied, as well as on each coral species. Similarity and ordination analysis were applied in order to explain similarities and significant differences of the phycological composition among the coral species. Scleractinian corals with algal assemblages were: Siderastrea siderea, Montastraea cavernosa, Pseudodiploria strigosa, Colpophylia natans, Stephanocoenia intersepta, Porites astreoides, Orbicella annularis, Orbicella faveolata. Thirty-two species of algae were identified from a total of 100 revised coral colonies which are represented in 3 divisions, 10 orders and 15 families. The corticated, foliose corticated and filamentous macroalgae were the most represented species. The most frequent algae on massive corals were Laurencia obtusa, Amphiroa rigida and Caulerpa chemnitzia. Massive corals with higher algal records were S. siderea (9 species), M. cavernosa (19 species) and P. strigosa (17 species). The algal assemblages on the massive corals presented low similarity. However, no significant dissimilar groups were detected. Only S. siderea and M. cavernosa are relatively similar in phycological composition. The results suggest that the massive corals of the Oro Verde reef are vulnerable to the colonization of algae, but it is necessary to investigate the conditions preceding algal settlement.

scholarly journals Divergência genética entre acessos de mentrasto do Estado do Tocantins através de marcadores RAPD

2013 ◽  
Vol 4 (4) ◽  
pp. 290-298
Author(s):  
Elainy Martins Oliveira ◽  
Waldesse Oliveira Junior ◽  
Jaqueline Oliveira ◽  
Henrique Guilhon De Castro
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Geographic Location ◽  
Genetic Distances ◽  
Similarity Coefficients ◽  
Ageratum Conyzoides ◽  
Genetic Studies ◽  
Low Degree ◽  
Medicinal Properties ◽  
Degree Of Association

Ageratum conyzoides (Asteraceae) is known in Brazil for its medicinal properties being mainly used as painkiller and anti-inflammatory. Due to the existence of few genetic studies for this species, this work aimed to characterize the genetic diversity among nine accessions from different sites at Tocantins state, to provide information about its genetic resources. Similarity coefficients obtained varied from 48% to 80%, result of amplification of 102 fragments, of which 72 (70.5%) were polymorphic. Groupment analysis allowed the differentiation in three groups. One of them was distinguished because it presented the highest similarity among all, being composed by ANA and NAT (80% similarity). In general, these data showed there is low degree of association between the geographic location of the accessions and the genetic distances. So, the collected accession ns in Tocantins state presented considerable genetic variability and the efficiency of RAPD markers for such characterization was here proven.

scholarly journals Biogeography and Independent Diversification in the Protist Symbiont Community of Heterotermes tenuis

2021 ◽  
Vol 9 ◽  
Author(s):  
Francesca De Martini ◽  
Nicole L. Coots ◽  
Daniel E. Jasso-Selles ◽  
Jordyn Shevat ◽  
Alison Ravenscraft ◽  
...  
Keyword(s):  
Regional Differences ◽  
Amplicon Sequencing ◽  
Genetic Distances ◽  
Species Level ◽  
Mantel Tests ◽  
Geographical Distances ◽  
Host Phylogeny ◽  
Single Cell Isolation ◽  
Host Genetic ◽  
Protist Species

The eukaryotic microbiome of “lower” termites is highly stable and host-specific. This is due to the mutually obligate nature of the symbiosis and the direct inheritance of protists by proctodeal trophallaxis. However, vertical transmission is occasionally imperfect, resulting in daughter colonies that lack one or more of the expected protist species. This phenomenon could conceivably lead to regional differences in protist community composition within a host species. Here, we have characterized the protist symbiont community of Heterotermes tenuis (Hagen) (Blattodea: Rhinotermitidae) from samples spanning South and Central America. Using light microscopy, single cell isolation, and amplicon sequencing, we report eight species-level protist phylotypes belonging to four genera in the phylum Parabasalia. The diversity and distribution of each phylotype’s 18S rRNA amplicon sequence variants (ASVs) mostly did not correlate with geographical or host genetic distances according to Mantel tests, consistent with the lack of correlation we observed between host genetic and geographical distances. However, the ASV distances of Holomastigotoides Ht3 were significantly correlated with geography while those of Holomastigotoides Ht1 were significantly correlated with host phylogeny. These results suggest mechanisms by which termite-associated protist species may diversify independently of each other and of their hosts, shedding light on the coevolutionary dynamics of this important symbiosis.

scholarly journals Genetic diversity of Collaborative Cross mice controls viral replication, clinical severity and brain pathology induced by Zika virus infection, independently of Oas1b

2019 ◽  
Author(s):  
Caroline Manet ◽  
Etienne Simon-Lorière ◽  
Grégory Jouvion ◽  
David Hardy ◽  
Matthieu Prot ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Viral Load ◽  
Viral Replication ◽  
Clinical Severity ◽  
Brain Pathology ◽  
Zikv Infection ◽  
Infected Cells ◽  
Host Genetic ◽  
Host Genes

ABSTRACTThe explosive spread of Zika virus (ZIKV) has been associated with major variations in severe disease and congenital afflictions among infected populations, suggesting an influence of host genes. We investigated how genome-wide variants could impact susceptibility to ZIKV infection in mice. We first describe that the susceptibility of Ifnar1 knockout mice is largely influenced by their genetic background. We then show that the broad genetic diversity of Collaborative Cross mice, which receptor to type I interferon (IFNAR) was blocked by anti-IFNAR antibody, expressed phenotypes ranging from complete resistance to severe symptoms and death with large variations in the peak and rate of decrease of plasma viral load, in brain viral load, in brain histopathology and in viral replication rate in infected cells. Differences of susceptibility between CC strains were correlated between Zika, Dengue and West Nile viruses. We identified highly susceptible and resistant mouse strains as new models to investigate the mechanisms of human ZIKV disease and other flavivirus infections. Genetic analyses revealed that phenotypic variations are driven by multiple genes with small effects, reflecting the complexity of ZIKV disease susceptibility in human population. Notably, our results rule out a role of the Oas1b gene in the susceptibility to ZIKV. Altogether, this study emphasizes the role of host genes in the pathogeny of ZIKV infection and lays the foundation for further genetic and mechanistic studies.IMPORTANCEIn recent outbreaks, ZIKV has infected millions of people and induced rare but potentially severe complications, including Guillain-Barré syndrome and encephalitis in adults. While several viral sequence variants were proposed to enhance the pathogenicity of ZIKV, the influence of host genetic variants in the clinical heterogeneity remains mostly unexplored. We have addressed this question using a mouse panel which models the genetic diversity of human population and a ZIKV strain from a recent clinical isolate. Through a combination of in vitro and in vivo approaches, we demonstrate that multiple host genetic variants determine viral replication in infected cells, and clinical severity, kinetics of blood viral load and brain pathology in mice. We describe new mouse models expressing high susceptibility or resistance to ZIKV and to other flaviviruses. These models will facilitate the identification and mechanistic characterization of host genes that influence ZIKV pathogenesis.

scholarly journals Causation without correlation: parasite-mediated frequency-dependent selection and infection prevalence

2021 ◽  
Author(s):  
Curtis M Lively ◽  
Julie Xu ◽  
Frida Ben-Ami
Keyword(s):  
Genetic Diversity ◽  
Natural Populations ◽  
Infection Prevalence ◽  
Strong Positive Correlation ◽  
Frequency Dependent ◽  
Frequency Dependent Selection ◽  
Host Diversity ◽  
Host Genetic ◽  
Host Parasite

Parasite-mediated selection is thought to maintain host genetic diversity for resistance. We might thus expect to find a strong positive correlation between host genetic diversity and infection prevalence across natural populations. Here we used computer simulations to examine host-parasite coevolution in 20 simi-isolated clonal populations across a broad range of values for both parasite virulence and parasite fecundity. We found that the correlation between host genetic diversity and infection prevalence can be significantly positive for intermediate values of parasite virulence and fecundity. But the correlation can also be weak and statistically non-significant, even when parasite-mediated frequency-dependent selection is the sole force maintaining host diversity. Hence correlational analyses of field populations, while useful, might underestimate the role of parasites in maintaining host diversity.

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