scholarly journals Epigenetic patterns associated with an ascidian invasion: a comparison of closely related clades in their native and introduced ranges

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Nicola A. Hawes ◽  
Achira Amadoru ◽  
Louis A. Tremblay ◽  
Xavier Pochon ◽  
Brendon Dunphy ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Dna Methylation ◽  
Phylogenetic Analyses ◽  
Native Range ◽  
Didemnum Vexillum ◽  
Colonial Ascidian ◽  
Introduced Populations ◽  
Clade B ◽  
Low Levels ◽  
Native And Introduced Ranges

Abstract Environmentally induced epigenetic modifications have been proposed as one mechanism underlying rapid adaptive evolution of invasive species. Didemnum vexillum is an invasive colonial ascidian that has established in many coastal waters worldwide. Phylogenetic analyses have revealed that D. vexillum populations consist of two distinct clades; clade B appears to be restricted to the native range (Japan), whereas clade A is found in many regions throughout the world, including New Zealand. The spread of D. vexillum clade A suggests that it might be intrinsically more invasive than clade B, despite low levels of genetic diversity compared to populations from the native region. This study investigated whether D. vexillum clade A exhibits epigenetic signatures (specifically differences in DNA methylation) associated with invasiveness. Global DNA methylation patterns were significantly different between introduced clade A colonies, and both clades A and B in the native range. Introduced colonies also showed a significant reduction in DNA methylation levels, which could be a mechanism for increasing phenotypic plasticity. High levels of DNA methylation diversity were maintained in the introduced population, despite reduced levels of genetic diversity, which may allow invasive populations to respond quickly to changes in new environments. Epigenetic changes induced during the invasion process could provide a means for rapid adaptation despite low levels of genetic variation in introduced populations.

scholarly journals Effects of temperature and salinity stress on DNA methylation in a highly invasive marine invertebrate, the colonial ascidian Didemnum vexillum

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5003 ◽  
Author(s):  
Nicola A. Hawes ◽  
Louis A. Tremblay ◽  
Xavier Pochon ◽  
Brendon Dunphy ◽  
Andrew E. Fidler ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Invasive Species ◽  
Marine Invertebrate ◽  
Salinity Gradient ◽  
Survival Rates ◽  
Global Dna Methylation ◽  
Didemnum Vexillum ◽  
Colonial Ascidian ◽  
Growth And Survival ◽  
Increasing Temperature

Environmentally induced epigenetic changes may contribute to phenotypic plasticity, increase adaptive potential in changing environments, and play a key role in the establishment and spread of invasive species in new habitats. In this study, we used methylation-sensitive amplified polymorphism (MSAP) to assess environmentally induced DNA methylation changes in a globally invasive clonal ascidian, Didemnum vexillum. We tested the effect of increasing temperature (19, 25 and 27 °C) and decreasing salinity (34, 32, 30, 28 and 26 practical salinity units (PSU)) on global DNA methylation, growth and survival rates. Exposure to 27 °C resulted in significant changes in DNA methylation over time. Growth also decreased in colonies exposed to high temperatures, suggesting they were under thermal stress. In contrast, no differences in growth nor DNA methylation patterns were observed in colonies exposed to a decreasing salinity gradient, potentially due to prior adaptation. The results of this study show that environmental stress can induce significant global DNA methylation changes in an invasive marine invertebrate on very rapid timescales, and that this response varies depending on the type, magnitude, and duration of the stressor. Changes in genomic DNA methylation and the rate of growth may act to ‘buy survival time’ under stressful conditions, expanding the distribution limits of this globally invasive species.

scholarly journals Genetic diversity and phylogenetic analyses of 11 cohorts of captive rhesus macaques from Chinese zoos

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6957
Author(s):  
Qian Su ◽  
Yongfang Yao ◽  
Qin Zhao ◽  
Diyan Li ◽  
Meng Xie ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Rhesus Macaques ◽  
Phylogenetic Analyses ◽  
Genetic Management ◽  
Southeastern China ◽  
Mitochondrial Dna Control Region ◽  
Clade B ◽  
In Captivity ◽  
High Level ◽  
Major Haplogroups

Rhesus macaques are raised in almost every Chinese zoo due to their likeability and ease in feeding; however, little is yet known about the genetic diversity of rhesus macaques in captivity. In this study, a 475-base pair nucleotide sequence of the mitochondrial DNA control region was obtained from the fecal DNA of 210 rhesus macaque individuals in captivity. A total of 69 haplotypes were defined, 51 of which (73.9%) were newly identified. Of all haplotypes, seven were shared between two zoos, and 62 haplotypes (89.8%) appeared only in a specific zoo, indicating a low rate of animal exchange between Chinese zoos. Moreover, there was a relatively high level of genetic diversity among the rhesus macaques (Hd = 0.0623 ± 0.0009, Pi = 0.979 ± 0.003, K = 28.974). Phylogenetic analysis demonstrated that all haplotypes were clearly clustered into two major haplogroups—Clade A (southeastern China) and Clade B (southwestern China)—and each major clade contained several small sub-haplogroups. The haplotypes of rhesus macaques from the same zoo were not clustered together for the most part, but scattered among several subclades on the phylogenetic tree. This indicates that the rhesus macaques in most Chinese zoos may originat from a diverse collection of geographical areas. Our results demonstrate that zoos play an important role in the conservation of the genetic diversity of rhesus macaques, as well as provide useful information on the genetic management of captive rhesus macaques.

scholarly journals High fusibility and chimera prevalence in an invasive colonial ascidian

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Maria Casso ◽  
Davide Tagliapietra ◽  
Xavier Turon ◽  
Marta Pascual
Keyword(s):  
Genetic Diversity ◽  
Whole Genome Amplification ◽  
Genetic Relatedness ◽  
Genotyping By Sequencing ◽  
Whole Genome ◽  
Didemnum Vexillum ◽  
Colonial Ascidian ◽  
Mediterranean Populations ◽  
Colony Fusion ◽  
Modular Organisms

Abstract The formation of chimeric entities through colony fusion has been hypothesized to favour colonisation success and resilience in modular organisms. In particular, it can play an important role in promoting the invasiveness of introduced species. We studied prevalence of chimerism and performed fusion experiments in Mediterranean populations of the worldwide invasive colonial ascidian Didemnum vexillum. We analysed single zooids by whole genome amplification and genotyping-by-sequencing and obtained genotypic information for more than 2,000 loci per individual. In the prevalence study, we analysed nine colonies and identified that 44% of them were chimeric, composed of 2–3 different genotypes. In the fusion experiment 15 intra- and 30 intercolony pairs were assayed but one or both fragments regressed and died in ~45% of the pairs. Among those that survived for the length of the experiment (30 d), 100% isogeneic and 31% allogeneic pairs fused. Fusion was unlinked to global genetic relatedness since the genetic distance between fused or non-fused intercolony pairs did not differ significantly. We could not detect any locus directly involved in allorecognition, but we cannot preclude the existence of a histocompatibility mechanism. We conclude that chimerism occurs frequently in D. vexillum and may be an important factor to enhance genetic diversity and promote its successful expansion.

Genetic Diversity and Drug Resistance of HIV-1 CRF55_01B in Guangdong, China

2020 ◽  
Vol 18 (3) ◽  
pp. 210-218
Author(s):  
Guolong Yu ◽  
Yan Li ◽  
Xuhe Huang ◽  
Pingping Zhou ◽  
Jin Yan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Drug Resistance ◽  
Reverse Transcriptase ◽  
Phylogenetic Analyses ◽  
Resistance Mutations ◽  
Protease Inhibition ◽  
Subtype B ◽  
Primary Drug Resistance ◽  
Hiv 1 ◽  
Primary Drug

Background: HIV-1 CRF55_01B was first reported in 2013. At present, no report is available regarding this new clade’s polymorphisms in its functionally critical regions protease and reverse transcriptase. Objective: To identify the diversity difference in protease and reverse transcriptase between CRF55_01B and its parental clades CRF01_AE and subtype B; and to investigate CRF55_01B’s drug resistance mutations associated with the protease inhibition and reverse transcriptase inhibition. Methods: HIV-1 RNA was extracted from plasma derived from a MSM population. The reverse transcription and nested PCR amplification were performed following our in-house PCR procedure. Genotyping and drug resistant-associated mutations and polymorphisms were identified based on polygenetic analyses and the usage of the HIV Drug Resistance Database, respectively. Results: A total of 9.24 % of the identified CRF55_01B sequences bear the primary drug resistance. CRF55_01B contains polymorphisms I13I/V, G16E and E35D that differ from those in CRF01_AE. Among the 11 polymorphisms in the RT region, seven were statistically different from CRF01_AE’s. Another three polymorphisms, R211K (98.3%), F214L (98.3%), and V245A/E (98.3 %.), were identified in the RT region and they all were statistically different with that of the subtype B. The V179E/D mutation, responsible for 100% potential low-level drug resistance, was found in all CRF55_01B sequences. Lastly, the phylogenetic analyses demonstrated 18 distinct clusters that account for 35% of the samples. Conclusions: CRF55_01B’s pol has different genetic diversity comparing to its counterpart in CRF55_01B’s parental clades. CRF55_01B has a high primary drug resistance presence and the V179E/D mutation may confer more vulnerability to drug resistance.

scholarly journals Genetic Diversity of Enteric Viruses in Children under Five Years Old in Gabon

Viruses ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 545
Author(s):  
Gédéon Prince Manouana ◽  
Paul Alvyn Nguema-Moure ◽  
Mirabeau Mbong Ngwese ◽  
C.-Thomas Bock ◽  
Peter G. Kremsner ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Preventive Measures ◽  
Phylogenetic Analyses ◽  
Enteric Viruses ◽  
Study Cohort ◽  
Viral Agent ◽  
A Genome ◽  
Stool Samples ◽  
Pcr Techniques ◽  
High Diversity

Enteric viruses are the leading cause of diarrhea in children globally. Identifying viral agents and understanding their genetic diversity could help to develop effective preventive measures. This study aimed to determine the detection rate and genetic diversity of four enteric viruses in Gabonese children aged below five years. Stool samples from children <5 years with (n = 177) and without (n = 67) diarrhea were collected from April 2018 to November 2019. Norovirus, astrovirus, sapovirus, and aichivirus A were identified using PCR techniques followed by sequencing and phylogenetic analyses. At least one viral agent was identified in 23.2% and 14.9% of the symptomatic and asymptomatic participants, respectively. Norovirus (14.7%) and astrovirus (7.3%) were the most prevalent in children with diarrhea, whereas in the healthy group norovirus (9%) followed by the first reported aichivirus A in Gabon (6%) were predominant. The predominant norovirus genogroup was GII, consisting mostly of genotype GII.P31-GII.4 Sydney. Phylogenetic analysis of the 3CD region of the aichivirus A genome revealed the presence of two genotypes (A and C) in the study cohort. Astrovirus and sapovirus showed a high diversity, with five different astrovirus genotypes and four sapovirus genotypes, respectively. Our findings give new insights into the circulation and genetic diversity of enteric viruses in Gabonese children.

scholarly journals Enteroviruses in Respiratory Samples from Paediatric Patients of a Tertiary Care Hospital in Germany

Viruses ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 882
Author(s):  
Susanne Baertl ◽  
Corinna Pietsch ◽  
Melanie Maier ◽  
Mario Hönemann ◽  
Sandra Bergs ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analyses ◽  
Tertiary Care ◽  
Oxygen Demand ◽  
Care Hospital ◽  
Paediatric Patients ◽  
Enterovirus A71 ◽  
Coxsackievirus A6 ◽  
Enterovirus D68 ◽  
Tract Infections

Enteroviruses are associated with various diseases accompanied by rare but severe complications. In recent years, outbreaks of enterovirus D68 and enterovirus A71 associated with severe respiratory infections and neurological complications have been reported worldwide. Since information on molecular epidemiology in respiratory samples is still limited, the genetic diversity of enteroviruses was retrospectively analysed over a 4-year period (2013–2016) in respiratory samples from paediatric patients. Partial viral major capsid protein gene (VP1) sequences were determined for genotyping. Enteroviruses were detected in 255 (6.1%) of 4187 specimens. Phylogenetic analyses of 233 (91.4%) strains revealed 25 different genotypes distributed to Enterovirus A (39.1%), Enterovirus B (34.3%), and Enterovirus D (26.6%). The most frequently detected genotypes were enterovirus D68 (26.6%), coxsackievirus A6 (15.9%), and enterovirus A71 (7.3%). Enterovirus D68 detections were associated with lower respiratory tract infections and increased oxygen demand. Meningitis/encephalitis and other neurological symptoms were related to enterovirus A71, while coxsackievirus A6 was associated with upper respiratory diseases. Prematurity turned out as a potential risk factor for increased oxygen demand during enterovirus infections. The detailed analysis of epidemiological and clinical data contributes to the non-polio enterovirus surveillance in Europe and showed high and rapidly changing genetic diversity of circulating enteroviruses, including different enterovirus D68 variants.

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