How ancient forest fragmentation and riparian connectivity generate high levels of genetic diversity in a micro-endemic Malagasy tree

AbstractUnderstanding landscape changes is central to predicting evolutionary trajectories and defining conservation practices. While human-driven deforestation is intense throughout Madagascar, exception in areas like the Loky-Manambato region (North) raises questions. This region also harbors a rich and endemic flora, whose evolutionary origin remains poorly understood.We assessed the genetic diversity of an endangered micro-endemic Malagasy olive species (Noronhia spinifolia) to better understand the vegetation dynamic in the Loky-Manambato region and its influence on past evolutionary processes. We characterized 72 individuals sampled across eight forests through nuclear and mitochondrial restriction associated sequencing data (RADseq) and chloroplast microsatellites (cpSSR).Extremely high genetic diversity was revealed in the three genomic compartments (chloroplast h = 0.99, mitochondrial h = 0.85, and nuclear HO = 0.07-0.20). Combined population and landscape genetics analyses indicate that N. spinifolia diversity is best explained by the current forest cover (R2 = 0.90), highlighting a long-standing forest fragmentation in the region. Our results further suggest a predominant role of forestdwelling organisms in mediating pollen and seed dispersals.This sustains a major and long-term role of riparian corridors in maintaining connectivity across those antique mosaic-habitats, calling for the study of organismal interactions that promote gene flow.

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Population structure of Cydia pomonella granulovirus isolates revealed by quantitative analysis of genetic variation

Virus Evolution ◽

10.1093/ve/veaa073 ◽

2020 ◽

Author(s):

Jiangbin Fan ◽

Johannes A Jehle ◽

Jörg T Wennmann

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Insect Pests ◽

Consensus Sequence ◽

Cydia Pomonella ◽

Next Generation Sequencing Data ◽

Snp Analysis ◽

Sequencing Data ◽

High Genetic Diversity ◽

Cydia Pomonella Granulovirus

Abstract Genetic diversity of viruses is driven by genomic mutations and selection through its host, resulting in differences in virulence as well as host responses. For baculoviruses, which are naturally occurring pathogens of insects and which are frequently sprayed on hundred thousands to millions of hectares as biocontrol agents of insect pests, the phenomenon of virus–host co-evolution is of particular scientific interest and economic importance because high virulence of baculovirus products is essential and emergence of host resistance needs to be avoided as much as possible. In the present study, the population structure of twenty isolates of the Cydia pomonella granulovirus (CpGV), including twelve isolates from different geographic origins and eight commercial formulations, were studied on the basis of next-generation sequencing data and by analyzing the distribution of single nucleotide polymorphisms (SNPs). An entirely consensus sequence-free quantitative SNP analysis was applied for the identification of 753 variant SNP sites being specific for single as well as groups of CpGV isolates. Based on the quantitative SNP analysis, homogenous, heterogenous as well as mixed isolates were identified and their proportions of genotypes were deciphered, revealing a high genetic diversity of CpGV isolates from around the world. Based on hierarchical clustering on principal components (HCPC), six distinct isolate/group clusters were identified, representing the proposed main phylogenetic lineages of CpGV but comprising full genome information from virus mixtures. The relative location of different isolates in HCPC reflected the proportion of variable compositions of different genotypes. The established methods provide novel analysis tools to decipher the molecular complexity of genotype mixtures in baculovirus isolates, thus depicting the population structure of baculovirus isolates in a more adequate form than consensus based analyses.

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High genetic diversity, distant phylogenetic relationships and intraspecies recombination events among natural populations of Yam mosaic virus: a contribution to understanding potyvirus evolution

Microbiology ◽

10.1099/0022-1317-81-1-243 ◽

2000 ◽

Vol 81 (1) ◽

pp. 243-255 ◽

Cited By ~ 76

Author(s):

M. Bousalem ◽

E. J. P. Douzery ◽

D. Fargette

Keyword(s):

Genetic Diversity ◽

Mosaic Virus ◽

Statistical Tests ◽

Phylogenetic Analyses ◽

Natural Populations ◽

High Genetic Diversity ◽

Single Clade ◽

Cultivated Species ◽

Selection Of

To evaluate the genetic diversity and understand the evolution of Yam mosaic virus (YMV), a highly destructive pathogen of yam (Dioscorea sp.), sequencing was carried out of the C-terminal part of the replicase (NIb), the coat protein (CP) and the 3′-untranslated region (3′-UTR) of 27 YMV isolates collected from the three main cultivated species (Dioscorea alata, the complex Dioscorea cayenensis–Dioscorea rotundata and Dioscorea trifida). YMV showed the most variable CP relative to eight other potyviruses. This high variability was structured into nine distant molecular groups, as revealed by phylogenetic analyses and validated by assessment of the molecular evolutionary noise. No correlation was observed between the CP and 3′-UTR diversities and phylogenies. The most diversified and divergent groups included isolates from Africa. The remaining groups clustered in a single clade and a geographical distinction between isolates from the Caribbean, South America and Africa was observed. The role of the host in the selection of particular isolates was illustrated by the case of a divergent cultivar from Burkina Faso. Phylogenetic topological incongruence and complementary statistical tests highlighted the fact that recombination events, with single and multiple crossover sites, largely contributed to the evolution of YMV. We hypothesise an African origin of YMV from the yam complex D. cayenensis–D. rotundata, followed by independent transfers to D. alata and D. trifida during virus evolution.

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Genetics of Host Protection against Helicobacter pylori Infections

International Journal of Molecular Sciences ◽

10.3390/ijms22063192 ◽

2021 ◽

Vol 22 (6) ◽

pp. 3192 ◽

Cited By ~ 1

Author(s):

Rosanna Capparelli ◽

Domenico Iannelli

Keyword(s):

Genetic Diversity ◽

Helicobacter Pylori ◽

T Regulatory Cells ◽

Protective Role ◽

Disease Genes ◽

Nucleotide Polymorphisms ◽

High Genetic Diversity ◽

Host Protection ◽

High Level

This narrative review discusses the genetics of protection against Helicobacter pylori (Hp) infection. After a brief overview of the importance of studying infectious disease genes, we provide a detailed account of the properties of Hp, with a view to those relevant for our topic. Hp displays a very high level of genetic diversity, detectable even between single colonies from the same patient. The high genetic diversity of Hp can be evaded by stratifying patients according to the infecting Hp strain. This approach enhances the power and replication of the study. Scanning for single nucleotide polymorphisms is generally not successful since genes rarely work alone. We suggest selecting genes to study from among members of the same family, which are therefore inclined to cooperate. Further, extending the analysis to the metabolism would significantly enhance the power of the study. This combined approach displays the protective role of MyD88, TIRAP, and IL1RL1 against Hp infection. Finally, several studies in humans have demonstrated that the blood T cell levels are under the genetic control of the CD39+ T regulatory cells (TREGS).

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Analysis of Segregation Ratio Distortion and Linkage Mapping in Two Switchgrass F1 Populations: Lowland-lowland and Lowland-upland Using Genotyping by Sequencing Data

10.21203/rs.2.15334/v1 ◽

2019 ◽

Author(s):

Rasyidah Razar ◽

Katrien Devos ◽

Ali Missaoui

Keyword(s):

Genetic Diversity ◽

Segregation Distortion ◽

Biomass Yield ◽

Genotyping By Sequencing ◽

Segregation Ratio ◽

Genetic Maps ◽

Linkage Maps ◽

Sequencing Data ◽

Target Number ◽

High Genetic Diversity

Abstract Background: Switchgrass is an emerging bioenergy crop due to its perennial nature, high biomass yield, and ability to grow in marginal land. The high genetic diversity in switchgrass germplasm can be exploited to capture favorable traits that increase the range of adaptation and biomass yield. Genetic diversity can be explored using single nucleotide polymorphisms (SNPs) that next-generation sequencing has made possible for high-throughput genotyping. We used genotyping-by-sequencing (GBS) of genomic fragments resulting from two methylation sensitive restriction enzymes: PstI and MspI . Two bi-parental F1 populations were developed from crosses between lowland B6 and lowland AP13 (AB population), and lowland B6 with upland VS16 genotypes (BV population), with a target number of 298 progenies in each population. Pseudo-testcross strategy was adopted to perform linkage analysis in these populations that are segregating for winter dormancy using single dose markers (SDA): heterozygous in one parent and homozygous in the other parent. We compared the amount of polymorphisms between the two crosses and examined the pattern of segregation distortion based on the SNPs data generated. Results: Two genetic maps were generated for each population, with 2772 markers in AB and 3766 markers in BV. The higher number of markers in the BV population was expected for since the parents originated from different ecotypes and verified to have the highest genetic distance. More segregation distortion was observed in markers located in the telomeric regions where more genes reside. More markers from the AB population exhibited segregation distortion compared to the BV, and the proportion of heterozygous alleles were significantly higher than homozygous alleles in AB population. The linkage maps showed strong collinearity with P. virgatum V5.1 reference genome with a very minimal number of markers originating from different chromosomes. Conclusion: Understanding the extent of segregation distortion in switchgrass crosses is important for the correct inclusion of markers based on their segregation ratio when constructing a linkage map. Switchgrass linkage maps should be a useful resource to dissect beneficial biomass traits linked to SNP markers.

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The genomic signature of wild-to-crop introgression during the domestication of scarlet runner bean (Phaseolus coccineus L.)

10.1101/2021.02.03.429668 ◽

2021 ◽

Author(s):

Azalea Guerra-García ◽

Idalia C. Rojas-Barrera ◽

Jeffrey Ross-Ibarra ◽

Roberto Papa ◽

Daniel Piñero

Keyword(s):

Genetic Diversity ◽

Demographic History ◽

Population Expansion ◽

Wild Relatives ◽

Small Scale ◽

List Type ◽

Sequencing Data ◽

North West ◽

Runner Bean ◽

Scarlet Runner Bean

SummaryThe scarlet runner bean is an open-pollinated legume from the highlands of Mesoamerica that is cultivated in small-scale agriculture for its dry seeds and immature pods. Demographic bottlenecks associated with domestication might reduce genetic diversity and facilitate the accumulation of deleterious mutations. Conversely, introgression from wild relatives could be a source of variation.Using Genotyping by Sequencing data (79,286 SNVs) from 237 cultivated and wild samples, we evaluated the demographic history of traditional varieties from different regions of Mexico and looked for evidence of introgression between sympatric wild and cultivated populations.Traditional varieties have high levels of diversity, even though there is evidence of a severe initial genetic bottleneck, followed by a population expansion. Introgression from wild to domesticated populations was detected, but not in the opposite direction. This asymmetric introgression might contribute to the recovery of genetic variation and it has occurred at different times: constantly in the center of Mexico; recently in the North West; and anciently in the South.Several factors are acting together to increase and maintain genetic diversity in P. coccineus cultivars, such as demographic expansion and introgression. Wild relatives represent a valuable genetic resource and have played a key role in scarlet runner bean evolution via introgression into traditional varieties.

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Dogs and Cats: Reservoirs for Highly Diverse Campylobacter jejuni and a Potential Source of Human Exposure

Animals ◽

10.3390/ani10050838 ◽

2020 ◽

Vol 10 (5) ◽

pp. 838

Author(s):

Amandine Thépault ◽

Valérie Rose ◽

Marilyne Queguiner ◽

Marianne Chemaly ◽

Katell Rivoal

Keyword(s):

Genetic Diversity ◽

Campylobacter Jejuni ◽

Human Exposure ◽

High Genetic Diversity ◽

Thermophilic Campylobacter ◽

Potential Link ◽

Genomic Characterization ◽

Partial Overlap ◽

Campylobacter Spp

Assessing the carriage of Campylobacter in animal reservoirs is essential to better understand Campylobacter epidemiology. Here, we evaluated the prevalence of thermophilic Campylobacter spp. in dogs and cats, hereafter defined as pets, and characterized Campylobacter jejuni (C. jejuni) isolates to assess their genetic diversity and their potential link with isolates from other animals or human cases. During a 6-month period, 304 feces samples were collected from pets. A significantly higher prevalence of thermophilic Campylobacter spp. was found in dogs compared with cats, as well as in dogs ≤ 1-year-old compared with older dogs. C. jejuni was the predominant species found in pets, and its genomic characterization revealed a high genetic diversity. Genotypes comparison with previously characterized isolates revealed a partial overlap between C. jejuni isolates from pets, chicken, cattle, and clinical cases. This overlap suggests the potential role of livestock and humans in pets’ exposure to Campylobacter, or vice versa. The isolation of pets’ specific profiles may suggest the existence of other sources of pet contamination or imply that pets may constitute a reservoir for Campylobacter. Because of the proximity between humans and pets, along with their frequent carriage of C. jejuni, human exposure to Campylobacter from pets can be more important than previously thought.

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Evolution and Genetic Diversity of Primate Cytomegaloviruses

Microorganisms ◽

10.3390/microorganisms8050624 ◽

2020 ◽

Vol 8 (5) ◽

pp. 624

Author(s):

Rachele Cagliani ◽

Diego Forni ◽

Alessandra Mozzi ◽

Manuela Sironi

Keyword(s):

Genetic Diversity ◽

Opportunistic Pathogen ◽

Clinical Samples ◽

High Genetic Diversity ◽

Viral Genetics ◽

Technological Advances ◽

Similar Genomic Organization ◽

Insight Into ◽

Core Genes

Cytomegaloviruses (CMVs) infect many mammals, including humans and non–human primates (NHPs). Human cytomegalovirus (HCMV) is an important opportunistic pathogen among immunocompromised patients and represents the most common infectious cause of birth defects. HCMV possesses a large genome and very high genetic diversity. NHP–infecting CMVs share with HCMV a similar genomic organization and coding content, as well as the course of viral infection. Recent technological advances have allowed the sequencing of several HCMV strains from clinical samples and provided insight into the diversity of NHP–infecting CMVs. The emerging picture indicates that, with the exclusion of core genes (genes that have orthologs in all herpesviruses), CMV genomes are relatively plastic and diverse in terms of gene content, both at the inter– and at the intra–species level. Such variability most likely underlies the strict species–specificity of these viruses, as well as their ability to persist lifelong and with relatively little damage to their hosts. However, core genes, despite their strong conservation, also represented a target of adaptive evolution and subtle changes in their coding sequence contributed to CMV adaptation to different hosts. Indubitably, important knowledge gaps remain, the most relevant of which concerns the role of viral genetics in HCMV–associated human disease.

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Species distribution, antibiotic resistance and virulence traits in canine and feline enterococci in Tunisia

Acta Veterinaria Hungarica ◽

10.1556/004.2017.018 ◽

2017 ◽

Vol 65 (2) ◽

pp. 173-184 ◽

Cited By ~ 7

Author(s):

Leila Ben Said ◽

Raoudha Dziri ◽

Nadia Sassi ◽

Carmen Lozano ◽

Karim Ben Slama ◽

...

Keyword(s):

Genetic Diversity ◽

Gel Electrophoresis ◽

Virulence Genes ◽

Pulsed Field Gel Electrophoresis ◽

High Genetic Diversity ◽

Antibiotic Resistant ◽

Faecal Samples ◽

Household Environment ◽

High Level

In order to investigate the possible role of dogs and cats in the carriage and potential dissemination of resistant enterococci, seventy faecal samples from dogs and cats were tested for enterococci. Fifty-eight enterococci were recovered. Isolates were identified as Enterococcus faecium (n = 31) and E. faecalis (n = 14) E. durans (n = 6), E. casseliflavus (n = 2), E. hirae and E. gallinarum (2 isolates each). Enterococcal isolates showed resistance to ciprofloxacin (n = 35), erythromycin (n = 31), tetracycline (n = 25), kanamycin (n = 15), streptomycin (n = 13), pristinamycin (n = 11), gentamicin (n = 10), chloramphenicol (n = 8), and linezolid (n = 6). The gene erm(B) was detected in 22 out of 31 erythromycin-resistant enterococci. All tetracycline-resistant enterococci carried tet(M) and/or tet(L) genes. The gene aac(6′)-Ie-aph(2″)-Ia was identified in five of high-level gentamicin-resistant isolates, the genes aph(3′)-IIIa and/or aac(6′)-Ie-aph(2″)-Ia in eleven high-level kanamycin-resistant isolates and the gene ant(6)-Ia in eleven high-level streptomycin-resistant isolates. Only one strain harboured cat(A) gene, and five strains contained vat(E) or vat(D) genes. Virulence genes gel(E) (21 strains), esp (11 strains) and cylA/cylB (5 strains) were detected. High genetic diversity was demonstrated among E. faecium isolates by pulsed-field gel electrophoresis (PFGE). Dogs and cats can be carriers of antibiotic-resistant enterococci in their faeces that could shed into the household environment.

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Detection of Multiple Variants of Grapevine Fanleaf Virus in Single Xiphinema index Nematodes

Viruses ◽

10.3390/v11121139 ◽

2019 ◽

Vol 11 (12) ◽

pp. 1139

Author(s):

Shahinez Garcia ◽

Jean-Michel Hily ◽

Véronique Komar ◽

Claude Gertz ◽

Gérard Demangeat ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Bottleneck ◽

Grapevine Fanleaf Virus ◽

High Genetic Diversity ◽

Genomic Rnas ◽

Xiphinema Index ◽

Virus Diversity ◽

Positive Sense ◽

Multiple Variants

Grapevine fanleaf virus (GFLV) is responsible for a widespread disease in vineyards worldwide. Its genome is composed of two single-stranded positive-sense RNAs, which both show a high genetic diversity. The virus is transmitted from grapevine to grapevine by the ectoparasitic nematode Xiphinema index. Grapevines in diseased vineyards are often infected by multiple genetic variants of GFLV but no information is available on the molecular composition of virus variants retained in X. index following nematodes feeding on roots. In this work, aviruliferous X. index were fed on three naturally GFLV-infected grapevines for which the virome was characterized by RNAseq. Six RNA-1 and four RNA-2 molecules were assembled segregating into four and three distinct phylogenetic clades of RNA-1 and RNA-2, respectively. After 19 months of rearing, single and pools of 30 X. index tested positive for GFLV. Additionally, either pooled or single X. index carried multiple variants of the two GFLV genomic RNAs. However, the full viral genetic diversity found in the leaves of infected grapevines was not detected in viruliferous nematodes, indicating a genetic bottleneck. Our results provide new insights into the complexity of GFLV populations and the putative role of X. index as reservoirs of virus diversity.

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