scholarly journals Population genomics of the facultatively asexual duckweed Spirodela polyrhiza

2019 ◽  
Author(s):  
Eddie Ho ◽  
Magdalena Bartkowska ◽  
Stephen I. Wright ◽  
Aneil Agrawal
Keyword(s):  
Genetic Diversity ◽  
Linkage Disequilibrium ◽  
Population Genomics ◽  
Low Frequency ◽  
Purifying Selection ◽  
Population Level ◽  
Abundant Species ◽  
List Type ◽  
Spirodela Polyrhiza ◽  
Individual Level

SummaryClonal propagation allows some plant species to achieve massive population sizes quickly but also reduces the evolutionary independence of different sites in the genome.We examine genome-wide genetic diversity in Spirodela polyrhiza, a duckweed that reproduces primarily asexually.We find that this geographically widespread and numerically abundant species has very low levels of genetic diversity. Diversity at nonsynonymous sites relative to synonymous sites is high, suggesting that purifying selection is weak. A potential explanation for this observation is that a very low frequency of sex renders selection in effective. However, there is a pronounced decay in linkage disequilibrium over 40 kb, suggesting that though sex may be rare at the individual level it is not too infrequent at the population level. In addition, neutral diversity is affected by the physical proximity of selected sites, which would be unexpected if sex was exceedingly rare at the population level.The amount of genetic mixing as assessed by the decay in linkage disequilibrium is not dissimilar from selfing species such as Arabidopsis thaliana, yet selection appears to be much less effective in duckweed. We discuss alternative explanations for the signature of weak purifying selection.

scholarly journals The population genomics of transposable element activation in the highly repressive genome of an agricultural pathogen

2020 ◽  
Author(s):  
Danilo Pereira ◽  
Ursula Oggenfuss ◽  
Bruce A. McDonald ◽  
Daniel Croll
Keyword(s):  
Genetic Diversity ◽  
Transposable Elements ◽  
Evolutionary Dynamics ◽  
Population Genomics ◽  
Sequence Data ◽  
Demographic History ◽  
Purifying Selection ◽  
Population Level ◽  
Wide Range ◽  
Genome Analyses

AbstractThe activity of transposable elements (TEs) can be an important driver of genetic diversity with TE-mediated mutations having a wide range of fitness consequences. To avoid deleterious effects of TE activity, some fungi evolved highly sophisticated genomic defences to reduce TE proliferation across the genome. Repeat-induced point (RIP) mutations is a fungal-specific TE defence mechanism efficiently targeting duplicated sequences. The rapid accumulation of RIP mutations is expected to deactivate TEs over the course of a few generations. The evolutionary dynamics of TEs at the population level in a species with highly repressive genome defences is poorly understood. Here, we analyze 366 whole-genome sequences of Parastagonospora nodorum, a fungal pathogen of wheat with efficient RIP. A global population genomics analysis revealed high levels of genetic diversity and signs of frequent sexual recombination. Contrary to expectations for a species with RIP, we identified recent TE activity in multiple populations. The TE composition and copy numbers showed little divergence among global populations regardless of the demographic history. Miniature inverted-repeat transposable elements (MITEs) and terminal repeat retrotransposons in miniature (TRIMs) were largely underlying recent intra-species TE expansions. We inferred RIP footprints in individual TE families and found that recently active, high-copy TEs have possibly evaded genomic defences. We find no evidence that recent positive selection acted on TE-mediated mutations rather that purifying selection maintained new TE insertions at low insertion frequencies in populations. Our findings highlight the complex evolutionary equilibria established by the joint action of TE activity, selection and genomic repression.Data SummaryAll Illumina sequence data is available from the NCBI SRA BioProject numbers PRJNA606320, PRJNA398070 and PRJNA476481 (https://www.ncbi.nlm.nih.gov/bioproject). The Methods and Supplementary Figures S1-S11 and Supplementary Tables S1-S4 provide all information on strain locations and outcomes of genome analyses.

scholarly journals Population genomics of transposable element activation in the highly repressive genome of an agricultural pathogen

2021 ◽  
Vol 7 (8) ◽  
Author(s):  
Danilo Pereira ◽  
Ursula Oggenfuss ◽  
Bruce A. McDonald ◽  
Daniel Croll
Keyword(s):  
Genetic Diversity ◽  
Transposable Elements ◽  
Evolutionary Dynamics ◽  
Population Genomics ◽  
Demographic History ◽  
Purifying Selection ◽  
Population Level ◽  
Copy Numbers ◽  
Wide Range ◽  
Parastagonospora Nodorum

The activity of transposable elements (TEs) can be an important driver of genetic diversity with TE-mediated mutations having a wide range of fitness consequences. To avoid deleterious effects of TE activity, some fungi have evolved highly sophisticated genomic defences to reduce TE proliferation across the genome. Repeat-induced point mutation (RIP) is a fungal-specific TE defence mechanism efficiently targeting duplicated sequences. The rapid accumulation of RIPs is expected to deactivate TEs over the course of a few generations. The evolutionary dynamics of TEs at the population level in a species with highly repressive genome defences is poorly understood. Here, we analyse 366 whole-genome sequences of Parastagonospora nodorum, a fungal pathogen of wheat with efficient RIP. A global population genomics analysis revealed high levels of genetic diversity and signs of frequent sexual recombination. Contrary to expectations for a species with RIP, we identified recent TE activity in multiple populations. The TE composition and copy numbers showed little divergence among global populations regardless of the demographic history. Miniature inverted-repeat transposable elements (MITEs) and terminal repeat retrotransposons in miniature (TRIMs) were largely underlying recent intra-species TE expansions. We inferred RIP footprints in individual TE families and found that recently active, high-copy TEs have possibly evaded genomic defences. We find no evidence that recent positive selection acted on TE-mediated mutations rather that purifying selection maintained new TE insertions at low insertion frequencies in populations. Our findings highlight the complex evolutionary equilibria established by the joint action of TE activity, selection and genomic repression.

scholarly journals Population genomics of Mycobacterium tuberculosis in the Inuit

2015 ◽  
Vol 112 (44) ◽  
pp. 13609-13614 ◽  
Author(s):  
Robyn S. Lee ◽  
Nicolas Radomski ◽  
Jean-Francois Proulx ◽  
Ines Levade ◽  
B. Jesse Shapiro ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mycobacterium Tuberculosis ◽  
Population Genomics ◽  
Purifying Selection ◽  
Synonymous Substitution ◽  
Nonsynonymous Snps ◽  
Recent Common Ancestor ◽  
Nucleotide Polymorphisms ◽  
Most Recent Common Ancestor ◽  
Bacterial Genetic

Nunavik, Québec suffers from epidemic tuberculosis (TB), with an incidence 50-fold higher than the Canadian average. Molecular studies in this region have documented limited bacterial genetic diversity among Mycobacterium tuberculosis isolates, consistent with a founder strain and/or ongoing spread. We have used whole-genome sequencing on 163 M. tuberculosis isolates from 11 geographically isolated villages to provide a high-resolution portrait of bacterial genetic diversity in this setting. All isolates were lineage 4 (Euro-American), with two sublineages present (major, n = 153; minor, n = 10). Among major sublineage isolates, there was a median of 46 pairwise single-nucleotide polymorphisms (SNPs), and the most recent common ancestor (MRCA) was in the early 20th century. Pairs of isolates within a village had significantly fewer SNPs than pairs from different villages (median: 6 vs. 47, P < 0.00005), indicating that most transmission occurs within villages. There was an excess of nonsynonymous SNPs after the diversification of M. tuberculosis within Nunavik: The ratio of nonsynonymous to synonymous substitution rates (dN/dS) was 0.534 before the MRCA but 0.777 subsequently (P = 0.010). Nonsynonymous SNPs were detected across all gene categories, arguing against positive selection and toward genetic drift with relaxation of purifying selection. Supporting the latter possibility, 28 genes were partially or completely deleted since the MRCA, including genes previously reported to be essential for M. tuberculosis growth. Our findings indicate that the epidemiologic success of M. tuberculosis in this region is more likely due to an environment conducive to TB transmission than a particularly well-adapted strain.

scholarly journals Neural Tracking of Sound Rhythms Correlates With Diagnosis, Severity, and Prognosis of Disorders of Consciousness

2021 ◽  
Vol 15 ◽  
Author(s):  
Chuan Xu ◽  
Jiajie Zou ◽  
Fangping He ◽  
Xinrui Wen ◽  
Jingqi Li ◽  
...  
Keyword(s):  
Low Frequency ◽  
Population Level ◽  
Disorders Of Consciousness ◽  
Family Counseling ◽  
Individual Level ◽  
Rehabilitation Programs ◽  
Diagnosis And Prognosis ◽  
The Individual ◽  
Effective Diagnosis ◽  
Potential Tool

Effective diagnosis and prognosis of patients with disorders of consciousness (DOC) provides a basis for family counseling, decision-making, and the design of rehabilitation programs. However, effective and objective bedside evaluation is a challenging problem. In this study, we explored electroencephalography (EEG) response tracking sound rhythms as potential neural markers for DOC evaluation. We analyzed the responses to natural speech and tones modulated at 2 and 41 Hz. At the population level, patients with positive outcomes (DOC-P) showed higher cortical synchronization to modulated tones at 41 Hz compared with patients with negative outcomes (DOC-N). At the individual level, phase coherence to modulated tones at 41 Hz was significantly correlated with Coma Recovery Scale-Revised (CRS-R) and Glasgow Outcome Scale-Extended (GOS-E) scores. Furthermore, SVM classifiers, trained using phase coherences in higher frequency bands or combination of the low frequency aSSR and speech tracking responses, performed very well in diagnosis and prognosis of DOC. These findings show that EEG response to auditory rhythms is a potential tool for diagnosis, severity, and prognosis of DOC.

scholarly journals Linkage disequilibrium patterns, population structure and diversity analysis in a worldwide durum wheat collection including Argentinian genotypes

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Pablo Federico Roncallo ◽  
Adelina Olga Larsen ◽  
Ana Laura Achilli ◽  
Carolina Saint Pierre ◽  
Cristian Andrés Gallo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Linkage Disequilibrium ◽  
Durum Wheat ◽  
Triticum Turgidum ◽  
Snp Array ◽  
Low Frequency ◽  
Germplasm Collection ◽  
Climate Change Scenarios ◽  
Allelic Variants

Abstract Background Durum wheat (Triticum turgidum L. ssp. durum Desf. Husn) is the main staple crop used to make pasta products worldwide. Under the current climate change scenarios, genetic variability within a crop plays a crucial role in the successful release of new varieties with high yields and wide crop adaptation. In this study we evaluated a durum wheat collection consisting of 197 genotypes that mainly comprised a historical set of Argentinian germplasm but also included worldwide accessions. Results We assessed the genetic diversity, population structure and linkage disequilibrium (LD) patterns in this collection using a 35 K SNP array. The level of polymorphism was considered, taking account of the frequent and rare allelic variants. A total of 1547 polymorphic SNPs was located within annotated genes. Genetic diversity in the germplasm collection increased slightly from 1915 to 2010. However, a reduction in genetic diversity using SNPs with rare allelic variants was observed after 1979. However, larger numbers of rare private alleles were observed in the 2000–2009 period, indicating that a high reservoir of rare alleles is still present among the recent germplasm in a very low frequency. The percentage of pairwise loci in LD in the durum genome was low (13.4%) in our collection. Overall LD and the high (r2 > 0.7) or complete (r2 = 1) LD presented different patterns in the chromosomes. The LD increased over three main breeding periods (1915–1979, 1980–1999 and 2000–2020). Conclusions Our results suggest that breeding and selection have impacted differently on the A and B genomes, particularly on chromosome 6A and 2A. The collection was structured in five sub-populations and modern Argentinian accessions (cluster Q4) which were clearly differentiated. Our study contributes to the understanding of the complexity of Argentinian durum wheat germplasm and to derive future breeding strategies enhancing the use of genetic diversity in a more efficient and targeted way.

scholarly journals Dioecy Is Associated with High Genetic Diversity and Adaptation Rates in the Plant Genus Silene

2020 ◽  
Author(s):  
Aline Muyle ◽  
Hélène Martin ◽  
Niklaus Zemp ◽  
Maéva Mollion ◽  
Sophie Gallina ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Genomics ◽  
Extinction Risk ◽  
Population Level ◽  
High Genetic Diversity ◽  
Geographic Ranges ◽  
Sexual Systems ◽  
Dead End ◽  
The Dead ◽  
Genus Silene

Abstract About 15,000 angiosperm species (∼6%) have separate sexes, a phenomenon known as dioecy. Why dioecious taxa are so rare is still an open question. Early work reported lower species richness in dioecious compared with nondioecious sister clades, raising the hypothesis that dioecy may be an evolutionary dead-end. This hypothesis has been recently challenged by macroevolutionary analyses that detected no or even positive effect of dioecy on diversification. However, the possible genetic consequences of dioecy at the population level, which could drive the long-term fate of dioecious lineages, have not been tested so far. Here, we used a population genomics approach in the Silene genus to look for possible effects of dioecy, especially for potential evidence of evolutionary handicaps of dioecy underlying the dead-end hypothesis. We collected individual-based RNA-seq data from several populations in 13 closely related species with different sexual systems: seven dioecious, three hermaphroditic, and three gynodioecious species. We show that dioecy is associated with increased genetic diversity, as well as higher selection efficacy both against deleterious mutations and for beneficial mutations. The results hold after controlling for phylogenetic inertia, differences in species census population sizes and geographic ranges. We conclude that dioecious Silene species neither show signs of increased mutational load nor genetic evidence for extinction risk. We discuss these observations in the light of the possible demographic differences between dioecious and self-compatible hermaphroditic species and how this could be related to alternatives to the dead-end hypothesis to explain the rarity of dioecy.

scholarly journals Review: Balancing Selection for Deleterious Alleles in Livestock

2021 ◽  
Vol 12 ◽  
Author(s):  
Martijn F. L. Derks ◽  
Marije Steensma
Keyword(s):  
Balancing Selection ◽  
Low Frequency ◽  
Purifying Selection ◽  
Population Level ◽  
Selection Strategy ◽  
Loss Of Function ◽  
Deleterious Alleles ◽  
Functional Consequences ◽  
Selection For ◽  
The Impact

Harmful alleles can be under balancing selection due to an interplay of artificial selection for the variant in heterozygotes and purifying selection against the variant in homozygotes. These pleiotropic variants can remain at moderate to high frequency expressing an advantage for favorable traits in heterozygotes, while harmful in homozygotes. The impact on the population and selection strength depends on the consequence of the variant both in heterozygotes and homozygotes. The deleterious phenotype expressed in homozygotes can range from early lethality to a slightly lower fitness in the population. In this review, we explore a range of causative variants under balancing selection including loss-of-function variation (i.e., frameshift, stop-gained variants) and regulatory variation (affecting gene expression). We report that harmful alleles often affect orthologous genes in different species, often influencing analogous traits. The recent discoveries are mainly driven by the increasing genomic and phenotypic resources in livestock populations. However, the low frequency and sometimes subtle effects in homozygotes prevent accurate mapping of such pleiotropic variants, which requires novel strategies to discover. After discovery, the selection strategy for deleterious variants under balancing selection is under debate, as variants can contribute to the heterosis effect in crossbred animals in various livestock species, compensating for the loss in purebred animals. Nevertheless, gene-assisted selection is a useful tool to decrease the frequency of the harmful allele in the population, if desired. Together, this review marks various deleterious variants under balancing selection and describing the functional consequences at the molecular, phenotypic, and population level, providing a resource for further study.

scholarly journals Recombination and Gene Conversion in a 170-kb Genomic Region of Arabidopsis thaliana

Genetics ◽  
2002 ◽  
Vol 161 (3) ◽  
pp. 1269-1278 ◽  
Author(s):  
Bernhard Haubold ◽  
Jürgen Kroymann ◽  
Andreas Ratzka ◽  
Thomas Mitchell-Olds ◽  
Thomas Wiehe
Keyword(s):  
Genetic Diversity ◽  
Arabidopsis Thaliana ◽  
Linkage Disequilibrium ◽  
Gene Conversion ◽  
Genomic Sequence ◽  
Genomic Region ◽  
Resistance To Herbivory ◽  
Linkage Disequilibria ◽  
Coalescent Simulations ◽  
The Mean

Abstract Arabidopsis thaliana is a highly selfing plant that nevertheless appears to undergo substantial recombination. To reconcile its selfing habit with the observations of recombination, we have sampled the genetic diversity of A. thaliana at 14 loci of ~500 bp each, spread across 170 kb of genomic sequence centered on a QTL for resistance to herbivory. A total of 170 of the 6321 nucleotides surveyed were polymorphic, with 169 being biallelic. The mean silent genetic diversity (πs) varied between 0.001 and 0.03. Pairwise linkage disequilibria between the polymorphisms were negatively correlated with distance, although this effect vanished when only pairs of polymorphisms with four haplotypes were included in the analysis. The absence of a consistent negative correlation between distance and linkage disequilibrium indicated that gene conversion might have played an important role in distributing genetic diversity throughout the region. We tested this by coalescent simulations and estimate that up to 90% of recombination is due to gene conversion.

scholarly journals Metagenomic analyses and genetic diversity of Tomato leaf curl Arusha virus affecting tomato plants in Kenya

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Edith Khamonya Avedi ◽  
Adedapo Olutola Adediji ◽  
Dora Chao Kilalo ◽  
Florence Mmogi Olubayo ◽  
Isaac Macharia ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Selection Pressure ◽  
Management Strategies ◽  
Purifying Selection ◽  
Tomato Leaf ◽  
Amino Acid Sequences ◽  
Virus Population ◽  
Tomato Production ◽  
Tomato Leaf Curl ◽  
Leaf Curl

Abstract Background Tomato production is threatened worldwide by the occurrence of begomoviruses which are associated with tomato leaf curl diseases. There is little information on the molecular properties of tomato begomoviruses in Kenya, hence we investigated the population and genetic diversity of begomoviruses associated with tomato leaf curl in Kenya. Methods Tomato leaf samples with virus-like symptoms were obtained from farmers’ field across the country in 2018 and Illumina sequencing undertaken to determine the genetic diversity of associated begomoviruses. Additionally, the occurrence of selection pressure and recombinant isolates within the population were also evaluated. Results Twelve complete begomovirus genomes were obtained from our samples with an average coverage of 99.9%. The sequences showed 95.7–99.7% identity among each other and 95.9–98.9% similarities with a Tomato leaf curl virus Arusha virus (ToLCArV) isolate from Tanzania. Analysis of amino acid sequences showed the highest identities in the regions coding for the coat protein gene (98.5–100%) within the isolates, and 97.1–100% identity with the C4 gene of ToLCArV. Phylogenetic algorithms clustered all Kenyan isolates in the same clades with ToLCArV, thus confirming the isolates to be a variant of the virus. There was no evidence of recombination within our isolates. Estimation of selection pressure within the virus population revealed the occurrence of negative or purifying selection in five out of the six coding regions of the sequences. Conclusions The begomovirus associated with tomato leaf curl diseases of tomato in Kenya is a variant of ToLCArV, possibly originating from Tanzania. There is low genetic diversity within the virus population and this information is useful in the development of appropriate management strategies for the disease in the country.

scholarly journals Blood Pressure Trajectories Across the Life Course

2021 ◽  
Vol 34 (3) ◽  
pp. 234-241
Author(s):  
Norrina B Allen ◽  
Sadiya S Khan
Keyword(s):  
Blood Pressure ◽  
Measurement Errors ◽  
Clinical Care ◽  
Population Level ◽  
Cumulative Exposure ◽  
Older Adulthood ◽  
Individual Level ◽  
The Life Course ◽  
Level Group ◽  
Improve Health

Abstract High blood pressure (BP) is a strong modifiable risk factor for cardiovascular disease (CVD). Longitudinal BP patterns themselves may reflect the burden of risk and vascular damage due to prolonged cumulative exposure to high BP levels. Current studies have begun to characterize BP patterns as a trajectory over an individual’s lifetime. These BP trajectories take into account the absolute BP levels as well as the slope of BP changes throughout the lifetime thus incorporating longitudinal BP patterns into a single metric. Methodologic issues that need to be considered when examining BP trajectories include individual-level vs. population-level group-based modeling, use of distinct but complementary BP metrics (systolic, diastolic, mean arterial, mid, and pulse pressure), and potential for measurement errors related to varied settings, devices, and number of readings utilized. There appear to be very specific developmental periods during which divergent BP trajectories may emerge, specifically adolescence, the pregnancy period, and older adulthood. Lifetime BP trajectories are impacted by both individual-level and community-level factors and have been associated with incident hypertension, multimorbidity (CVD, renal disease, cognitive impairment), and overall life expectancy. Key unanswered questions remain around the additive predictive value of BP trajectories, intergenerational contributions to BP patterns (in utero BP exposure), and potential genetic drivers of BP patterns. The next phase in understanding BP trajectories needs to focus on how best to incorporate this knowledge into clinical care to reduce the burden of hypertensive-related outcomes and improve health equity.

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