Faculty Opinions recommendation of Strain-level genomic variation in natural populations of Lebetimonas from an erupting deep-sea volcano.

Abstract Genomic variation in the model plant Arabidopsis thaliana has been extensively used to understand evolutionary processes in natural populations, mainly focusing on single-nucleotide polymorphisms. Conversely, structural variation has been largely ignored in spite of its potential to dramatically affect phenotype. Here, we identify 155,440 indels and structural variants ranging in size from 1 bp to 10 kb, including presence/absence variants (PAVs), inversions, and tandem duplications in 1,301 A. thaliana natural accessions from Morocco, Madeira, Europe, Asia, and North America. We show evidence for strong purifying selection on PAVs in genes, in particular for housekeeping genes and homeobox genes, and we find that PAVs are concentrated in defense-related genes (R-genes, secondary metabolites) and F-box genes. This implies the presence of a “core” genome underlying basic cellular processes and a “flexible” genome that includes genes that may be important in spatially or temporally varying selection. Further, we find an excess of intermediate frequency PAVs in defense response genes in nearly all populations studied, consistent with a history of balancing selection on this class of genes. Finally, we find that PAVs in genes involved in the cold requirement for flowering (vernalization) and drought response are strongly associated with temperature at the sites of origin.

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Population differentiation and structural variation in the genome of Manduca sexta across the United States

10.1101/2020.11.01.364000 ◽

2020 ◽

Author(s):

Andrew J. Mongue ◽

Akito Y. Kawahara

Keyword(s):

Manduca Sexta ◽

Sex Chromosome ◽

Natural Habitat ◽

Natural Populations ◽

The United States ◽

Genomic Variation ◽

The Other ◽

Z Chromosome ◽

Scientific Disciplines ◽

Two Populations

AbstractMany species that are extensively studied in the laboratory are less well characterized in their natural habitat, and laboratory strains represent only a small fraction of the variation in a species’ genome. Here we investigate genomic variation in three natural populations of an agricultural pest and a model insect for many scientific disciplines, the tobacco hornworm (Manduca sexta). We show that hornworms from Arizona, Kansas, and North Carolina are genetically distinct, with Arizona being particularly differentiated from the other two populations. Specifically, two segregating inversions and a potential pseudogene are found only in the Arizona population. One inversion on the Z chromosome may enhance adaptive evolution of the sex chromosome, while the significance of the other, autosomal inversion remains unclear. The pseudogene may be involved in the exploitation of a novel hostplant in Arizona, but functional genetic assays will be required to confirm this hypothesis. Nevertheless, our results reveal undiscovered natural variation and provide useful genomic data for a model insect species.

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Long-read sequencing to interrogate strain-level variation among adherent-invasive Escherichia coli isolated from human intestinal tissue

10.1101/2020.03.10.985440 ◽

2020 ◽

Author(s):

Jeremy Wang ◽

Rachel Bleich ◽

Sandra Zarmer ◽

Janelle Arthur

Keyword(s):

Escherichia Coli ◽

Crohn’S Disease ◽

Crohn's Disease ◽

Pathogenic Bacteria ◽

Genomic Variation ◽

Strain Level ◽

Level Variation ◽

Intestinal Tissue ◽

E Coli ◽

Long Read

AbstractAdherent-invasive Escherichia coli (AIEC) are a pathovar linked to inflammatory bowel diseases (IBD), especially Crohn’s disease, and colorectal cancer. AIEC have no known molecular or genomic markers, but instead are defined by in vitro functional attributes. Futhermore, it is unknown if strains classified as AIEC truly colonize intestinal tissues better than non-AIEC strains. To evaluate strain-level variation among tissue-associated E. coli, we must develop a sequencing approach capable of long reads and with the ability to exclude mammalian DNA. We also must evaluate genomic variation among strains that have demonstrated ability to colonize intestinal tissues. Here we have assembled complete genomes using ultra-long-read nanopore sequencing for a model AIEC strain, NC101, and seven strains isolated from the intestinal mucosa of Crohn’s disease and non-Crohn’s tissues. We show these strains can colonize the intestinal tissue in a Crohn’s disease mouse model and induce varying levels of inflammatory cytokines from cultured macrophages. We demonstrate these strains can be quantified and distinguished in the presence of 99.5% mammalian DNA and from within a fecal population. Analysis of global genomic structure and specific sequence variation within the ribosomal RNA operon provides a framework for efficiently tracking strain-level variation of closely-related E. coli and likely other commensal/pathogenic bacteria impacting intestinal inflammation in mice and IBD patients.

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TfoX-Based Genetic Mapping Identifies Vibrio fischeri Strain-Level Differences and Reveals a Common Lineage of Laboratory Strains

Journal of Bacteriology ◽

10.1128/jb.02347-14 ◽

2015 ◽

Vol 197 (6) ◽

pp. 1065-1074 ◽

Cited By ~ 9

Author(s):

John F. Brooks ◽

Mattias C. Gyllborg ◽

Acadia A. Kocher ◽

Laura E. H. Markey ◽

Mark J. Mandel

Keyword(s):

Genetic Mapping ◽

Vibrio Fischeri ◽

Natural Populations ◽

Culture Conditions ◽

Strain Level ◽

Wild Type ◽

Random Mutation ◽

Genetic Traits ◽

Content Type ◽

Glycerol Utilization

Bacterial strain variation exists in natural populations of bacteria and can be generated experimentally through directed or random mutation. The advent of rapid and cost-efficient whole-genome sequencing has facilitated strain-level genotyping. Even with modern tools, however, it often remains a challenge to map specific traits to individual genetic loci, especially for traits that cannot be selected under culture conditions (e.g., colonization level or pathogenicity). Using a combination of classical and modern approaches, we analyzed strain-level variation inVibrio fischeriand identified the basis by which some strains lack the ability to utilize glycerol as a carbon source. We proceeded to reconstruct the lineage of the commonly usedV. fischerilaboratory strains. Compared to the wild-type ES114 strain, we identify in ES114-L a 9.9-kb deletion with endpoints intadB2andglpF; restoration of the missing portion ofglpFrestores the wild-type phenotype. The widely used strains ESR1, JRM100, and JRM200 contain the same deletion, and ES114-L is likely a previously unrecognized intermediate strain in the construction of many ES114 derivatives. ES114-L does not exhibit a defect in competitive squid colonization but ESR1 does, demonstrating that glycerol utilization is not required for early squid colonization. Our genetic mapping approach capitalizes on the recently discovered chitin-based transformation pathway, which is conserved in theVibrionaceae; therefore, the specific approach used is likely to be useful for mapping genetic traits in otherVibriospecies.

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Genomic Variation Shaped by Environmental and Geographical Factors in Prairie Cordgrass Natural Populations Collected across Its Native Range in the USA

Genes ◽

10.3390/genes12081240 ◽

2021 ◽

Vol 12 (8) ◽

pp. 1240

Author(s):

Jia Guo ◽

Patrick J. Brown ◽

Albert L. Rayburn ◽

Carolyn J. Butts-Wilmsmeyer ◽

Arvid Boe ◽

...

Keyword(s):

Abiotic Stress Tolerance ◽

Natural Populations ◽

Genomic Variation ◽

Biofuel Production ◽

Breeding Value ◽

Grass Species ◽

Gene Pools ◽

Ploidy Levels ◽

Geographical Factors ◽

Prairie Cordgrass

Prairie cordgrass (Spartina pectinata Link) is a native perennial warm-season (C4) grass common in North American prairies. With its high biomass yield and abiotic stress tolerance, there is a high potential of developing prairie cordgrass for conservation practices and as a dedicated bioenergy crop for sustainable cellulosic biofuel production. However, as with many other undomesticated grass species, little information is known about the genetic diversity or population structure of prairie cordgrass natural populations as compared to their ecotypic and geographic adaptation in North America. In this study, we sampled and characterized a total of 96 prairie cordgrass natural populations with 9315 high quality SNPs from a genotyping-by-sequencing (GBS) approach. The natural populations were collected from putative remnant prairie sites throughout the Midwest and Eastern USA, which are the major habitats for prairie cordgrass. Partitioning of genetic variance using SNP marker data revealed significant variance among and within populations. Two potential gene pools were identified as being associated with ploidy levels, geographical separation, and climatic separation. Geographical factors such as longitude and altitude, and environmental factors such as annual temperature, annual precipitation, temperature of the warmest month, precipitation of the wettest month, precipitation of Spring, and precipitation of the wettest month are important in affecting the intraspecific distribution of prairie cordgrass. The divergence of prairie cordgrass natural populations also provides opportunities to increase breeding value of prairie cordgrass as a bioenergy and conservation crop.

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Ancestral Admixture Is the Main Determinant of Global Biodiversity in Fission Yeast

Molecular Biology and Evolution ◽

10.1093/molbev/msz126 ◽

2019 ◽

Vol 36 (9) ◽

pp. 1975-1989 ◽

Cited By ~ 14

Author(s):

Sergio Tusso ◽

Bart P S Nieuwenhuis ◽

Fritz J Sedlazeck ◽

John W Davey ◽

Daniel C Jeffares ◽

...

Keyword(s):

Single Molecule ◽

Phenotypic Variation ◽

Natural Populations ◽

Strand Break ◽

Transgressive Segregation ◽

Genomic Variation ◽

Population History ◽

Structural Genomic ◽

History Of ◽

Reproductive Compatibility

Abstract Mutation and recombination are key evolutionary processes governing phenotypic variation and reproductive isolation. We here demonstrate that biodiversity within all globally known strains of Schizosaccharomyces pombe arose through admixture between two divergent ancestral lineages. Initial hybridization was inferred to have occurred ∼20–60 sexual outcrossing generations ago consistent with recent, human-induced migration at the onset of intensified transcontinental trade. Species-wide heritable phenotypic variation was explained near-exclusively by strain-specific arrangements of alternating ancestry components with evidence for transgressive segregation. Reproductive compatibility between strains was likewise predicted by the degree of shared ancestry. To assess the genetic determinants of ancestry block distribution across the genome, we characterized the type, frequency, and position of structural genomic variation using nanopore and single-molecule real-time sequencing. Despite being associated with double-strand break initiation points, over 800 segregating structural variants exerted overall little influence on the introgression landscape or on reproductive compatibility between strains. In contrast, we found strong ancestry disequilibrium consistent with negative epistatic selection shaping genomic ancestry combinations during the course of hybridization. This study provides a detailed, experimentally tractable example that genomes of natural populations are mosaics reflecting different evolutionary histories. Exploiting genome-wide heterogeneity in the history of ancestral recombination and lineage-specific mutations sheds new light on the population history of S. pombe and highlights the importance of hybridization as a creative force in generating biodiversity.

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Evolution as an ecosystem process: insights from genomics

Genome ◽

10.1139/gen-2017-0044 ◽

2018 ◽

Vol 61 (4) ◽

pp. 298-309 ◽

Cited By ~ 5

Author(s):

Blake Matthews ◽

Rebecca J. Best ◽

Philine G.D. Feulner ◽

Anita Narwani ◽

Romana Limberger

Keyword(s):

Evolutionary Dynamics ◽

Genome Structure ◽

Natural Populations ◽

Genomic Variation ◽

Ecosystem Dynamics ◽

Genomic Diversity ◽

Ecosystem Change ◽

Ecosystem Process ◽

Integrative Research ◽

Genomic Studies

Evolution is a fundamental ecosystem process. The study of genomic variation of organisms can not only improve our understanding of evolutionary processes, but also of contemporary and future ecosystem dynamics. We argue that integrative research between the fields of genomics and ecosystem ecology could generate new insights. Specifically, studies of biodiversity and ecosystem functioning, evolutionary rescue, and eco-evolutionary dynamics could all benefit from information about variation in genome structure and the genetic architecture of traits, whereas genomic studies could benefit from information about the ecological context of evolutionary dynamics. We propose new ways to help link research on functional genomic diversity with (reciprocal) interactions between phenotypic evolution and ecosystem change. Despite numerous challenges, we anticipate that the wealth of genomic data being collected on natural populations will improve our understanding of ecosystems.

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Sardines at a junction: seascape genomics reveals ecological and oceanographic drivers of variation in the NW Mediterranean Sea

10.22541/au.162854295.58977249/v1 ◽

2021 ◽

Author(s):

Aglaia Antoniou ◽

Tereza Manousaki ◽

Francisco Ramírez ◽

Alessia Cariani ◽

Rita Cannas ◽

...

Keyword(s):

Local Adaptation ◽

Dynamic Equilibrium ◽

Natural Populations ◽

Spatial Dimension ◽

Western Mediterranean ◽

Genomic Variation ◽

Entire Genome ◽

Outlier Loci ◽

Genomic Approach ◽

Nw Mediterranean

By evaluating genetic variation across the entire genome, one can address existing questions in a novel way while new can be asked. Such questions include how different local environments influence both adaptive and neutral genomic variation within and among populations, providing insights not only into local adaptation of natural populations, but also into their responses to global change and the exploitation-induced evolution. Here, under a seascape genomic approach, ddRAD genomic data were used along with environmental information to uncover the underlying processes (migration, selection) shaping European sardines (Sardina pilchardus) of the Western Mediterranean and adjacent Atlantic waters. This information can be relevant to the (re)definition of fishery stocks, and their short-term adaptive potential. We found that studied sardine samples form two clusters, detected using both neutral and adaptive (outlier) loci suggesting that natural selection and local adaptation play a key role in driving genetic change among the Atlantic and the Mediterranean sardines. Temperature and especially the trend in the number of days with sea surface temperature (SST) above 19oC was crucial at all levels of population structuring with implications on species’ key biological processes, especially reproduction. Our findings provide evidence for a dynamic equilibrium where population structure is maintained by physical and biological factors under the opposing influences of migration and selection. Given its dynamic nature, such a system postulates a continuous monitoring under a seascape genomic approach that can benefit by incorporating a temporal as well as a more detailed spatial dimension.

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