scholarly journals Contrasting evolutionary genome dynamics between domesticated and wild yeasts

2017 ◽  
Vol 49 (6) ◽  
pp. 913-924 ◽  
Author(s):  
Jia-Xing Yue ◽  
Jing Li ◽  
Louise Aigrain ◽  
Johan Hallin ◽  
Karl Persson ◽  
...  
Keyword(s):  
Evolutionary Dynamics ◽  
Phenotypic Diversity ◽  
Population Level ◽  
Structural Rearrangements ◽  
Reciprocal Translocations ◽  
Genome Dynamics ◽  
Long Read ◽  
Wild Yeasts ◽  
Definition Of ◽  
Genome Assemblies

Abstract Structural rearrangements have long been recognized as an important source of genetic variation, with implications in phenotypic diversity and disease, yet their detailed evolutionary dynamics remain elusive. Here we use long-read sequencing to generate end-to-end genome assemblies for 12 strains representing major subpopulations of the partially domesticated yeast Saccharomyces cerevisiae and its wild relative Saccharomyces paradoxus. These population-level high-quality genomes with comprehensive annotation enable precise definition of chromosomal boundaries between cores and subtelomeres and a high-resolution view of evolutionary genome dynamics. In chromosomal cores, S. paradoxus shows faster accumulation of balanced rearrangements (inversions, reciprocal translocations and transpositions), whereas S. cerevisiae accumulates unbalanced rearrangements (novel insertions, deletions and duplications) more rapidly. In subtelomeres, both species show extensive interchromosomal reshuffling, with a higher tempo in S. cerevisiae. Such striking contrasts between wild and domesticated yeasts are likely to reflect the influence of human activities on structural genome evolution.

scholarly journals Contrasting genome dynamics between domesticated and wild yeasts

2016 ◽  
Author(s):  
Jia-Xing Yue ◽  
Jing Li ◽  
Louise Aigrain ◽  
Johan Hallin ◽  
Karl Persson ◽  
...  
Keyword(s):  
Evolutionary Dynamics ◽  
Phenotypic Diversity ◽  
Accumulation Rate ◽  
Population Level ◽  
Structural Rearrangements ◽  
Chromosome Partitioning ◽  
Long Read ◽  
Definition Of ◽  
Genome Assemblies ◽  
Reference Genomes

AbstractStructural rearrangements have long been recognized as an important source of genetic variation with implications in phenotypic diversity and disease, yet their evolutionary dynamics are difficult to characterize with short-read sequencing. Here, we report long-read sequencing for 12 strains representing major subpopulations of the partially domesticated yeastSaccharomyces cerevisiaeand its wild relativeSaccharomyces paradoxus. Complete genome assemblies and annotations generate population-level reference genomes and allow for the first explicit definition of chromosome partitioning into cores, subtelomeres and chromosome-ends. High-resolution view of structural dynamics uncovers that, in chromosomal cores,S. paradoxusexhibits higher accumulation rate of balanced structural rearrangements (inversions, translocations and transpositions) whereasS. cerevisiaeaccumulates unbalanced rearrangements (large insertions, deletions and duplications) more rapidly. In subtelomeres, recurrent interchromosomal reshuffling was found in both species, with higher rate inS. cerevisiae. Such striking contrasts between wild and domesticated yeasts reveal the influence of human activities on structural genome evolution.

scholarly journals Nanopore sequencing and Hi-C scaffolding provide insight into the evolutionary dynamics of transposable elements and piRNA production in wild strains of Drosophila melanogaster

2019 ◽  
Vol 48 (1) ◽  
pp. 290-303 ◽  
Author(s):  
Christopher E Ellison ◽  
Weihuan Cao
Keyword(s):  
Drosophila Melanogaster ◽  
Evolutionary Dynamics ◽  
De Novo ◽  
Population Level ◽  
Chromosome Length ◽  
Nanopore Sequencing ◽  
Long Reads ◽  
Wild Strains ◽  
Genome Assemblies ◽  
Insight Into

Abstract Illumina sequencing has allowed for population-level surveys of transposable element (TE) polymorphism via split alignment approaches, which has provided important insight into the population dynamics of TEs. However, such approaches are not able to identify insertions of uncharacterized TEs, nor can they assemble the full sequence of inserted elements. Here, we use nanopore sequencing and Hi-C scaffolding to produce de novo genome assemblies for two wild strains of Drosophila melanogaster from the Drosophila Genetic Reference Panel (DGRP). Ovarian piRNA populations and Illumina split-read TE insertion profiles have been previously produced for both strains. We find that nanopore sequencing with Hi-C scaffolding produces highly contiguous, chromosome-length scaffolds, and we identify hundreds of TE insertions that were missed by Illumina-based methods, including a novel micropia-like element that has recently invaded the DGRP population. We also find hundreds of piRNA-producing loci that are specific to each strain. Some of these loci are created by strain-specific TE insertions, while others appear to be epigenetically controlled. Our results suggest that Illumina approaches reveal only a portion of the repetitive sequence landscape of eukaryotic genomes and that population-level resequencing using long reads is likely to provide novel insight into the evolutionary dynamics of repetitive elements.

scholarly journals Rate, spectrum, and evolutionary dynamics of spontaneous epimutations

2015 ◽  
Vol 112 (21) ◽  
pp. 6676-6681 ◽  
Author(s):  
Adriaan van der Graaf ◽  
René Wardenaar ◽  
Drexel A. Neumann ◽  
Aaron Taudt ◽  
Ruth G. Shaw ◽  
...  
Keyword(s):  
Cytosine Methylation ◽  
Evolutionary Dynamics ◽  
Phenotypic Diversity ◽  
Natural Populations ◽  
Population Level ◽  
Genomic Context ◽  
Term Selection ◽  
Comprehensive Picture ◽  
Dynamic Interplay

Stochastic changes in cytosine methylation are a source of heritable epigenetic and phenotypic diversity in plants. Using the model plant Arabidopsis thaliana, we derive robust estimates of the rate at which methylation is spontaneously gained (forward epimutation) or lost (backward epimutation) at individual cytosines and construct a comprehensive picture of the epimutation landscape in this species. We demonstrate that the dynamic interplay between forward and backward epimutations is modulated by genomic context and show that subtle contextual differences have profoundly shaped patterns of methylation diversity in A. thaliana natural populations over evolutionary timescales. Theoretical arguments indicate that the epimutation rates reported here are high enough to rapidly uncouple genetic from epigenetic variation, but low enough for new epialleles to sustain long-term selection responses. Our results provide new insights into methylome evolution and its population-level consequences.

scholarly journals Horizontal transfer and proliferation of Tsu4 in Saccharomyces paradoxus

2018 ◽  
Author(s):  
Casey M. Bergman
Keyword(s):  
Horizontal Transfer ◽  
Sensu Stricto ◽  
South American ◽  
Patchy Distribution ◽  
Reciprocal Translocations ◽  
Saccharomyces Paradoxus ◽  
Long Read ◽  
History Of ◽  
Genome Assemblies ◽  
Donor Species

AbstractBackgroundRecent evidence suggests that horizontal transfer plays a significant role in the evolution of of transposable elements (TEs) in eukaryotes. Many cases of horizontal TE transfer (HTT) been reported in animals and plants, however surprisingly few examples of HTT have been reported in fungi.FindingsHere I report evidence for a novel HTT event in fungi involving Tsu4 in Saccharomyces paradoxus based on (i) high similarity between Tsu4 elements in S. paradoxus and S. uvarum, (ii) a patchy distribution of Tsu4 in S. paradoxus and general absence from its sister species S. cerevisiae, and (iii) discordance between the phylogenetic history of Tsu4 sequences and species in the Saccharomyces sensu stricto group. Available data suggests the HTT event likely occurred somewhere in the Nearctic, Neotropic or Indo-Australian part of the S. paradoxus species range, and that a lineage related to S. uvarum or S. eubayanus was the donor species. The HTT event has led to massive proliferation of Tsu4 in the South American lineage of S. paradoxus, which exhibits partial reproductive isolation with other strains of this species because of multiple reciprocal translocations. Full-length Tsu4 elements are associated with both breakpoints of one of these reciprocal translocations.ConclusionsThis work shows that comprehensive analysis of TE sequences in essentially-complete genome assemblies derived from long-read sequencing provides new opportunities to detect HTT events in fungi and other organisms. This work also provides support for the hypothesis that HTT and subsequent TE proliferation can induce genome rearrangements that contribute to post-zygotic isolation in yeast.

scholarly journals Genotyping of structural variation using PacBio high-fidelity sequencing

2021 ◽  
Author(s):  
Zhiliang Zhang ◽  
Jijin Zhang ◽  
Lipeng Kang ◽  
Xuebing Qiu ◽  
Beirui Niu ◽  
...  
Keyword(s):  
Comprehensive Evaluation ◽  
Phenotypic Diversity ◽  
Population Level ◽  
High Fidelity ◽  
Structural Variations ◽  
Plant Genomes ◽  
Sequencing Technologies ◽  
Long Read ◽  
Low Coverage ◽  
The Impact

Background: Structural variations (SVs) pervade the genome and contribute substantially to the phenotypic diversity of species. However, most SVs were ineffectively assayed because of the complexity of plant genomes and the limitations of sequencing technologies. Recent advancement of third-generation sequencing technologies, particularly the PacBio high-fidelity (HiFi) sequencing, which generates both long and highly accurate reads, offers an unprecedented opportunity to characterize SVs and reveal their functionality. Since HiFi sequencing is new, it is crucial to evaluate HiFi reads in SV detection before applying the technology at scale. Results: We sequenced wheat genomes using HiFi, then conducted a comprehensive evaluation of SV detection using mainstream long-read aligners and SV callers. The results showed the accuracy of SV discovery depends more on aligners rather than callers. For aligners, pbmm2 and NGMLR provided the most accurate results while detecting deletion and insertion, respectively. Likewise, cuteSV and SVIM achieved the best performance across all SV callers. We demonstrated that the combination of the aligners and callers mentioned above is optimal for SV detection. Furthermore, we evaluated the impact of sequencing depth on the accuracy of SV detection. The results showed that low-coverage HiFi sequencing is capable of generating high-quality SV genotyping. Conclusions: This study provides a robust benchmark of SV discovery with HiFi reads, showing the remarkable potential of long-read sequencing to investigate structural variations in plant genomes. The high accuracy SV discovery from low-coverage HiFi sequencing indicates that skim HiFi sequencing is an ideal approach to study structural variations at the population level.

scholarly journals Hapo-G, haplotype-aware polishing of genome assemblies with accurate reads

2021 ◽  
Vol 3 (2) ◽  
Author(s):  
Jean-Marc Aury ◽  
Benjamin Istace
Keyword(s):  
Single Molecule ◽  
Direct Consequence ◽  
High Quality ◽  
Sequencing Errors ◽  
Coding Regions ◽  
Sequencing Technologies ◽  
Long Reads ◽  
Oxford Nanopore ◽  
Long Read ◽  
Genome Assemblies

Abstract Single-molecule sequencing technologies have recently been commercialized by Pacific Biosciences and Oxford Nanopore with the promise of sequencing long DNA fragments (kilobases to megabases order) and then, using efficient algorithms, provide high quality assemblies in terms of contiguity and completeness of repetitive regions. However, the error rate of long-read technologies is higher than that of short-read technologies. This has a direct consequence on the base quality of genome assemblies, particularly in coding regions where sequencing errors can disrupt the coding frame of genes. In the case of diploid genomes, the consensus of a given gene can be a mixture between the two haplotypes and can lead to premature stop codons. Several methods have been developed to polish genome assemblies using short reads and generally, they inspect the nucleotide one by one, and provide a correction for each nucleotide of the input assembly. As a result, these algorithms are not able to properly process diploid genomes and they typically switch from one haplotype to another. Herein we proposed Hapo-G (Haplotype-Aware Polishing Of Genomes), a new algorithm capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes.

scholarly journals Contiguity: Contig adjacency graph construction and visualisation

2015 ◽  
Author(s):  
Mitchell J Sullivan ◽  
Nouri L Ben Zakour ◽  
Brian M Forde ◽  
Mitchell Stanton-Cook ◽  
Scott A Beatson
Keyword(s):  
De Novo ◽  
Reference Sequence ◽  
De Bruijn Graph ◽  
Interactive Software ◽  
Graph Exploration ◽  
Adjacency Graph ◽  
Highly Sensitive ◽  
Long Read ◽  
Genome Assemblies ◽  
Adjacency Graphs

Contiguity is an interactive software for the visualization and manipulation of de novo genome assemblies. Contiguity creates and displays information on contig adjacency which is contextualized by the simultaneous display of a comparison between assembled contigs and reference sequence. Where scaffolders allow unambiguous connections between contigs to be resolved into a single scaffold, Contiguity allows the user to create all potential scaffolds in ambiguous regions of the genome. This enables the resolution of novel sequence or structural variants from the assembly. In addition, Contiguity provides a sequencing and assembly agnostic approach for the creation of contig adjacency graphs. To maximize the number of contig adjacencies determined, Contiguity combines information from read pair mappings, sequence overlap and De Bruijn graph exploration. We demonstrate how highly sensitive graphs can be achieved using this method. Contig adjacency graphs allow the user to visualize potential arrangements of contigs in unresolvable areas of the genome. By combining adjacency information with comparative genomics, Contiguity provides an intuitive approach for exploring and improving sequence assemblies. It is also useful in guiding manual closure of long read sequence assemblies. Contiguity is an open source application, implemented using Python and the Tkinter GUI package that can run on any Unix, OSX and Windows operating system. It has been designed and optimized for bacterial assemblies. Contiguity is available at http://mjsull.github.io/Contiguity .

scholarly journals Perspectives from animal demography on incorporating evolutionary mechanism into plant population dynamics

2018 ◽  
Author(s):  
Maria Paniw
Keyword(s):  
Environmental Change ◽  
Evolutionary Dynamics ◽  
Natural Populations ◽  
Population Level ◽  
Plant Population ◽  
Future Research ◽  
Phenotypic Traits ◽  
Plant Population Dynamics ◽  
Future Research Agenda ◽  
Powerful Approach

AbstractWith a growing number of long-term, individual-based data on natural populations available, it has become increasingly evident that environmental change affects populations through complex, simultaneously occurring demographic and evolutionary processes. Analyses of population-level responses to environmental change must therefore integrate demography and evolution into one coherent framework. Integral projection models (IPMs), which can relate genetic and phenotypic traits to demographic and population-level processes, offer a powerful approach for such integration. However, a rather artificial divide exists in how plant and animal population ecologists use IPMs. Here, I argue for the integration of the two sub-disciplines, particularly focusing on how plant ecologists can diversify their toolset to investigate selection pressures and eco-evolutionary dynamics in plant population models. I provide an overview of approaches that have applied IPMs for eco-evolutionary studies and discuss a potential future research agenda for plant population ecologists. Given an impending extinction crisis, a holistic look at the interacting processes mediating population persistence under environmental change is urgently needed.

scholarly journals The blind choreographer: evolution of social norms and correlated equilibria

2018 ◽  
Author(s):  
Bryce Morsky ◽  
Erol Akçay
Keyword(s):  
Social Norms ◽  
Social Life ◽  
Evolutionary Dynamics ◽  
Population Level ◽  
Nash Bargaining ◽  
Game Of Chicken ◽  
Nash Bargaining Game ◽  
Satisfactory Account ◽  
Environmental Events ◽  
Natural Classes

AbstractSocial norms regulate and coordinate most aspects of human social life, yet they emerge and change as a result of individual behaviours, beliefs, and expectations. A satisfactory account for the evolutionary dynamics of social norms therefore has to link individual beliefs and expectations to population-level dynamics, where individual norms change according to their consequences for individuals. Here we present a new model of evolutionary dynamics of social norms that encompasses this objective and addresses the emergence of social norms. In this model, a norm is a set of behavioural prescriptions and a set of environmental descriptions that describe the expected behaviours of those with whom the norm holder will interact. These pre-scriptions and descriptions are functions of exogenous environmental events. These events have no intrinsic meaning or effect on the payoffs to individuals, yet beliefs/- superstitions regarding them can effectuate coordination. Though a norm's prescriptions and descriptions are dependent upon one another, we show how they emerge from random accumulations of beliefs. We categorize the space of social norms into several natural classes and study the evolutionary competition between these classes of norms. We apply our model to the Game of Chicken and the Nash Bargaining Game. Further, we show how the space of norms and evolutionary stability is dependent upon the correlation structure of the environment, and under which such correlation structures social dilemmas can be ameliorated or exacerbated.

scholarly journals Daptomycin treatment impacts resistance in off-target populations of vancomycin-resistant Enterococcus faecium

PLoS Biology ◽  
2020 ◽  
Vol 18 (12) ◽  
pp. e3000987
Author(s):  
Clare L. Kinnear ◽  
Elsa Hansen ◽  
Valerie J. Morley ◽  
Kevin C. Tracy ◽  
Meghan Forstchen ◽  
...  
Keyword(s):  
Enterococcus Faecium ◽  
Evolutionary Dynamics ◽  
Temporal Dynamics ◽  
Phenotypic Diversity ◽  
Target Selection ◽  
Quantitative Measure ◽  
Target Population ◽  
Control Group ◽  
Antibiotic Exposure ◽  
Hospital System

The antimicrobial resistance crisis has persisted despite broad attempts at intervention. It has been proposed that an important driver of resistance is selection imposed on bacterial populations that are not the intended target of antimicrobial therapy. But to date, there has been limited quantitative measure of the mean and variance of resistance following antibiotic exposure. Here we focus on the important nosocomial pathogen Enterococcus faecium in a hospital system where resistance to daptomycin is evolving despite standard interventions. We hypothesized that the intravenous use of daptomycin generates off-target selection for resistance in transmissible gastrointestinal (carriage) populations of E. faecium. We performed a cohort study in which the daptomycin resistance of E. faecium isolated from rectal swabs from daptomycin-exposed patients was compared to a control group of patients exposed to linezolid, a drug with similar indications. In the daptomycin-exposed group, daptomycin resistance of E. faecium from the off-target population was on average 50% higher than resistance in the control group (n = 428 clones from 22 patients). There was also greater phenotypic diversity in daptomycin resistance within daptomycin-exposed patients. In patients where multiple samples over time were available, a wide variability in temporal dynamics were observed, from long-term maintenance of resistance to rapid return to sensitivity after daptomycin treatment stopped. Sequencing of isolates from a subset of patients supports the argument that selection occurs within patients. Our results demonstrate that off-target gastrointestinal populations rapidly respond to intravenous antibiotic exposure. Focusing on the off-target evolutionary dynamics may offer novel avenues to slow the spread of antibiotic resistance.

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