scholarly journals Selective ancestral sorting and de novo evolution in the agricultural invasion of Amaranthus tuberculatus

2021 ◽  
Author(s):  
Julia M. Kreiner ◽  
Amalia Caballero ◽  
Stephen I. Wright ◽  
John R. Stinchcombe
Keyword(s):  
De Novo ◽  
Sequence Data ◽  
Sex Differentiation ◽  
Common Garden ◽  
Whole Genome Sequence ◽  
Secondary Contact ◽  
Natural Environments ◽  
Relative Role ◽  
Standing Variation ◽  
Amaranthus Tuberculatus

The relative role of hybridization, de novo evolution, and standing variation in weed adaptation to agricultural environments is largely unknown. In Amaranthus tuberculatus, a widespread North American agricultural weed, adaptation is likely influenced by recent secondary contact and admixture of two previously isolated subspecies. We characterized the extent of adaptation and phenotypic differentiation accompanying the spread of A. tuberculatus into agricultural environments and the contribution of subspecies divergence. We generated phenotypic and whole-genome sequence data from a manipulative common garden experiment, using paired samples from natural and agricultural populations. We found strong latitudinal, longitudinal, and sex differentiation in phenotypes, and subtle differences among agricultural and natural environments that were further resolved with ancestry-based inference. The transition into agricultural environments has favoured southwestern var. rudis ancestry that leads to higher biomass and environment-specific phenotypes: increased biomass and earlier flowering under reduced water availability, and reduced plasticity in fitness-related traits. We also detected de novo adaptation to agricultural habitats independent of ancestry effects, including marginally higher biomass and later flowering in agricultural populations, and a time to germination home advantage. Therefore, the invasion of A. tuberculatus into agricultural environments has drawn on adaptive variation across multiple timescales—through both preadaptation via the preferential sorting of var. rudis ancestry and de novo local adaptation.

scholarly journals The Genome Sequence of the Anthelmintic-Susceptible New Zealand Haemonchus contortus

2019 ◽  
Vol 11 (7) ◽  
pp. 1965-1970 ◽  
Author(s):  
Nikola Palevich ◽  
Paul H Maclean ◽  
Abdul Baten ◽  
Richard W Scott ◽  
David M Leathwick
Keyword(s):  
Genome Sequence ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Sequence Data ◽  
Animal Health ◽  
Draft Genome ◽  
Whole Genome Sequence ◽  
Parasitic Nematodes ◽  
Hybrid Assembly ◽  
Genetic Structures

Abstract Internal parasitic nematodes are a global animal health issue causing drastic losses in livestock. Here, we report a H. contortus representative draft genome to serve as a genetic resource to the scientific community and support future experimental research of molecular mechanisms in related parasites. A de novo hybrid assembly was generated from PCR-free whole genome sequence data, resulting in a chromosome-level assembly that is 465 Mb in size encoding 22,341 genes. The genome sequence presented here is consistent with the genome architecture of the existing Haemonchus species and is a valuable resource for future studies regarding population genetic structures of parasitic nematodes. Additionally, comparative pan-genomics with other species of economically important parasitic nematodes have revealed highly open genomes and strong collinearities within the phylum Nematoda.

Characterizing mutagenic effects of recombination through a sequence-level genetic map

Science ◽  
2019 ◽  
Vol 363 (6425) ◽  
pp. eaau1043 ◽  
Author(s):  
Bjarni V. Halldorsson ◽  
Gunnar Palsson ◽  
Olafur A. Stefansson ◽  
Hakon Jonsson ◽  
Marteinn T. Hardarson ◽  
...  
Keyword(s):  
Genetic Map ◽  
Meiotic Recombination ◽  
De Novo ◽  
Sequence Data ◽  
Mutagenic Effect ◽  
Whole Genome Sequence ◽  
De Novo Mutation ◽  
Base Pairs ◽  
Males And Females ◽  
Mutagenic Effects

Genetic diversity arises from recombination and de novo mutation (DNM). Using a combination of microarray genotype and whole-genome sequence data on parent-child pairs, we identified 4,531,535 crossover recombinations and 200,435 DNMs. The resulting genetic map has a resolution of 682 base pairs. Crossovers exhibit a mutagenic effect, with overrepresentation of DNMs within 1 kilobase of crossovers in males and females. In females, a higher mutation rate is observed up to 40 kilobases from crossovers, particularly for complex crossovers, which increase with maternal age. We identified 35 loci associated with the recombination rate or the location of crossovers, demonstrating extensive genetic control of meiotic recombination, and our results highlight genes linked to the formation of the synaptonemal complex as determinants of crossovers.

scholarly journals Genome-wide patterns of divergence and introgression after secondary contact between Pungitius sticklebacks

2020 ◽  
Vol 375 (1806) ◽  
pp. 20190548 ◽  
Author(s):  
Yo Y. Yamasaki ◽  
Ryo Kakioka ◽  
Hiroshi Takahashi ◽  
Atsushi Toyoda ◽  
Atsushi J. Nagano ◽  
...  
Keyword(s):  
Gene Flow ◽  
Reproductive Isolation ◽  
Sequence Data ◽  
Continuous Process ◽  
Sympatric Species ◽  
Whole Genome Sequence ◽  
Secondary Contact ◽  
Pungitius Pungitius ◽  
Hybrid Male ◽  
Differential Adaptation

Speciation is a continuous process. Although it is known that differential adaptation can initiate divergence even in the face of gene flow, we know relatively little about the mechanisms driving complete reproductive isolation and the genomic patterns of divergence and introgression at the later stages of speciation. Sticklebacks contain many pairs of sympatric species differing in levels of reproductive isolation and divergence history. Nevertheless, most previous studies have focused on young species pairs. Here, we investigated two sympatric stickleback species, Pungitius pungitius and P. sinensis , whose habitats overlap in eastern Hokkaido; these species show hybrid male sterility, suggesting that they may be at a late stage of speciation. Our demographic analysis using whole-genome sequence data showed that these species split 1.73 Ma and came into secondary contact 37 200 years ago after a period of allopatry. This long period of allopatry might have promoted the evolution of intrinsic incompatibility. Although we detected on-going gene flow and signatures of introgression, overall genomic divergence was high, with considerable heterogeneity across the genome. The heterogeneity was significantly associated with variation in recombination rate. This sympatric pair provides new avenues to investigate the late stages of the stickleback speciation continuum. This article is part of the theme issue ‘Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers’.

scholarly journals Plasmid Profiler: Comparative Analysis of Plasmid Content in WGS Data

2017 ◽  
Author(s):  
Adrian Zetner ◽  
Jennifer Cabral ◽  
Laura Mataseje ◽  
Natalie C Knox ◽  
Philip Mabon ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
De Novo ◽  
Sequence Data ◽  
Health Agency ◽  
R Package ◽  
Whole Genome Sequence ◽  
Reference Sequence ◽  
Supplementary Information ◽  
Plasmid Content ◽  
Link Type

AbstractSummaryComparative analysis of bacterial plasmids from whole genome sequence (WGS) data generated from short read sequencing is challenging. This is due to the difficulty in identifying contigs harbouring plasmid sequence data, and further difficulty in assembling such contigs into a full plasmid. As such, few software programs and bioinformatics pipelines exist to perform comprehensive comparative analyses of plasmids within and amongst sequenced isolates. To address this gap, we have developed Plasmid Profiler, a pipeline to perform comparative plasmid content analysis without the need forde novoassembly. The pipeline is designed to rapidly identify plasmid sequences by mapping reads to a plasmid reference sequence database. Predicted plasmid sequences are then annotated with their incompatibility group, if known. The pipeline allows users to query plasmids for genes or regions of interest and visualize results as an interactive heat map.Availability and ImplementationPlasmid Profiler is freely available software released under the Apache 2.0 open source software license. A stand-alone version of the entire Plasmid Profiler pipeline is available as a Docker container athttps://hub.docker.com/r/phacnml/plasmidprofiler_0_1_6/.The conda recipe for the Plasmid R package is available at:https://anaconda.org/bioconda/r-plasmidprofilerThe custom Plasmid Profiler R package is also available as a CRAN package athttps://cran.r-project.org/web/packages/Plasmidprofiler/index.htmlGalaxy tools associated with the pipeline are available as a Galaxy tool suite athttps://toolshed.g2.bx.psu.edu/repository?repository_id=55e082200d16a504The source code is available at:https://github.com/phac-nml/plasmidprofilerThe Galaxy implementation is available at:https://github.com/phac-nml/plasmidprofiler-galaxyContactEmail:[email protected]: National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, CanadaSupplementary informationDocumentation:http://plasmid-profiler.readthedocs.io/en/latest/

scholarly journals PopDel identifies medium-size deletions simultaneously in tens of thousands of genomes

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Sebastian Niehus ◽  
Hákon Jónsson ◽  
Janina Schönberger ◽  
Eythór Björnsson ◽  
Doruk Beyter ◽  
...  
Keyword(s):  
Large Scale ◽  
De Novo ◽  
Sequence Data ◽  
Whole Genome Sequence ◽  
Medium Size ◽  
Phenotypic Traits ◽  
Structural Variants ◽  
High Confidence ◽  
Sequencing Studies ◽  
Genomic Structural Variants

AbstractThousands of genomic structural variants (SVs) segregate in the human population and can impact phenotypic traits and diseases. Their identification in whole-genome sequence data of large cohorts is a major computational challenge. Most current approaches identify SVs in single genomes and afterwards merge the identified variants into a joint call set across many genomes. We describe the approach PopDel, which directly identifies deletions of about 500 to at least 10,000 bp in length in data of many genomes jointly, eliminating the need for subsequent variant merging. PopDel scales to tens of thousands of genomes as we demonstrate in evaluations on up to 49,962 genomes. We show that PopDel reliably reports common, rare and de novo deletions. On genomes with available high-confidence reference call sets PopDel shows excellent recall and precision. Genotype inheritance patterns in up to 6794 trios indicate that genotypes predicted by PopDel are more reliable than those of previous SV callers. Furthermore, PopDel’s running time is competitive with the fastest tested previous tools. The demonstrated scalability and accuracy of PopDel enables routine scans for deletions in large-scale sequencing studies.

scholarly journals De Novo Gene Evolution of Antifreeze Glycoproteins in Codfishes Revealed by Whole Genome Sequence Data

2017 ◽  
Vol 35 (3) ◽  
pp. 593-606 ◽  
Author(s):  
Helle Tessand Baalsrud ◽  
Ole Kristian Tørresen ◽  
Monica Hongrø Solbakken ◽  
Walter Salzburger ◽  
Reinhold Hanel ◽  
...  
Keyword(s):  
Genome Sequence ◽  
De Novo ◽  
Gene Evolution ◽  
Sequence Data ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Antifreeze Glycoproteins ◽  
Genome Sequence Data ◽  
De Novo Gene

scholarly journals PopDel identifies medium-size deletions jointly in tens of thousands of genomes

2019 ◽  
Author(s):  
Sebastian Niehus ◽  
Hákon Jónsson ◽  
Janina Schönberger ◽  
Eythór Björnsson ◽  
Doruk Beyter ◽  
...  
Keyword(s):  
Large Scale ◽  
De Novo ◽  
Sequence Data ◽  
Whole Genome Sequence ◽  
Medium Size ◽  
Phenotypic Traits ◽  
Structural Variants ◽  
Novel Approach ◽  
Sequencing Studies ◽  
Genomic Structural Variants

AbstractThousands of genomic structural variants segregate in the human population and can impact phenotypic traits and diseases. Their identification in whole-genome sequence data of large cohorts is a major computational challenge. We describe a novel approach, PopDel, which jointly identifies deletions of about 500 to at least 10,000 bp in length in many genomes together. PopDel scales to tens of thousands of genomes as we demonstrate in evaluations on up to 49,962 genomes. We show that PopDel reliably reports common, rare and de novo deletions. On genomes with available high-confidence reference call sets PopDel shows excellent recall and precision. Genotype inheritance patterns in up to 6,794 trios indicate that genotypes predicted by PopDel are more reliable than those of previous SV callers. Furthermore, PopDel’s running time is competitive with the fastest tested previous tools. The demonstrated scalability and accuracy of PopDel enables routine scans for deletions in large-scale sequencing studies.

scholarly journals Assembly of whole-chromosome pseudomolecules for polyploid plant genomes using outcrossed mapping populations

2017 ◽  
Author(s):  
Chenxi Zhou ◽  
Bode Olukolu ◽  
Dorcus C. Gemenet ◽  
Shan Wu ◽  
Wolfgang Gruneberg ◽  
...  
Keyword(s):  
De Novo ◽  
Sequence Data ◽  
Genotyping By Sequencing ◽  
Whole Genome Sequence ◽  
Sequencing Data ◽  
Ipomoea Trifida ◽  
High Coverage ◽  
Potato Genome ◽  
Plant Genomes ◽  
Mapping Populations

ABSTRACTThe assembly of whole-chromosome pseudomolecules for plant genomes remains challenging due to polyploidy and high repeat content. We developed an approach for constructing complete pseudomolecules for polyploid species using genotyping-by-sequencing data from outcrossing mapping populations coupled with high coverage whole genome sequence data of a reference genome. Our approach combines de novo assembly with linkage mapping to arrange scaffolds into pseudomolecules. We show that the method is able to reconstruct simulated chromosomes for both diploid and tetraploid genomes. Comparisons to three existing genetic mapping tools show that our method outperforms the other methods in accuracy on both grouping and ordering, and is robust to the presence of substantial amounts of missing data and genotyping errors. We applied our method to three real datasets including a diploid Ipomoea trifida and two tetraploid potato mapping populations. The linkage maps show significant concordance with the reference chromosomes. We resolved seven assembly errors for the published Ipomoea trifida genome assembly as well as anchored an unplaced scaffold in the published potato genome.

Sporadic Occurrence of Recent Selective Sweeps from Standing Variation in Humans as Revealed by an Approximate Bayesian Computation Approach

Genetics ◽  
2021 ◽  
Author(s):  
Guillaume Laval ◽  
Etienne Patin ◽  
Pierre Boutillier ◽  
Lluis Quintana-Murci
Keyword(s):  
Approximate Bayesian Computation ◽  
Sequence Data ◽  
Machine Learning Algorithms ◽  
Whole Genome Sequence ◽  
Bayesian Computation ◽  
Human Adaptation ◽  
Selective Sweeps ◽  
Standing Variation ◽  
Genome Wide ◽  
Approximate Bayesian

Abstract During their dispersals over the last 100,000 years, modern humans have been exposed to a large variety of environments, resulting in genetic adaptation. While genome-wide scans for the footprints of positive Darwinian selection have increased knowledge of genes and functions potentially involved in human local adaptation, they have globally produced evidence of a limited contribution of selective sweeps in humans. Conversely, studies based on machine learning algorithms suggest that recent sweeps from standing variation are widespread in humans, an observation that has been recently questioned. Here, we sought to formally quantify the number of recent selective sweeps in humans, by leveraging approximate Bayesian computation and whole-genome sequence data. Our computer simulations revealed suitable ABC estimations, regardless of the frequency of the selected alleles at the onset of selection and the completion of sweeps. Under a model of recent selection from standing variation, we inferred that an average of 68 (from 56 to 79) and 140 (from 94 to 198) sweeps occurred over the last 100,000 years of human history, in African and Eurasian populations, respectively. The former estimation is compatible with human adaptation rates estimated since divergence with chimps, and reveal numbers of sweeps per generation per site in the range of values estimated in Drosophila. Our results confirm the rarity of selective sweeps in humans and show a low contribution of sweeps from standing variation to recent human adaptation.

scholarly journals A reference dataset of 5.4 million phased human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree

2016 ◽  
Author(s):  
Michael A. Eberle ◽  
Epameinondas Fritzilas ◽  
Peter Krusche ◽  
Morten Källberg ◽  
Benjamin L. Moore ◽  
...  
Keyword(s):  
De Novo ◽  
Sequence Data ◽  
Objective Assessment ◽  
Variant Calling ◽  
Whole Genome Sequence ◽  
Reference Dataset ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Transmission Information

AbstractImprovement of variant calling in next-generation sequence data requires a comprehensive, genome-wide catalogue of high-confidence variants called in a set of genomes for use as a benchmark. We generated deep, whole-genome sequence data of seventeen individuals in a three-generation pedigree and called variants in each genome using a range of currently available algorithms. We used haplotype transmission information to create a phased “platinum” variant catalogue of 4.7 million single nucleotide variants (SNVs) plus 0.7 million small (1-50bp) insertions and deletions (indels) that are consistent with the pattern of inheritance in the parents and eleven children of this pedigree. Platinum genotypes are highly concordant with the current catalogue of the National Institute of Standards and Technology for both SNVs (>99.99%) and indels (99.92%), and add a validated truth catalogue that has 26% more SNVs and 45% more indels. Analysis of 334,652 SNVs that were consistent between informatics pipelines yet inconsistent with haplotype transmission (“non-platinum”) revealed that the majority of these variants are de novo and cell-line mutations or reside within previously unidentified duplications and deletions. The reference materials from this study are a resource for objective assessment of the accuracy of variant calls throughout genomes.

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