CeNDR, theCaenorhabditis elegansnatural diversity resource

Nucleic Acids Research, Journal Year: 2016, Volume and Issue: 45(D1), P. D650 - D657

Published: Oct. 3, 2016

Studies in model organisms have yielded considerable insights into the etiology of disease and our understanding evolutionary processes. Caenorhabditis elegans is among most powerful used to understand biology. However, C. not as extensively other investigate how natural variation shapes traits, especially through use genome-wide association (GWA) analyses. Here, we introduce a new platform, Natural Diversity Resource (CeNDR) enable statistical genetics genomics studies connect results human disease. CeNDR provides research community with wild strains, sequence variant data for every strain, GWA mapping portal studying elegans. Additionally, researchers outside can benefit from public mappings integrated tools comparative uses several databases that are continually updated addition sequencing data, results. The accessible freely available web located at http://www.elegansvariation.org or an application programming interface.

Language: Английский

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A Species-Wide Inventory of NLR Genes and Alleles in Arabidopsis thaliana

Cell, Journal Year: 2019, Volume and Issue: 178(5), P. 1260 - 1272.e14

Published: Aug. 1, 2019

Infectious disease is both a major force of selection in nature and prime cause yield loss agriculture. In plants, resistance often conferred by nucleotide-binding leucine-rich repeat (NLR) proteins, intracellular immune receptors that recognize pathogen proteins their effects on the host. Consistent with extensive balancing positive selection, NLRs are encoded one most variable gene families but true extent intraspecific NLR diversity has been unclear. Here, we define nearly complete species-wide pan-NLRome Arabidopsis thaliana based sequence enrichment long-read sequencing. The largely saturates approximately 40 well-chosen wild strains, half being present accessions. We chart architectural diversity, identify new architectures, quantify selective forces act specific domains. Our study provides blueprint for defining pan-NLRomes.

Language: Английский

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Host–parasite co-evolution and its genomic signature

Nature Reviews Genetics, Journal Year: 2020, Volume and Issue: 21(12), P. 754 - 768

Published: Aug. 28, 2020

Language: Английский

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Phylogenomic approaches to detecting and characterizing introgression

Genetics, Journal Year: 2021, Volume and Issue: 220(2)

Published: Nov. 11, 2021

Abstract Phylogenomics has revealed the remarkable frequency with which introgression occurs across tree of life. These discoveries have been enabled by rapid growth methods designed to detect and characterize from whole-genome sequencing data. A large class phylogenomic makes use data species infer based on expectations multispecies coalescent. range simple tests, such as D-statistic, model-based approaches for inferring phylogenetic networks. Here, we provide a detailed overview various signals that different modes are expected leave in genome, how current them. We discuss strengths pitfalls these identify areas future development, highlighting introgression, power each method conclude discussion challenges they could potentially be addressed.

Language: Английский

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Cycles of satellite and transposon evolution in Arabidopsis centromeres

Nature, Journal Year: 2023, Volume and Issue: 618(7965), P. 557 - 565

Published: May 17, 2023

Language: Английский

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Plastome phylogeny and early diversification of Brassicaceae

BMC Genomics, Journal Year: 2017, Volume and Issue: 18(1)

Published: Feb. 16, 2017

The family Brassicaceae encompasses diverse species, many of which have high scientific and economic importance. Early diversifications phylogenetic relationships between major lineages or clades remain unclear. Here we re-investigate phylogeny with complete plastomes from 51 species representing all four 5 6 (A, B, C, E F) as identified in earlier studies. Bayesian maximum likelihood analyses using a partitioned supermatrix 77 protein coding genes resulted nearly identical tree topologies exemplified by highly supported clades. All were well interrelationships them resolved. previously defined Clade C was found to be paraphyletic (the genus Megadenia formed separate lineage), while the remaining monophyletic. (lineage III) sister B + rather than core (clades A I II), suggested previous transcriptome study. Molecular dating based on plastome origin late Oligocene early Miocene, following radiative diversification across took place within short timescale. In addition, gene losses occurred multiple times during evolutionary family. Plastome illustrates cruciferous species. This will facilitate our further understanding evolution adaptation numerous model Brassicaceae.

Language: Английский

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The Aquilegia genome provides insight into adaptive radiation and reveals an extraordinarily polymorphic chromosome with a unique history

eLife, Journal Year: 2018, Volume and Issue: 7

Published: Oct. 16, 2018

The columbine genus Aquilegia is a classic example of an adaptive radiation, involving wide variety pollinators and habitats. Here we present the genome assembly A. coerulea 'Goldsmith', complemented by high-coverage sequencing data from 10 wild species covering world-wide distribution. Our analyses reveal extensive allele sharing among demonstrate that introgression selection played role in radiation. We also remarkable discovery evolutionary history entire chromosome differs rest - phenomenon do not fully understand, but which highlights need to consider chromosomes context.

Language: Английский

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Ancestral Hybridization Facilitated Species Diversification in the Lake Malawi Cichlid Fish Adaptive Radiation

Molecular Biology and Evolution, Journal Year: 2019, Volume and Issue: 37(4), P. 1100 - 1113

Published: Dec. 6, 2019

The adaptive radiation of cichlid fishes in East African Lake Malawi encompasses over 500 species that are believed to have evolved within the last 800,000 years from a common founder population. It has been proposed hybridization between ancestral lineages can provide genetic raw material fuel such exceptionally high diversification rates, and evidence for this recently presented Victoria region superflock. Here, we report genomes also show two split 3-4 Ma, today represented by cichlids riverine Astatotilapia sp. "ruaha blue." ancestries present large blocks several kilobases, but there is little variation pattern species, suggesting large-scale mosaic structure was largely established prior radiation. Nevertheless, tens thousands polymorphic variants apparently derived interspersed genomes. These loci striking excess differentiation across ecological subgroups assemblage, parental alleles sort differentially into benthic pelagic lineages, consistent with strong differential selection on these during divergence. Furthermore, enriched genes involved immune response vision, including opsin previously identified as important speciation. Our results reinforce role explosive demonstrating its significance one largest recent vertebrate radiations.

Language: Английский

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Reference-guided de novo assembly approach improves genome reconstruction for related species

BMC Bioinformatics, Journal Year: 2017, Volume and Issue: 18(1)

Published: Nov. 10, 2017

The development of next-generation sequencing has made it possible to sequence whole genomes at a relatively low cost. However, de novo genome assemblies remain challenging due short read length, missing data, repetitive regions, polymorphisms and errors. As more are sequenced, reference-guided assembly approaches can be used assist the process. previous methods mostly focused on other genotypes within same species. We adapted extended approach, which enables usage related reference guide assembly. In order compare evaluate our approaches, we simulated data set heterozygotic plant genome. approach almost always outperforms corresponding program even when different species is used. Similar improvements observed in high coverage situations. addition, show that single evaluation metric, like widely N50 not enough properly rate as points best evaluated with criteria. Therefore, summed z-scores 36 statistics assemblies. combination mapping provides powerful tool improve reconstruction by integrating information Our extension application this strategy only but also between Finally, often straight forward, truth known. Thus one should use metrics, try assess continuity accuracy an

Language: Английский

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Methylome evolution in plants

Genome biology, Journal Year: 2016, Volume and Issue: 17(1)

Published: Dec. 1, 2016

Despite major progress in dissecting the molecular pathways that control DNA methylation patterns plants, little is known about mechanisms shape plant methylomes over evolutionary time. Drawing on recent intra- and interspecific epigenomic studies, we show methylome evolution long timescales largely a byproduct of genomic changes. By contrast, short appears to be driven mainly by spontaneous epimutational events. We argue novel methods based analyses site frequency spectrum (mSFS) natural populations can provide deeper insights into forces act at each timescale.

Language: Английский

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