Highly contiguous assemblies of 101 drosophilid genomes

eLife, Journal Year: 2021, Volume and Issue: 10

Published: July 19, 2021

Over 100 years of studies in Drosophila melanogaster and related species the genus have facilitated key discoveries genetics, genomics, evolution. While high-quality genome assemblies exist for several this group, they only encompass a small fraction genus. Recent advances long-read sequencing allow tens or even hundreds to be efficiently generated. Here, we utilize Oxford Nanopore build an open community resource 101 lines 93 drosophilid encompassing 14 groups 35 sub-groups. The genomes are highly contiguous complete, with average contig N50 10.5 Mb greater than 97% BUSCO completeness 97/101 assemblies. We show that Nanopore-based accurate coding regions, particularly respect insertions deletions. These assemblies, along detailed laboratory protocol assembly pipelines, released as public will serve starting point addressing broad questions ecology, evolution at scale species.

Language: Английский

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Stress response, behavior, and development are shaped by transposable element-induced mutations in Drosophila

PLoS Genetics, Journal Year: 2019, Volume and Issue: 15(2), P. e1007900 - e1007900

Published: Feb. 12, 2019

Most of the current knowledge on genetic basis adaptive evolution is based analysis single nucleotide polymorphisms (SNPs). Despite increasing evidence for their causal role, contribution structural variants to remains largely unexplored. In this work, we analyzed population frequencies 1,615 Transposable Element (TE) insertions annotated in reference genome Drosophila melanogaster, 91 samples from 60 worldwide natural populations. We identified a set 300 polymorphic TEs that are present at high frequencies, and located genomic regions with recombination rate, where efficiency selection high. The age length these consistent relatively young long reaching due action positive selection. Besides, 21 fixed also likely be adaptive. Indeed, we, others, found 84 TE insertions. genes nearby candidate suggested functional response related GO categories stimulus, behavior, development. further showed subset affects expression genes, five them have already been linked an ecologically relevant phenotypic effect. Our results provide more complete understanding variation fitness-related traits evolution. Similar studies should help uncover importance TE-induced mutations other species as well.

Language: Английский

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Drosophila Evolution over Space and Time (DEST): A New Population Genomics Resource

Molecular Biology and Evolution, Journal Year: 2021, Volume and Issue: 38(12), P. 5782 - 5805

Published: Sept. 1, 2021

Abstract Drosophila melanogaster is a leading model in population genetics and genomics, growing number of whole-genome data sets from natural populations this species have been published over the last years. A major challenge integration disparate sets, often generated using different sequencing technologies bioinformatic pipelines, which hampers our ability to address questions about evolution species. Here we these issues by developing bioinformatics pipeline that maps pooled (Pool-Seq) reads D. hologenome consisting fly symbiont genomes estimates allele frequencies either heuristic (PoolSNP) or probabilistic variant caller (SNAPE-pooled). We use generate largest repository genomic available for date, encompassing 271 previously unpublished samples 100 locations >20 countries on four continents. Several sampled at seasons across multiple This set, call Evolution Space Time (DEST), coupled with sampling environmental metadata. web-based genome browser web portal provide easy access SNP set. further guidelines how Pool-Seq model-based demographic inference. Our aim scalable platform as community resource can be easily extended via future efforts an even more extensive cosmopolitan will enable geneticists analyze spatiotemporal genetic patterns evolutionary dynamics unprecedented detail.

Language: Английский

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Highly contiguous assemblies of 101 drosophilid genomes

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2020, Volume and Issue: unknown

Published: Dec. 15, 2020

Over 100 years of studies in Drosophila melanogaster and related species the genus have facilitated key discoveries genetics, genomics, evolution. While high-quality genome assemblies exist for several this group, they only encompass a small fraction genus. Recent advances long read sequencing allow high quality tens or even hundreds to be generated. Here, we utilize Oxford Nanopore build an open community resource 101 lines 95 drosophilid encompassing 14 groups 35 sub-groups with average contig N50 10.5 Mb greater than 97% BUSCO completeness 97/101 assemblies. These assemblies, along detailed wet lab protocol assembly pipelines, are released as public will serve starting point addressing broad questions ecology, evolution within group.

Language: Английский

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Demographic analyses of a new sample of haploid genomes from a Swedish population of Drosophila melanogaster

Scientific Reports, Journal Year: 2020, Volume and Issue: 10(1)

Published: Dec. 29, 2020

Abstract European and African natural populations of Drosophila melanogaster have been the focus several studies aiming at inferring demographic adaptive processes based on genetic variation data. However, in these analyses little attention has given to gene flow between samples. Here we present a dataset consisting 14 fully sequenced haploid genomes sampled from population northern species range (Umeå, Sweden). We co-analyzed this new data with an compare likelihood competing scenarios for show that improves fit models

Language: Английский

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T-lex3: an accurate tool to genotype and estimate population frequencies of transposable elements using the latest short-read whole genome sequencing data

Bioinformatics, Journal Year: 2019, Volume and Issue: 36(4), P. 1191 - 1197

Published: Sept. 26, 2019

Transposable elements (TEs) constitute a significant proportion of the majority genomes sequenced to date. TEs are responsible for considerable fraction genetic variation within and among species. Accurate genotyping in is therefore crucial complete identification differences individuals, populations species.In this work, we present new version T-lex, computational pipeline that accurately genotypes estimates population frequencies reference TE insertions using short-read high-throughput sequencing data. In version, have re-designed T-lex algorithm integrate BWA-MEM aligner, which one most accurate mappers can be launched on longer short-reads (e.g. reads >150 bp). We added filtering steps increase accuracy genotyping, parameters allow user control both minimum maximum number reads, strains genotype insertion. also showed first time T-lex3 provides calls plant genome.To test T-lex3, called 1630 individual Drosophila melanogaster, 1600 humans, 3067 rice genome. broadly applicable tool estimating organisms with different genome sizes contents. available at Github: https://github.com/GonzalezLab/T-lex3.Supplementary data Bioinformatics online.

Language: Английский

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Museum Genomics of an Agricultural Super-Pest, the Colorado Potato Beetle, Leptinotarsa decemlineata (Chrysomelidae), Provides Evidence of Adaptation from Standing Variation

Integrative and Comparative Biology, Journal Year: 2022, Volume and Issue: 62(6), P. 1827 - 1837

Published: Aug. 24, 2022

Despite extensive research on agricultural pests, our knowledge about their evolutionary history is often limited. A mechanistic understanding of the demographic changes and modes adaptation remains an important goal, as it improves organismal responses to environmental change ability sustainably manage pest populations. Emerging genomic datasets now allow for characterization adaptive processes, but face limits when they are drawn from contemporary samples, especially in context strong change, repeated selection, or involving modest shifts allele frequency at many loci. Temporal sampling, however, can improve reconstruct events. Here, we leverage museum samples examine whether population diversity structure has changed over time, identify regions that appear be under selection. We focus Colorado potato beetle (CPB), Leptinotarsa decemlineata (Say 1824; Coleoptera: Chrysomelidae), which widely regarded a super-pest due its rapid, repeated, evolution insecticides. By combining whole genome resequencing data 78 with modern demonstrate CPB expanded rapidly 19th century, leading reduction limited genetic Midwest Northeast United States. scans provide evidence selection acting resistant field populations Wisconsin New York, including numerous known insecticide resistance genes. also validate these results by showing selective sweeps identified scan. Perhaps most importantly, temporal analysis indicates standing variation, find parallel two geographical regions. Parallel involves range phenotypic traits not previously CPB, such reproductive morphological functional pathways might habitats.

Language: Английский

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Drosophila Evolution over Space and Time (DEST) - A New Population Genomics Resource

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2021, Volume and Issue: unknown

Published: Feb. 1, 2021

Abstract Drosophila melanogaster is a leading model in population genetics and genomics, growing number of whole-genome datasets from natural populations this species have been published over the last 20 years. A major challenge integration these disparate datasets, often generated using different sequencing technologies bioinformatic pipelines, which hampers our ability to address questions about evolution structure species. Here we issues by developing bioinformatics pipeline that maps pooled (Pool-Seq) reads D. hologenome consisting fly symbiont genomes estimates allele frequencies either heuristic (PoolSNP) or probabilistic variant caller (SNAPE-pooled). We use generate largest data repository genomic available for date, encompassing 271 samples 100 locations >20 countries on four continents based combination 121 unpublished 150 previously datasets. Several sampled at seasons across multiple This dataset, call Evolution Space Time (DEST), coupled with sampling environmental meta-data. web-based genome browser web portal provide easy access SNP dataset. Our aim scalable platform as community resource can be easily extended via future efforts an even more extensive cosmopolitan will enable geneticists analyze spatio-temporal genetic patterns evolutionary dynamics unprecedented detail.

Language: Английский

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Genetics and Population Analysis

Elsevier eBooks, Journal Year: 2018, Volume and Issue: unknown, P. 363 - 378

Published: June 14, 2018

Language: Английский

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De Novo Transcriptomic Resources in the Brain of Vespa velutina for Invasion Control

Insects, Journal Year: 2020, Volume and Issue: 11(2), P. 101 - 101

Published: Feb. 3, 2020

The invasion of Vespa velutina presents a great threat to the agriculture economy, ecological environment, and human health. An effective strategy for this hornet control is urgently required, but limited genome information restricts application molecular-genomic tools targeted management. Therefore, we conducted large-scale transcriptome profiling brain obtain functional target genes molecular markers. Using an Illumina HiSeq platform, more than 41 million clean reads were obtained de novo assembled into 182,087 meaningful unigenes. A total 56,400 unigenes annotated against publicly available protein sequence databases set reliable Simple Sequence Repeats (SSRs) Single Nucleotide Polymorphisms (SNP) markers developed. homologous encoding crucial behavior regulation factors, odorant binding proteins (OBPs), vitellogenin, also identified from highly expressed transcripts. This study provides abundant targets invasive further promotes genetic velutina.

Language: Английский

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