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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Single-fly genome assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life

PLoS Biology, Journal Year: 2024, Volume and Issue: 22(7), P. e3002697 - e3002697

Published: July 18, 2024

Long-read sequencing is driving rapid progress in genome assembly across all major groups of life, including species the family Drosophilidae, a longtime model system for genetics, genomics, and evolution. We previously developed cost-effective hybrid Oxford Nanopore (ONT) long-read Illumina short-read approach used it to assemble 101 drosophilid genomes from laboratory cultures, greatly increasing number assemblies this taxonomic group. The next challenge address culture bias taxon sampling by that cannot easily be reared lab. Here, we build upon our previous methods perform amplification-free ONT single wild flies obtained either directly field or ethanol-preserved specimens museum collections, improving representation lesser studied taxa whole-genome data. Using Novaseq X Plus P2 sequencers with R10.4.1 chemistry, set new benchmark inexpensive at US $150 per while assembling as little 35 ng genomic DNA fly. present 183 179 resource systematics, phylogenetics, comparative genomics. Of these genomes, 62 are pooled lab strains 121 adult flies. Despite sample limitations working small insects, most single-fly diploid comparable contiguity (>1 Mb contig N50), completeness (>98% complete dipteran BUSCOs), accuracy (>QV40 genome-wide R10.4.1) inbred lines. well-resolved multi-locus phylogeny 360 4 outgroup encompassing publicly available (as August 2023) Finally, Progressive Cactus whole-genome, reference-free alignment built subset 298 suitably high-quality genomes. alignment, along updated protocols computational pipelines, released an open tool studying evolution scale entire insect family.

Language: Английский

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Hematopoietic plasticity mapped in Drosophila and other insects

eLife, Journal Year: 2022, Volume and Issue: 11

Published: Aug. 3, 2022

Hemocytes, similar to vertebrate blood cells, play important roles in insect development and immunity, but it is not well understood how they perform their tasks. New technology, particular single-cell transcriptomic analysis combination with

Language: Английский

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Desiccation resistance differences in Drosophila species can be largely explained by variations in cuticular hydrocarbons

eLife, Journal Year: 2022, Volume and Issue: 11

Published: Dec. 6, 2022

Maintaining water balance is a universal challenge for organisms living in terrestrial environments, especially insects, which have essential roles our ecosystem. Although the high surface area to volume ratio insects makes them vulnerable loss, evolved different levels of desiccation resistance adapt diverse environments. To withstand desiccation, use lipid layer called cuticular hydrocarbons (CHCs) reduce evaporation from body surface. It has long been hypothesized that water-proofing capability this CHC layer, can confer resistance, depends on its chemical composition. However, it unknown components are important contributors and how these determine differences resistance. In study, we used machine-learning algorithms, correlation analyses, synthetic CHCs investigate affect 50 Drosophila related species. We showed across species be largely explained by variation particular, length subset CHCs, methyl-branched (mbCHCs), key determinant There also significant between evolution longer mbCHCs higher Given almost ubiquitous suggest evolutionary changes insect general mechanism adaptation changing

Language: Английский

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Decoupled evolution of the Sex Peptide gene family and Sex Peptide Receptor in Drosophilidae

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(3)

Published: Jan. 12, 2024

Across internally fertilising species, males transfer ejaculate proteins that trigger wide-ranging changes in female behaviour and physiology. Much theory has been developed to explore the drivers of protein evolution. The accelerating availability high-quality genomes now allows us test how these are evolving at fine taxonomic scales. Here, we use from 264 species chart evolutionary history Sex Peptide (SP), a potent regulator post-mating responses

Language: Английский

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Unistrand piRNA clusters are an evolutionarily conserved mechanism to suppress endogenous retroviruses across the Drosophila genus

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Nov. 13, 2023

Abstract The PIWI-interacting RNA (piRNA) pathway prevents endogenous genomic parasites, i.e. transposable elements, from damaging the genetic material of animal gonadal cells. Specific regions in genome, called piRNA clusters, are thought to define each species’ repertoire and therefore its capacity recognize silence specific transposon families. unistrand cluster flamenco ( flam ) is essential somatic compartment Drosophila ovary restrict Gypsy -family transposons infecting neighbouring germ Disruption results de-repression sterility, yet it remains unknown whether this silencing mechanism present more widely. Here, we systematically characterise 119 species identify five additional -like clusters separated by up 45 million years evolution. Small RNA-sequencing validated these as bona-fide expressed cells ovary, where they selectively target family. Together, our study provides compelling evidence a widely conserved that co-evolved with virus-like transposons.

Language: Английский

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The Physiological and Evolutionary Ecology of Sperm Thermal Performance

Frontiers in Physiology, Journal Year: 2022, Volume and Issue: 13

Published: March 24, 2022

Ongoing anthropogenic climate change has increased attention on the ecological and evolutionary consequences of thermal variation. Most research in this field focused physiology behavior diploid whole organisms. The performance haploid gamete stages directly tied to reproductive success received comparatively little attention, especially context ecology wild (i.e., not domesticated) Here, we review evidence for effects temperature sperm phenotypes, emphasizing data from organisms whenever possible. We find that are pervasive, above normal temperatures particular detrimental. That said, there is traits can evolve adaptively response change, adaptive phenotypic plasticity also place results curves, encourage framework be used as a guide experimental design maximize relevance well comparability across studies. highlight gaps our understanding require more fully understand adaptation global change.

Language: Английский

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Single-fly assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Oct. 2, 2023

Abstract Long-read sequencing is driving rapid progress in genome assembly across all major groups of life, including species the family Drosophilidae, a longtime model system for genetics, genomics, and evolution. We previously developed cost-effective hybrid Oxford Nanopore (ONT) long-read Illumina short-read approach used it to assemble 101 drosophilid genomes from laboratory cultures, greatly increasing number assemblies this taxonomic group. The next challenge address culture bias taxon sampling by that cannot easily be reared lab. Here, we build upon our previous methods perform amplification-free ONT single wild flies obtained either directly field or ethanol-preserved specimens museum collections, improving representation lesser studied taxa whole-genome data. Using Novaseq X Plus P2 sequencers with R10.4.1 chemistry, set new benchmark inexpensive at US $150 per while assembling as little 35 ng genomic DNA fly. present 183 179 resource systematics, phylogenetics, comparative genomics. Of these genomes, 62 are pooled lab strains 121 adult flies. Despite sample limitations working small insects, most single-fly diploid comparable contiguity (>1Mb contig N50), completeness (>98% complete dipteran BUSCOs), accuracy (>QV40 genome-wide R10.4.1) inbred lines. well-resolved multi-locus phylogeny 360 4 outgroup encompassing publicly available (as August 2023) Finally, Progressive Cactus whole-genome, reference-free alignment built subset 298 suitably high-quality genomes. alignment, along updated protocols computational pipelines, released an open tool studying evolution scale entire insect family.

Language: Английский

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Co-option of the trichome-forming network initiated the evolution of a morphological novelty in Drosophila eugracilis

Current Biology, Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 1, 2024

Language: Английский

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Phylogenomic Analysis Reveals Evolutionary Relationships of Tropical Drosophilidae: From Drosophila to Scaptodrosophila

Ecology and Evolution, Journal Year: 2025, Volume and Issue: 15(3)

Published: March 1, 2025

ABSTRACT Species radiation in the family Drosophilidae has led to a diversity of species occupying wide range ecological niches. Despite high within this family, with over thousands and more than hundred recorded Thailand Malay Peninsula, taxonomic classifications remain complicated due morphological plasticity inconsistent phylogenetic reconstructions based on limited genetic data. In study, we assemble new mitochondrial genomes from Drosophila Scaptodrosophila collected Thailand, expanding genomic resources for these underexplored tropical regions. Phylogenetic analyses 13 protein‐coding genes revealed well‐supported evolutionary relationships, forming distinct lineage several subgroups, such as ananassae , montium melanogaster exhibiting monophyly. Notable discrepancies were observed placement suzukii subgroup, which was not recovered monophyletic, position punjabiensis reflecting complexities sorting hybridization events. This comprehensive analysis provides accurate understanding relationships Drosophilidae's diversification tropics.

Language: Английский

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