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

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  • Additional Information
    • Source:
      Publisher: Public Library of Science Country of Publication: United States NLM ID: 101183755 Publication Model: eCollection Cited Medium: Internet ISSN: 1545-7885 (Electronic) Linking ISSN: 15449173 NLM ISO Abbreviation: PLoS Biol Subsets: MEDLINE
    • Publication Information:
      Original Publication: San Francisco, CA : Public Library of Science, [2003]-
    • Subject Terms:
      Phylogeny* ; Drosophilidae*/genetics ; Drosophilidae*/classification ; Genome, Insect* ; Genomics*/methods; Animals ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods
    • Abstract:
      Long-read sequencing is driving rapid progress in genome assembly across all major groups of life, including species of the family Drosophilidae, a longtime model system for genetics, genomics, and evolution. We previously developed a cost-effective hybrid Oxford Nanopore (ONT) long-read and Illumina short-read sequencing approach and used it to assemble 101 drosophilid genomes from laboratory cultures, greatly increasing the number of genome assemblies for this taxonomic group. The next major challenge is to address the laboratory culture bias in taxon sampling by sequencing genomes of species that cannot easily be reared in the lab. Here, we build upon our previous methods to perform amplification-free ONT sequencing of single wild flies obtained either directly from the field or from ethanol-preserved specimens in museum collections, greatly improving the representation of lesser studied drosophilid taxa in whole-genome data. Using Illumina Novaseq X Plus and ONT P2 sequencers with R10.4.1 chemistry, we set a new benchmark for inexpensive hybrid genome assembly at US $150 per genome while assembling genomes from as little as 35 ng of genomic DNA from a single fly. We present 183 new genome assemblies for 179 species as a resource for drosophilid systematics, phylogenetics, and comparative genomics. Of these genomes, 62 are from pooled lab strains and 121 from single adult flies. Despite the sample limitations of working with small insects, most single-fly diploid assemblies are comparable in contiguity (>1 Mb contig N50), completeness (>98% complete dipteran BUSCOs), and accuracy (>QV40 genome-wide with ONT R10.4.1) to assemblies from inbred lines. We present a well-resolved multi-locus phylogeny for 360 drosophilid and 4 outgroup species encompassing all publicly available (as of August 2023) genomes for this group. Finally, we present a Progressive Cactus whole-genome, reference-free alignment built from a subset of 298 suitably high-quality drosophilid genomes. The new assemblies and alignment, along with updated laboratory protocols and computational pipelines, are released as an open resource and as a tool for studying evolution at the scale of an entire insect family.
      Competing Interests: The authors have declared that no competing interests exist.
      (Copyright: © 2024 Kim et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
    • Comments:
      Update of: bioRxiv. 2023 Oct 02:2023.10.02.560517. doi: 10.1101/2023.10.02.560517. (PMID: 37873137)
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    • Grant Information:
      R35 GM122592 United States GM NIGMS NIH HHS; F32 GM135998 United States GM NIGMS NIH HHS; R35 GM148244 United States GM NIGMS NIH HHS; T32 HG000044 United States HG NHGRI NIH HHS; R35 GM118165 United States GM NIGMS NIH HHS; R35 GM137834 United States GM NIGMS NIH HHS; K99 GM137041 United States GM NIGMS NIH HHS
    • Publication Date:
      Date Created: 20240718 Date Completed: 20240718 Latest Revision: 20240725
    • Publication Date:
      20240726
    • Accession Number:
      PMC11257246
    • Accession Number:
      10.1371/journal.pbio.3002697
    • Accession Number:
      39024225