Single-fly assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life
Status PubMed-not-MEDLINE Jazyk angličtina Země Spojené státy americké Médium electronic
Typ dokumentu preprinty, časopisecké články
Grantová podpora
R35 GM122592
NIGMS NIH HHS - United States
F32 GM135998
NIGMS NIH HHS - United States
R35 GM148244
NIGMS NIH HHS - United States
R35 GM138286
NIGMS NIH HHS - United States
T32 HG000044
NHGRI NIH HHS - United States
R35 GM118165
NIGMS NIH HHS - United States
R35 GM137834
NIGMS NIH HHS - United States
K99 GM137041
NIGMS NIH HHS - United States
PubMed
37873137
PubMed Central
PMC10592941
DOI
10.1101/2023.10.02.560517
PII: 2023.10.02.560517
Knihovny.cz E-zdroje
- Publikační typ
- časopisecké články MeSH
- preprinty MeSH
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 (>1Mb 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.
Baylor College of Medicine USA
Center for Reproductive Evolution Department of Biology Syracuse University USA
Daintree Rainforest Observatory James Cook University Australia
Department of Biological and Environmental Science University of Jyväskylä Finland
Department of Biological Sciences Hokkaido University Japan
Department of Biological Sciences Michigan Technological University USA
Department of Biological Sciences Tokyo Metropolitan University Japan
Department of Biological Sciences Virginia Tech USA
Department of Biology Case Western Reserve University USA
Department of Biology Stanford University USA
Department of Biology University of North Carolina Chapel Hill USA
Department of Cell and Molecular Biology University of California Berkeley United States
Department of Complexity Science and Engineering The University of Tokyo Japan
Department of Developmental Biology Stanford University USA
Department of Ecology and Evolutionary Biology Yale University USA
Department of Entomology Cornell University USA
Department of Evolution and Ecology University of California Davis USA
Department of Zoology The University of British Columbia
Hawaii Invertebrate Program Division of Forestry and Wildlife State of Hawaii USA
Hokkaido University Museum Hokkaido University Japan
Howard Hughes Medical Institute University of California Berkeley United States
Institute of Ecology and Evolution University of Edinburgh UK
Institute of Entomology Biology Centre Czech Academy of Sciences Czechia
Pacific Biosciences Research Center University of Hawai'i Mānoa USA
School of Environmental and Natural Sciences Bangor University UK
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