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G3 (Bethesda, Md.)
04 11, 2023;13 (4):

Draft genome assemblies of the avian louse Brueelia nebulosa and its associates using long-read sequencing from an individual specimen.

Andrew D Sweet, Daniel R Browne, Alvaro G Hernandez, Kevin P Johnson, Stephen L Cameron
Author Information
  1. Andrew D Sweet: Department of Biological Sciences, Arkansas State University, 2713 Pawnee Street, Jonesboro, AR 72401, USA.
  2. Daniel R Browne: Pacific Biosciences, 1305 O'Brien Drive, Menlo Park, CA 94025, USA.
  3. Alvaro G Hernandez: Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
  4. Kevin P Johnson: Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, IL 61820, USA.
  5. Stephen L Cameron: Department of Entomology, Purdue University, West Lafayette, IN 47907, USA.
PMID: 36735822 DOI: 10.1093/g3journal/jkad030

Abstract

Sequencing high molecular weight (HMW) DNA with long-read and linked-read technologies has promoted a major increase in more complete genome sequences for nonmodel organisms. Sequencing approaches that rely on HMW DNA have been limited to larger organisms or pools of multiple individuals, but recent advances have allowed for sequencing from individuals of small-bodied organisms. Here, we use HMW DNA sequencing with PacBio long reads and TELL-Seq linked reads to assemble and annotate the genome from a single individual feather louse (Brueelia nebulosa) from a European Starling (Sturnus vulgaris). We assembled a genome with a relatively high scaffold N50 (637 kb) and with BUSCO scores (96.1%) comparable to louse genomes assembled from pooled individuals. We annotated a number of genes (10,938) similar to the human louse (Pediculus humanus) genome. Additionally, calling phased variants revealed that the Brueelia genome is more heterozygous (∼1%) then expected for a highly obligate and dispersal-limited parasite. We also assembled and annotated the mitochondrial genome and primary endosymbiont (Sodalis) genome from the individual louse, which showed evidence for heteroplasmy in the mitogenome and a reduced genome size in the endosymbiont compared to its free-living relative. Our study is a valuable demonstration of the capability to obtain high-quality genomes from individual small, nonmodel organisms. Applying this approach to other organisms could greatly increase our understanding of the diversity and evolution of individual genomes.

Keywords

Sturnus vulgaris PacBio TELL-Seq ectoparasite endosymbiont historical effective population size mitogenome

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MeSH Term

Animals
Humans
Phthiraptera
Sequence Analysis, DNA
Genome, Mitochondrial
Genome Size
DNA
High-Throughput Nucleotide Sequencing

Chemicals

DNA
Journal Article Research Support, U.S. Gov't, Non-P.H.S.
Article has an altmetric score of 1

Word Cloud

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