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Measuring Genome Sizes Using Read-Depth, k-mers, and Flow Cytometry: Methodological Comparisons in Beetles (Coleoptera)

Authors
  • Pflug, James M.1
  • Holmes, Valerie Renee2
  • Burrus, Crystal2
  • Johnston, J. Spencer2
  • Maddison, David R.1
  • 1 Department of Integrative Biology, Oregon State University, Corvallis, OR 97331
  • 2 Department of Entomology, Texas A&M University, College Station, TX 77843
Type
Published Article
Journal
G3 Genes|Genome|Genetics
Publisher
The Genetics Society of America
Publication Date
Jun 29, 2020
Volume
10
Issue
9
Pages
3047–3060
Identifiers
DOI: 10.1534/g3.120.401028
PMID: 32601059
PMCID: PMC7466995
Source
PubMed Central
Keywords
License
Green

Abstract

Measuring genome size across different species can yield important insights into evolution of the genome and allow for more informed decisions when designing next-generation genomic sequencing projects. New techniques for estimating genome size using shallow genomic sequence data have emerged which have the potential to augment our knowledge of genome sizes, yet these methods have only been used in a limited number of empirical studies. In this project, we compare estimation methods using next-generation sequencing (k-mer methods and average read depth of single-copy genes) to measurements from flow cytometry, a standard method for genome size measures, using ground beetles (Carabidae) and other members of the beetle suborder Adephaga as our test system. We also present a new protocol for using read-depth of single-copy genes to estimate genome size. Additionally, we report flow cytometry measurements for five previously unmeasured carabid species, as well as 21 new draft genomes and six new draft transcriptomes across eight species of adephagan beetles. No single sequence-based method performed well on all species, and all tended to underestimate the genome sizes, although only slightly in most samples. For one species, Bembidion sp. nr. transversale , most sequence-based methods yielded estimates half the size suggested by flow cytometry.

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