Journal
G3-GENES GENOMES GENETICS
Volume 10, Issue 9, Pages 3047-3060Publisher
GENETICS SOCIETY AMERICA
DOI: 10.1534/g3.120.401028
Keywords
Genome Size; K-mer; Carabidae; Flow Cytometry; Insect Genomes
Categories
Funding
- Harold E. and Leona M. Rice Endowment Fund at Oregon State University
- NSF [DEB-1702062]
Ask authors/readers for more resources
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,Bembidionsp. nr.transversale, most sequence-based methods yielded estimates half the size suggested by flow cytometry.
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available