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

Area of Science:

• Genomics
• Evolutionary Biology
• Bioinformatics

Background:

• Genome size is crucial for understanding genome evolution and guiding sequencing projects.
• Emerging sequence-based methods offer potential for genome size estimation but require empirical validation.

Purpose of the Study:

• To compare next-generation sequencing (k-mer, average read depth) genome size estimation methods against flow cytometry.
• To introduce a new protocol for estimating genome size using read depth of single-copy genes.
• To expand genome size data for ground beetles (Carabidae) and Adephagan beetles.

Main Methods:

• Utilized k-mer methods and average read depth of single-copy genes for genome size estimation.
• Employed flow cytometry as the standard measurement technique.
• Developed and tested a novel read-depth protocol for genome size estimation.
• Generated new draft genomes and transcriptomes for multiple beetle species.

Main Results:

• No single sequence-based method consistently performed well across all tested species.
• Sequence-based methods generally underestimated genome sizes, with significant underestimation in *Bembidion* sp. nr. *transversale*.
• Provided new flow cytometry measurements for five carabid species and new genomic data for eight Adephagan species.

Conclusions:

• Current sequence-based genome size estimation methods require refinement for broader applicability.
• Flow cytometry remains a reliable standard for genome size measurement.
• The study highlights the need for careful method selection and validation in genomic studies.