Do DNA and cytometric measures agree on genome sizes?

Measurement of DNA contents of genomes is valuable for understanding genome biology, including assessments of genome assemblies, but it is not a trivial problem. Measuring contents of DNA shotgun reads is complicated by several factors: biological contents of genomes, laboratory methods, sequencing technology and computational processing. This compares and shares complications with cytometric measures of genome size and contents. There is an obvious discrepancy between cytometry and current long-read assemblies: assemblies average significantly below cytometric sizes. Measures of population changes within a species will control some of these complications. This report examines five species population sets with published cytometric and DNA data sets: Arabidopsis thaliana and A. arenosa, Arctic plants of Cochlearia genus, clonal populations of a rotifer Brachionus asplanchnoidis, and Zea mays corn plants. Results of this are clear, if complicated: DNA and cytometry do measure the same genome sizes, when done carefully with controls or adjustments for errors. Population changes in genome sizes are found by assembly-mapped measures of DNA, including environment or regional effects of latitude and altitude. Copy numbers of repeats, transposons and genes are changing. Kmer-based measures of DNA generally fail to match cytometry, miss population changes, and are opaque to understanding measurement errors. Oxford Nanopore technology produces the least biased DNA for measurement, with recent ONT.R10 Simplex data a match to cytometric sizes for corn, tomato plants, zebra fish and zebra finch bird. Assemblies of these species DNA average 12% below measured sizes, incomplete for duplicated content. New assembly of this ONT Simplex DNA reaches the size measured by cytometry and Gnodes, in 4 of 5 species. rRNA gene duplications measure one aspect of this discrepancy: the genome assemblies examined all are missing many rRNA genes. New experiments that measure both cytometry and DNA, controlling error factors, are warranted to clarify these results and suggest improvements for genome projects.