Gnodes#3 draft document, 2023 June-Dec.

Measure of major contents in animal and plant genomes, using Gnodes, finds under-assemblies of model plant, Daphnia, fire ant and others.
by Donald G. Gilbert; Indiana Univ., Bloomington, IN, USA; gilbert.bionet@gmail.com 

Abstract

Significant discrepancies in genome sizes measured by cytometric methods versus DNA sequence estimates are frequent, including recent long-read DNA assemblies of plant and animal genomes.  A new DNA sequence measure using the baseline of unique conserved genes, Gnodes, finds the larger cytometric measures are often accurate.  Many DNA-informatic measures of size, as well as assembly methods, have errors in methodology that under-measure duplicated genome spans.  

Major contents of several model and discrepant genomes are analyzed here, including human,  corn, chicken, insects, crustaceans, and the model plant.  Transposons dominate larger genomes, structural repeats are often a major portion of smaller ones.  Gene coding sequences are found in similar amounts across the taxonomic spread.  The largest contributors to size discrepancies are higher-order repeats, but duplicated coding sequences are a significant missed content, and transposons in some examined species.

Informatics of measuring DNA and producing assemblies, including recent long-read telomere to telomere approaches, are subject to mistakes in operation and/or interpretation, which are often biased against repeats and duplications.  Mistaken aspects include alignment methods that are inaccurate for high-copy duplicated spans; misclassification of true repetitive sequence as heterozygosity and artifact; software default settings that exclude high-copy DNA; and overly conservative data processing that reduces duplicated genomic spans.  Re-assemblies of long read DNA with balanced methods for problem genomes including model plant, water fleas, and fire ant, recovers the missing genome portions.