Holiday 2023 Genomics Puzzle

Cytometric methods of genome size estimation are well established, and are not known to be biased. A majority of recent animal and plant genome assemblies (2020-2023 long-reads) are well below cytometric sizes, from 15% to over 50% below.

Q: What are causes, and cures, of this discrepancy?
A1. cytometry is high-biased, because of .. ?
A2. long-read assembly is low-biased, because of .. ?
A3. genomics is complicated, both measures are right and wrong..

My answer: This trend of smaller assemblies can be examined through measure of a third evidence, the major contents of the raw DNA sequence used to build these assemblies.

gnodes_doc3d.pdf : "Measure of major contents in animal and plant genomes, using Gnodes, finds under-assemblies of model plant, Daphnia, fire ant and others."

Fig I1. Genome sizes as Assembly / Cytometric size percentage in relation to cytometric sizes, for arthropods, birds, fishes, mammals and plants.

-- Don Gilbert, 2023 December