Genome size estimation and genome assembly completeness assessment.

Abstract

Evaluation of genome size has been extensively used in different fields. In many studies, it has been employed to test correlation with other parameters such as metabolic rates, longevity and ecological/geographical distribution. Moreover, genome size assessed with cytometrical methods can be useful to evaluate the completeness of genome assemblies. In this latter case, knowledge of the accuracy of cytometry-based genome size measurement is fundamental, and a pivotal factor is the internal standard used during measurement. In the present article, I tested the correlation between cytometry-measured genome sizes and assembly sizes, finding a probable systemic error. Indeed, the two most widely used internal standard, i.e., human and chicken, are traditionally set equal to 3.5 and 1.25 pg, respectively. With the advent of telomere-to-telomere genome assembly, we can now know the real genome size for several species, being actually 3.19 pg for human and 1.12 pg for chicken. Recalculating the genome size for 912 vertebrate species, I assessed the level of genome assembly completeness, explored the influence of factors such as sequencing platform and gave some suggestions for future studies.