Re-calibration of flow cytometry standards for plant genome size estimation

The evolution of long-read sequencing technologies has advanced the development of genome assemblies that are now frequently presented as gap-free or nearly gapless, reflecting substantial improvements in sequencing accuracy and completeness. However, discrepancies between the genome size estimates derived from genome assemblies and flow cytometry create ambiguity regarding the accuracy of these complementary approaches. Accurate genome size estimation via flow cytometry relies on use of an internal standard with a genome of known size. Historically, the genome size of these standards was often calibrated against incomplete genome assemblies or non-plant genomes, such as the human male genome, which was previously considered to be 7 pg but is now known to be around 6.15 pg after 20 years of advancements. Calibrating plant references against non-plant standards is not recommended due to differential staining properties. Therefore, we recalibrated the size of five plant genomes commonly used as reference standards in flow cytometry, by utilizing a recent gapless, telomere-to-telomere (T2T) genome assembly of Nipponbare rice. Our results indicate a significant overestimation of around 20% in previous flow cytometry-based estimates for Pisum sativum and Nicotiana benthamiana, around 10% for Arabidopsis thaliana, and less than 5% for Sorghum bicolor, and Gossypium hirsutum. The close alignment of the recalibrated GS estimates to the reference genome assemblies and recalculated estimates from different studies confirms their suitability as reference standards for more accurate measurement of plant genome size.