Rhythmidia: A modern tool for circadian period analysis of filamentous fungi

• Published in: PLoS computational biology 2024-08, Vol.20 (8), p.e1012167
• Main Authors: Keeley, Alex T, Lotthammer, Jeffrey M, Pelham, Jacqueline F
• Format: Article
• Language: English
• Subjects: Biology and Life Sciences; Circadian rhythms; Environmental aspects; Fungi; Physical Sciences; Physiological aspects; Research and Analysis Methods; Software
• ISSN: 1553-7358; 1553-734X; 1553-7358
• DOI: 10.1371/journal.pcbi.1012167

Circadian rhythms are ubiquitous across the kingdoms of life and serve important roles in regulating physiology and behavior at many levels. These rhythms occur in ~24-hour cycles and are driven by a core molecular oscillator. Circadian timekeeping enables organisms to anticipate daily changes by timing their growth and internal processes. Neurospora crassa is a model organism with a long history in circadian biology, having conserved eukaryotic clock properties and observable circadian phenotypes. A core approach for measuring circadian function in Neurospora is to follow daily oscillations in the direction of growth and spore formation along a thin glass tube (race tube). While leveraging robust phenotypic readouts is useful, interpreting the outputs of large-scale race tube experiments by hand can be time-consuming and prone to human error. To provide the field with an efficient tool for analyzing race tubes, we present Rhythmidia, a graphical user interface (GUI) tool written in Python for calculating circadian periods and growth rates of Neurospora. Rhythmidia is open source, has been benchmarked against the current state-of-the-art, and is easily accessible on GitHub.