Fig. 1: Transcriptional states of Arabidopsis cell types change during leaf ageing.

a, Images of 29-day-old (day 1 of the experiment) (left) and 37-day-old (day 9 of the experiment) (right) Arabidopsis rosettes with leaf stage indicated (scale bar, 1 cm). Below, leaf area of each leaf stage sampled at the beginning (day 1) (left) and end (day 9) (right) of the time course is shown (bars indicates mean, n = 3 leaves per stage). b, A total of 647 individual leaves spanning 15 leaf developmental stages across the 9-day time course were profiled at single-nucleus resolution using sci-RNA-seq3. c, Schematic illustrating the leaf stages and time points sampled across the experiment. d, A leaf transcriptional atlas was assembled from 264,183 nuclei, with nine leaf cell types identified using established marker genes. e, Epidermal nuclei subclustered and coloured by the leaf stage from which they were sourced. f, Expression patterns of CYCD1;1,CYCB1;2, PME5, RD29A and KMD1 within the epidermal subcluster. g, Pseudobulked expression profiles of CYCD1;1 and KMD1 in the epidermis subcluster, arranged by leaf stage and day of sampling. h, Normalized expression profiles of CYCD1;1, CYCB1;2, PME5, RD29A and KMD1 in the epidermis subcluster across leaf age. Curve shows quadratic model fit (solid lines) with 95% CI indicated by shaded area. i, The z-score normalized expression trends of 115 genes upregulated specifically within the epidermis subcluster during leaf maturation. Curves show quadratic model fit (solid lines), with 99% CIs indicated by shaded areas. Select gene names are shown.