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. 2020 Sep 1;38(1):31–47. doi: 10.1093/molbev/msaa217

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© The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

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Fig. 1. — Bacillus subtilis biofilm growth is a highly regulated and punctuated process exhibiting a phylogeny−ontogeny recapitulation pattern. (a) Gross morphology of B. subtilis biofilms on solid agar plates at 6 h (6H), 12 h (12H), 1 day (1D), 2 days (2D), 3 days (3D), 5 days (5D), 7 days (7D), 14 days (14D), 1 month (1M), and 2 months (2M) after inoculation with LC (see supplementary file S3, Supplementary Material online). (b) Pearson’s correlation coefficients between timepoints of biofilm ontogeny in all-against-all comparison. Early (6H−1D), mid (3D−7D), and late (1M−2M) periods, together with transition stages at 2D and 14D, are marked. (c) Average transcript expression profiles of the 31 most populated gene clusters (for all 64 clusters see supplementary file S5, Supplementary Material online). (d) Hypothetical profiles of phylogeny−ontogeny correlations. Solid line displays no correlation, dotted line the recapitulation model and dashed line the hourglass model. (e) Transcriptome age index (TAI) and (g) proteome age index (PAI) profiles of B. subtilis biofilm ontogeny show recapitulation pattern. (f) Transcriptome nonsynonymous divergence index (TdNI) and (h) proteome nonsynonymous divergence index (PdNI) profiles show that genes conserved at nonsynonymous sites are used early in the biofilm ontogeny, whereas more divergent ones later during biofilm ontogeny. Nonsynonymous divergence rates were estimated in B. subtilis–B. licheniformis comparison. Depicted P values are obtained by the flat line test and gray shaded areas represent ±one standard deviation estimated by permutation analysis (see Materials and Methods, e−h). Early (red), mid (blue), and late (green) periods of biofilm growth are color coded (c, e−h).