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. 2022 Feb 10;12:764843. doi: 10.3389/fpls.2021.764843

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Copyright © 2022 Jhu, Farhi, Wang, Zumstein and Sinha.

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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Heatmaps and gene-coexpression networks (GCNs) of C. campestris haustorial tissues across three developmental stages. (A) A heatmap of gene expression profiles in z-scores for SOM5, which includes genes that are highly expressed in the early stage. (B) A GCN of genes in SOM5. This SOM5 GCN is composed of four major modules. Magenta indicates genes in Module 1, which has enriched biological process GO term including “response to abiotic and biotic stimulus, stress, hormone, far-red light.” The transcription factor HB7 is enlarged and labeled in yellow. (C) GCN of genes that are classified in SOM5 Module 1. PL, pectin lyase-like superfamily protein. A, auxin response factor 1. E, ethylene signaling-related genes. (D) A heatmap of gene expression profiles in z-scores for SOM3, which includes genes that are highly expressed in the mature stage. (E) A GCN of genes that are in SOM3. The SOM3 GCN is composed of five major modules. Cyan indicates genes in Module 2, which has enriched biological process GO term including “root radial pattern formation.” Selected pectin methyl-esterase inhibitor (PMEI) is enlarged and labeled in yellow. (F) GCN of genes that are classified in SOM3 Module 2. PMEI, pectin methyl-esterase inhibitor. EX, expansin. (G) A heatmap of gene expression profiles in z-scores for SOM6, which includes genes that are relatively highly expressed in the early and mature stage. (H) A GCN of genes in SOM6. This SOM6 GCN is composed of four major modules. Magenta indicates genes in Module 1, which has enriched biological process GO term including “response to stimulus, hormone, organic substance.” Ethylene responsive element binding factor 1 (ERF1) is enlarged and labeled in yellow. The transcription factor LBD25 is enlarged and labeled in cyan as other genes in Module 2. (I) GCN of genes that are classified in SOM6 Module 1. PL, pectin lyase-like superfamily protein. A, auxin transporter or auxin-responsive protein; E, ethylene signaling-related genes; PL, pectin lyase-like superfamily protein; PME, pectin methylesterase; PMT, pectin methyltransferase-like; PAE, pectin acetylesterase family protein. The complete gene lists for all SOM units with SOM distances and PCA principal component values are included in Supplementary Table 1. The selected SOM gene lists were used for constructing the GCN based on the expression profiles in C. campestris LCM data with the following normal quantile cutoffs. The SOM5 GCN cutoff = 0.97. The SOM3 GCN cutoff = 0.98. The SOM6 GCN cutoff = 0.95.