Genome Wide Identification and Characterization of LIM Domain Associated Gene Superfamily in Common Bean ( Phaseolus vulgaris L.)

Figures

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  Figure 1. Position of PvLIM genes on chromosomes of Phaseolus vulgaris.

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  Figure 2. Exon–intron distribution of 17 PvLIM genes predicted from GSDS 2.0 (Left). Ten identified Motif distribution over 17 PvLIM genes alongside their respective domains using Meme Suite (Right).

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  Figure 3. Phylogenetic analysis of LIM proteins from P. vulgaris, A. thaliana, B. rapa, C. quinoa, G. max, V. radiata, and S. lycopersicum. The phylogenetic tree was prepared in MEGA‐11 by neighbor joining method with 1000 bootstrap replicates.

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  Figure 4. Syntenic relationship among P. vulgaris, A. thaliana, B. rapa, C. quinoa, G. max, V. radiata, and S. lycopersicum only showing the best hits using “score/max” ratio coloring. Blue signifies less than 50% similarity (discarded). Green represents 50%–75% similarity (discarded). Orange indicates a similarity range of 75%–99.999% and red denotes 100% similarity.

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  Figure 6. Tertiary structures of all 17 PvLIM proteins. The most highly conserved residues are in maroon and least conserved are in cyan. The log range of the conservation color gradient was from −1.4 to 1.4.

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  Figure 7. Seven distinguished protein–protein interactions network structure found in Phaseolus vulgaris LIM genes. The interacting proteins are marked with their respective uniprot accession. The color scales represent the relative signal intensity scores. Known interactions are distinguished by light blue lines for interactions sourced from curated databases and pink lines for those experimentally determined. Predicted interactions are represented with green lines for gene neighborhood associations, red lines for gene fusions, and dark blue lines for gene co‐occurrence. Additionally, other types of data include text mining results, shown with yellow lines, co‐expression represented by black lines, and protein homology indicated with purple lines.

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  Figure 8. Cis acting elements identified in 17 PvLIM genes.

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  Figure 9. Heat map showing expression level of PvLIM genes in different tissues. Median normalized RPKM values are plotted against respective tissues. Name of the tissues presented are Leaf Young, Leaf 21DAE, Stem, Shoot, Flower, Pod Young, Pod 9 cm, Pod 10 cm, Pod 12 cm, Seed 7 mg, Seed 50 mg, Seed 140 mg, Root Tip, Root Young, Root 21 DAE.

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  Figure 10. Co‐expression heat map based on Pearson’s correlation coefficient (r). The value is calculated using the RPKM values in leaves of different tissues of Phaseolus vulgaris retrieved from the P. vulgaris gene expression atlas (no treatment).