Genome-wide identification and expression analysis of the CHYR gene family in Phaseolus vulgaris under abiotic stress at the seeding stage

Figures & data

Figure 1. Location of the PvCHYRs. The ruler on the left represents its location on chromosomes on the reference genome. The tightness of the line represents the density of genes. All this information was provided by the Ensembl Plants database.

Table 1. The detailed information of PvCHYRs.

Gene name	Gene Bank	Gene accession	Gene_id	Chr	Location	Protein length	CDS length	Isoelectric point	Molecular weight	Instability index	Aliphatic index
PvCHYR01	ESW33271.1	CM002288.1	Phvul.001G056800	1	6662038–6667903	307	924	6.18	35574.43	58.01	51.07
PvCHYR02	ESW32384.1	CM002289.1	Phvul.002G317800	2	47797468–47807211	1236	3711	5.78	139569.56	53.72	74.88
PvCHYR03	ESW26137.1	CM002290.1	Phvul.003G094000	3	19455085–19461272	628	1887	6.65	70542.93	60.08	65.57
PvCHYR04	ESW26227.1	CM002290.1	Phvul.003G101500	3	24803372–24807416	267	804	6.3	31110.37	58.28	57.94
PvCHYR05	ESW27352.1	CM002290.1	Phvul.003G194400	3	40691734–40702409	1256	3771	6.41	145479.33	53.09	53.09
PvCHYR06	ESW19866.1	CM002293.1	Phvul.006G162000	6	27326977–27330404	267	804	6.58	31141.53	56.66	59.06
PvCHYR07	ESW09085.1	CM002296.1	Phvul.009G099000	9	15095014–15100759	305	918	7.19	34923.05	50.61	62.26
PvCHYR08	ESW04328.1	CM002298.1	Phvul.011G086000	11	8292810–8299636	221	666	7.13	25411.16	38.34	61.18

Figure 3. The motifs and gene structure analysis of PvCHYRs. (A) The evolution of PvCHYRs; (B) The motifs of PvCHYRs. Ten squares with different colors represent different motifs; (C) The gene structure of PvCHYRs. The green squares represent the UTR region, the yellow squares represent the CDS region, and the pink squares represent the sequence coding CHY domain.

Figure 2. The evolutionary analysis of PvCHYRs. The arc shapes with different colors represent subgroups I, II, and III.

Figure 4. The evolution, motifs, and gene structure analysis of CHYR members in five species, Arabidopsis, rice, maize, soybean, and common bean. Different colored backgrounds represent different subgroups. The outer ring is the motif analysis, while the inner ring is the gene structure analysis of CHYR members.

Figure 5. The cis-acting elements analysis of PvCHYRs. (A) The evolution of PvCHYRs. (B) The cis-acting elements of PvCHYRs. The red ones represent the hormone-related elements, the blue ones represent stress-related elements, and the yellow ones represent sprout-related elements.

Figure 6. The collinearity analysis of PvCHYRs. (A) The collinear relationship of PvCHYRs. Two middle rings represent the gene density of the genome. (B) The collinear relationship of PvCHYRs with soybean and Arabidopsis. Green squares are common bean’s chromosomes; yellow ones are soybean chromosomes, while red ones represent Arabidopsis’s chromosomes. Red lines represent the collinear relationship with soybean, and blue lines represent the collinear relationship with Arabidopsis.

Figure 7. The expression pattern analysis of PvCHYRs in different tissues at the seeding stage. (A) The expression pattern analysis of PvCHYRs in silico. Different colored backgrounds represent different subgroups. The color of the squares, from blue to red, represent the expression level from low to high, respectively. (B-I) The expression pattern analysis of PvCHYRs by qRT-PCR analysis. The columns of three colors represent cotyledons, hypocotyls, and radicles, respectively. The different letters on the column represent the significance (P < 0.05).

Figure 8. The expression pattern analysis of PvCHYRs in radicle at the seeding stage under abiotic stress. The columns of three colors represent control, salt, and cold, respectively. The different letters on the column represent the significance (P < 0.05).

Data availability statement

All data generated or analyzed during this study are included in this manuscript.