In Silico Expression Profiling and PPI Analysis of Potassium Transport Genes

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In Silico Expression Profiling and PPI Analysis of Potassium Transport Genes

December 15, 2021 by Muhmmad Waqas0
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In Silico Expression Profiling and PPI Analysis of Potassium Transport Genes

The expression pattern of K+ transport genes was analyzed in two different cultivars of C. cajan (AKPR303, AKCMS11, TTB7). For this purpose, RNA-seq data (SRR6780151, SRR6780152, SRR6780153, SRR6780154, SRR6785590, SRR6785591) were downloaded from NCBI-SRA (https://www.ncbi.nlm.nih.gov/sra (accessed on 14 August 2021)). Moreover, to analyze the expression pattern of potassium-transporting genes in C. cajan under heat stress at different time points (30 min, 03 h) and salt stress in ICP7: salt-tolerant and ICP1071: salt susceptible, data (heat: SRR11856663 SRR11856664, SRR11856665, salt: SRR5451688, SRR5451689, SRR5451690, SRR5451691) were downloaded from the NCBI-SRA database. These paired-end clean reads were mapped to the C. cajan genome. C. cajan genome was downloaded from NCBI and indexes were built using bowtie2. The cufflinks program was used to calculate the expression level of annotated genes in the reference genome using the GFF format of the genome. The normalized FPKM value was used to construct a heatmap using TBtools. Furthermore, these identified potassium transporters and channels were subjected to STRING v11.0 (https://string-db.org/ (accessed on 14 August 2021)) to analyze network of protein–protein interactions (PPIs). The minimum required interaction score was 0.400, corresponding to medium confidence.

Results of In Silico Expression Analysis

Comparative expression of K+ transporting genes in the flower bud of two different cultivars of C. cajan (AKPR303 and AKCMS11) was analyzed. The average for two biological replicates was used for each cultivar. Most of the genes were expressed in both cultivars, except for some genes that showed zero expression. Some HAK family members (HAK-3, -4, -5, -6, -7, -8, -10, -12, -13, -15, -16, -17) and some TPK-KCO family members (KCO-1, -2, -3, and -4) were found to be highly expressed in both cultivars, while other HAK family members, i.e., HAK-9, -11, -14 and KEA family members, i.e., KEA-1, -2, were found slightly expressed in both cultivars. Specifically, CcHAK15 was highly expressed (up to six units). CcHAK2CcHKT1, and CcKAT3 showed no expression in all three cultivars.

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