Volume 18, Issue 3 (12-2023)
MGj 2023, 18(3): 267-278 |
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Amini S, Maali-Amiri R, Poormazaheri H. Genome-wide evolutionary characterization and digital expression analysis related to polyamine biosynthetic genes in chickpea. MGj 2023; 18 (3) : 3
URL: http://mg.genetics.ir/article-1-1788-en.html
URL: http://mg.genetics.ir/article-1-1788-en.html
University of Tehran
Abstract: (370 Views)
In plants, putrescine (Put), spermidine (Spd), and spermine (Spm), all belong to the polyamine family, and their roles in several biological processes such as growth, development, and various responses to stimuli have been little studied. This report deals with the in-silico genome-wide evolutionary characterization of polyamine biosynthetic genes family members (including arginine/ornithine decarboxylase (ADC/ODC), Spd synthase (SPDS), and Spm synthase (SPMS), respectively) and their digital gene expression profiling analysis in different tissues along with gene ontology (GO) and gene-gene based network analysis in chickpea (Cicer arietinum L.). Based on bioinformatics analysis, identified five different putative polyamine biosynthetic gene pathways located on chromosomes 2, 4, 5, 6 and 7, respectively. Their open reading frames ranged in size from 990 to 2199 bp, encoding proteins with lengths of 329 to 732 aa. The MW values for these 5 sequences ranged from 36.59 to 78.74 kDa while pI values were 5.08 to 6.67. CaADC, CaSPDSs and CaSPMSs were predicted to localize in apoplast (extracellular). CaODC were found primarily in mitochondria. The prediction of the three-dimensional shape (3-D) of these proteins shows their structural diversity. The analysis of the second structure showed that these proteins have different percentages of Alpha-helices, Beta sheet, Random coil and Turn. Analysis of gene structure showed that the sequence of ADC and ODC were singleton while the SPDS and SPMS sequence showed dispersed duplication. The phylogenetic analysis provides further insights into the evolutionary relations between these proteins, as well as their putative functions. Multiple alignments revealed high similarity in their conserved domain but divergence in the N- and C-terminals. The phylogenetic tree showed that the ADC and ODC sequences in chickpea have very conserved protein motifs and there are no introns in the sequence of these two genes. SPDSs and SPMSs are divided into two distinct groups based on the presence of similar protein motifs. The results indicate that SPDSs and SPMSs contain seven to ten introns and most of these isoforms have the same number of exons but different lengths of exons and introns. Analyzing digital gene expression during developmental processes revealed that polyamine biosynthetic genes play a more significant role in fine-tuning plant life cycle. According to the results of data mining in the EST database, high expression levels of PAs biosynthesis genes, especially ADC, were identified in leaf and root, while, ODC had low or no expression level in all of this tissues. When considered together, these results provide valuable information for future research with regard to polyamine biosynthetic gene family members' function and structure in plants and also provide applying and manipulation of PA biosynthetic gene pathways in chickpea breeding programs.
Article number: 3
Type of Study: Applicable |
Subject:
Subject 01
Received: 2022/09/19 | Accepted: 2023/10/7 | Published: 2023/12/31
Received: 2022/09/19 | Accepted: 2023/10/7 | Published: 2023/12/31
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