Borhan Ahmed

Calcineurin B-like proteins (CBLs) are plant-specific Ca ²⁺ sensors that, in synergy with CBL-interacting protein kinases (CIPKs), regulate Ca ²⁺ signaling in responses to environmental stimuli. Although their roles are extensively characterized in Arabidopsis thaliana and other model plant species, an exhaustive analysis of jute species ( Corchorus olitorius and C. capsularis ) remains elusive. This research identified nine CBL s and 19 CIPK s in C. capsularis , and eight CBL s and 18 CIPK s in C. olitorius . We conducted a meticulous analysis of their physicochemical properties, gene structure, subcellular localization, chromosomal localization, synteny, collinearity, conserved domains, and motifs. Gene structure and phylogenetic analyses categorized CBL and CIPK genes into four distinct clades based on conserved protein architectures and motifs. Subcellular localization predictions indicated a predominantly cytoplasmic distribution for most CIPKs and plasma membrane localization for most CBLs. Promoter analysis of cis- regulatory elements reveals that numerous CBL and CIPK genes from both species are involved in various abiotic stress responses. Expression analyses of these bast fiber-producing Corchorus species suggest the pivotal roles of CBL5 , CIPK6 , CIPK10 , and CIPK25 in fiber cell development, while those of CBL8 , CIPK21 , and CIPK23 in reproductive organ development in both jute species. Waterlogging stress significantly upregulated the expression of CBL5 , CBL8 , CIPK7 , CIPK10 , and CIPK24 in both jute species. Salt stress triggered the upregulation of CBL4 , CBL10 , CIPK2 , CIPK6 , CIPK10 , CIPK14 , CIPK24 , and CIPK25 , while drought treatments led to the upregulation of CBL3 , CIPK5 , CIPK6 , CIPK7 , CIPK10 , and CIPK24 in both jute species. These transcriptome-based expression findings provide putative insights that lay the groundwork for future studies of CBLs and CIPKs in jute, enhancing our understanding of their roles in environmental stress adaptation and improving crop performance.

Mitogen activated protein kinase (MAPK) cascade is evolutionary conserved universal signal transduction module that plays central role in the growth and development of plants as well as in biotic and abiotic stress response. Although, MAPKs have been investigated in several model plants, no systematic analysis has been conducted in jute species ( Corchorus olitorius and C. capsularis ) even though, their genome sequencing has been completed. In the present study we identified 11 and 12 putative MAPKs in C. olitorius and C. capsularis using their genomic database, respectively. Here we provide a comprehensive bioinformatics analysis of the MAPK family from both Corchorus species including identification and nomenclature, chromosomal localization, sequence alignment, domain and Motif, gene structure, phylogenetic, functional analysis and investigation of expression analysis in response to abiotic stress and fiber cell development. The phylogenetic analysis of predicted MAPKs were clustered into four different clades and assigned with specific name based on their orthology based evolutionary relationship with Arabidopsis . Structural analysis of the MAPK genes revealed that there was a large variation among the exon number in both Corchorus species ranged from 2 to 11 but genes with the same clade had similar exon-intron structure. The sequence alignment analysis concede the presence of several conserved domain and motif including crucial signature phosphorylation motif TDY or TEY where first one is harbor in group D sequence and rest of the sequence contain TEY motif in their activation loop. Transcriptome analysis against salinity, drought along with fiber cell formation showed that MAPK4-1 genes in both jute genome highly expressed and may play a potential role in jute on adverse condition as well as jute fiber formation. These findings yielded new insights into the transcriptional control of MAPK gene expression, provide an improved understanding of abiotic stress responses and signaling transduction in jute, that lead to potential applications in the genetic improvement of jute cultivars.

Na ⁺ /H ⁺ exchangers (NHXs) are secondary ion transporter to exchange H+ and transfer Na ⁺ or K ⁺ across membrane plays crucial role in cellular pH and Na ⁺ and K ⁺ homeostasis in plant. In the present study, we have performed genomewide identification, characterization and comparative analysis of NHXs genes in two cultivated jute species and found seven Co and Cc NHXs in each genome. Subsequently phylogenetic analysis demonstrated that Co and Cc NHXs have three sub-group that correlate with other plant species containing 10-12 transmembrane helices (TMH) and a hydrophilic C-terminal domain in the cytoplasmic region, the TMH compose a hollow cylinder to provide the channel for Na ⁺ and H ⁺ transport. Promoter profiling of both species NHXs genes revealed in enrichment of cis element involved in stress responsiveness reflecting their potential involvement against abiotic stress. Transcriptome data and real time PCR of Co and Cc NHXs gene expression analysis under saline and drought condition showed significant differences, which suggest their potential role in abiotic stress conditions. This is the first comprehensive analysis providing baseline information of Co and Cc NHXs genes in abiotic stress condition which can be used for the development of abiotic stress tolerant jute variety.

Mesta yellow vein mosaic disease (MYVMD), one of the major diseases circulating mesta growing regions of Indian sub-continent, is responsible for serious yield loss in mesta crops. A complex of monopartite begomovirus, Mesta yellow vein mosaic virus (MYVMV) and associated betasatellite, is reported in several studies as the causal agent of MYVMD. However, all-inclusive molecular evolutionary analysis of so far available MYVMVs and associated betasatellites disseminating in this region is still lacking. In this study, by estimating and analyzing various indexes of population genetics and evolutionary parameters, we discussed the sources of genetic variations, population dynamics and different forces acting on the evolution of MYVMVs and associated betasatellites. The study finds recombination as a vital force in the evolution and diversification of begomovirus complexes in different geographic locations however, betasatellites were found to be exposed to more diverse recombination events compared to MYVMVs. Indian isolates are reported to have high frequency of polymorphism in this study which suggests a balancing selection or expansion occurring in Indian populations of begomoviruses. Higher degree of genetic differentiation and lower rate of gene flow calculated between the viral populations of Bangladesh and Pakistan is justified by the relatively far geographical distance between these two countries. Although the study detects overall purifying selection, the degrees of constraints acting on individual gene tested are found different. Coat protein (AV1) is estimated with very high nucleotide substitution rate which is very likely to result from the strongest purifying selection pressure ( d _N /d _S = 0.131) calculated in this study on coat protein. The findings of this study on different evolutionary forces that shape the emergence and diversification of MYVMVs and associated betasatellites may provide directions towards future evolutionary trend analysis and development of comprehensive disease control strategies for begomoviruses.