Identification of resistance gene analogs of the NBS-LRR family through transcriptome probing and in silico prediction of the expressome of Dalbergia sissoo under dieback disease stress

Abstract

Dalbergia sissoo is an important timber tree, and dieback disease poses a dire threat to it toward extinction. The genomic record of D. sissoo is not available yet on any database; that is why it is challenging to probe the genetic elements involved in stress resistance. Hence, we attempted to unlock the genetics involved in dieback resistance through probing the NBS-LRR family, linked with mostly disease resistance in plants. We analyzed the transcriptome of D. sissoo under dieback challenge through DOP-rtPCR analysis using degenerate primers from conserved regions of NBS domain-encoded gene sequences. The differentially expressed gene sequences were sequenced and in silico characterized for predicting the expressome that contributes resistance to D. sissoo against dieback. The molecular and bioinformatic analyses predicted the presence of motifs including ATP/GTP-binding site motif A (P-loop NTPase domain), GLPL domain, casein kinase II phosphorylation site, and N-myristoylation site that are the attributes of proteins encoded by disease resistance genes. The physicochemical characteristics of identified resistance gene analogs, subcellular localization, predicted protein fingerprints, in silico functional annotation, and predicted protein structure proved their role in disease and stress resistance.

In silico structural-functional characterization of three differentially expressed resistance gene analogs identified in Dalbergia sissoo against dieback disease reveals their role in immune response regulation

“…Subcellular localization confirms their location in the nuclear, mitochondrial, plasma membrane, and extracellular space. The extracellular location was also assessed with tobacco and Arabidopsis ( Ijaz et al., 2022 ). The dynamic-related protein of rice (OsDRP1E) has a mitochondrial cellular location ( Li et al., 2017 ) which defines their role in plants’ defense mechanism upon pathogenic attack.…”

“…If a pathogen overcomes it, then the second level initiates. This level includes resistance (R) genes or their product and starts a molecular cascade of signal transductions in response to the attack ( Ijaz et al., 2022 ). The controlling signals include kinases, phytoalexin, peroxidases, reactive oxygen species, and guanine nucleotide-binding proteins ( Zhong et al., 2019 ).…”

Identification of the Function of the Pathogenesis-Related Protein GmPR1L in the Resistance of Soybean to Cercospora sojina Hara

“…Numerous studies have validated that transcription factors are important factors affecting biotic and abiotic stresses in plants [ 47 , 48 , 49 ]. The main transcription factors involved in disease resistance in plants include WRKY , MYB , ZFP , and ZIP .…”

In silico characterization of differentially expressed short-read nucleotide sequences identified in dieback stress-induced transcriptomic analysis reveals their role as antimicrobial peptides

“…These RGAs were of short nucleotide sequence length and expressed only in dieback-resistant D. sissoo plants. These differentially expressed short-read nucleotide sequences were identified in dieback stress-induced transcriptomic analysis ( Ijaz et al., 2022 ). Primer detail is given in Supplementary Table S1 .…”