Genome-Wide Identification and Analysis of the SBP-Box Family Genes under Phytophthora capsici Stress in Pepper (Capsicum annuum L.)

Abstract

SQUAMOSA promoter binding protein (SBP)-box genes encode plant-specific transcription factors that are extensively involved in many physiological and biochemical processes, including growth, development, and signal transduction. However, pepper (Capsicum annuum L.) SBP-box family genes have not been well characterized. We investigated SBP-box family genes in the pepper genome and characterized these genes across both compatible and incompatible strain of Phytophthora capsici, and also under different hormone treatments. The results indicated that total 15 members were identified and distributed on seven chromosomes of pepper. Phylogenetic analysis showed that SBP-box genes of pepper can be classified into six groups. In addition, duplication analysis within pepper genome, as well as between pepper and Arabidopsis genomes demonstrated that there are four pairs of homology of SBP-box genes in the pepper genome and 10 pairs between pepper and Arabidopsis genomes. Tissue-specific expression analysis of the CaSBP genes demonstrated their diverse spatiotemporal expression patterns. The expression profiles were similarly analyzed following exposure to P. capsici inoculation and hormone treatments. It was shown that nine of the CaSBP genes (CaSBP01, 02, 03, 04, 05, 06, 11, 12, and 13) exhibited a dramatic up-regulation after compatible HX-9 strain (P. capsici) inoculation, while CaSBP09 and CaSBP15 were down-regulated. In case of PC strain (P. capsici) infection six of the CaSBP genes (CaSBP02, 05, 06, 11, 12, and 13) were arose while CaSBP14 was down regulated. Furthermore, Salicylic acid, Methyl jasmonate and their biosynthesis inhibitors treatment indicated that some of the CaSBP genes are potentially involved in these hormone regulation pathways. This genome-wide identification, as well as characterization of evolutionary relationships and expression profiles of the pepper CaSBP genes, will help to improve pepper stress tolerance in the future.

Classification and Genome-Wide Analysis of Chitin-Binding Proteins Gene Family in Pepper (Capsicum annuum L.) and Transcriptional Regulation to Phytophthora capsici, Abiotic Stresses and Hormonal Applications

“…The expression of the CABPR1 gene in pepper was higher in the virulent strain interaction versus the avirulent interaction [60]. However, in contrast to our previous studies [61], it was found that the expression of most CaSBPs was comparatively greater in the avirulent interaction than in the compatible interaction. Some other studies have revealed that the expression of oxysterol-binding protein gene ( CanOBP ) and a novel peroxidase gene ( CanPOD ) were higher in the incompatible interaction [62,63] and the defense-related genes such as b-1, 3-glucanase gene ( CABGLU ), disease-associated protein gene ( CABPR1 ), and peroxidase gene ( CAPO1 ) were expressed in a similar pattern, after the inoculation of virulent and avirulent strains of Phytophthora capsici on the roots of pepper as reported by Wang et al (2013) [62].…”

“…“PF00187.17” was collected from Pfam database () as described in our previous study [61,77]. To further authenticate the CaChi family members, the CaChi were aligned with DNAMAN to cross check in both CM334 (Available online: ) [40] and Zunla-1 (Available online: ) [78] databases of pepper, while the obtained sequences were from the latest versions, i.e., v1.55 and v2.0, respectively.…”

“…Information about the chromosomal location of CaChi genes were obtained from Pepper Genome Platform (PGP) (Available online: ) as described by Zhang et al (2016) [61], and the genes were mapped on chromosomes using MapDraw [87]. Duplication analysis within the pepper genome was carried out with the criteria depicted by Gu et al (2002) [88] further detail as: (1) the FASTA-alignable region among the two proteins should be more than 80% of the longer protein sequence; and (2) the identity between the two protein sequences (I) should be I ≥ 30% if the alignable region is longer than 150 amino acid and I ≥ 0.01 n + 4.8L −0.32(1 + exp(−L/1000) otherwise, where n = 6 and L is the alignable length between the two protein sequences of the gene [88,89].…”

“…The method used for P. capsici inoculation was same as described by Khan et al (2018) and Zhang et al (2016) [61,77]. The root samples were amassed 0, 6, 12, 24, 48 and 72 h post inoculation (hpi) of P. capsici .…”

Molecular Evolution, Genome-Wide Characterization and Codon Bias Analysis of the SBP-Box Family in Cucumis sativus

“…In tomato, silencing the LeSPL-CNR gene could inhibit fruit ripening [17]. In pepper (Capsicum annuum L), CaSBP genes tended to be involved in pathogen resistance pathway against phytophthora capsici, which caused blight and fruit rot [27]. In sorghum (Sorghum bicolor L), SbSBPs tended to be involved in the ABA signaling pathway for abiotic stress response [28].…”