Genome-Wide Identification of BTB Domain-Containing Gene Family in Grapevine (Vitis vinifera L.)

Abstract

BTB (broad-complex, tram track and bric-a-brac) proteins have broad functions in different growth processes and biotic and abiotic stresses. However, the biological role of these proteins has not yet been explored in grapevine, which draws our attention towards the BTB gene family. Herein, we identified 69 BTB genes (VvBTB) in the Vitis vinifera genome and performed comprehensive in silico analysis. Phylogenetic analysis classified VvBTB proteins into five groups, and further domain analysis revealed the presence of other additional functional domains. The majority of BTB proteins were localized in the nucleus. We also performed differential expression analysis by harnessing RNA- seq data of 10 developmental stages and different biotic and abiotic stresses. Our findings revealed the plausible roles of the BTB gene family in developmental stages; Fifty VvBTB were differentially expressed at different developmental stages. In addition, 47 and 16 VvBTB were responsive towards abiotic and biotic stresses, respectively. Interestingly, 13 VvBTB genes exhibited differential expression in at least one of the developmental stages and biotic and abiotic stresses. Further, miRNA target prediction of 13 VvBTB genes revealed that vvi-miR482 targets VvBTB56, and multiple miRNAs, such as vvi-miR172, vvi-miR169 and vvi-miR399, target VvBTB24, which provides an insight into the essential role of the BTB family in the grapevine. Our study provides the first comprehensive analysis and essential information that can potentially be used for further functional investigation of BTB genes in this economically important fruit crop.

Bioinformatic Analysis of the BTB Gene Family in Paulownia fortunei and Functional Characterization in Response to Abiotic and Biotic Stresses

“…The analysis of the cisacting elements of the PfBTB genes promoter revealed the presence of light-responsive elements, stress-responsive elements, and hormone-responsive elements (Figure 4). Among them, light-responsive elements are ubiquitous and most abundant, which is consistent with the analysis results of different species of grape [34], sugar beet [35], and tomato [5], indicating that the transcriptional regulation of PfBTB may be generally affected by light signals. Meanwhile, hormone-responsive elements, such as SA, GA, IAA, MeJA, and ABA, were also contained on the PfBTB gene promoter.…”

“…The number of BTB family members in plants varies greatly among different species: 69 members in grape [ 34 ], 49 members in sugar beet [ 35 ], 38 members in tomato [ 5 ], and 158 members in rice [ 4 ]. Using the recent determination of the P. fortunei genome, we identified 62 BTB members for the first time in Paulownia ( Table 1 ).…”

“…Among the 62 PfBTB genes, PfBTB41 in the Armadillo subfamily has the most exons (19), while PfBTB56 in the other subfamily only has one exon ( Figure 2 ). We observed very different patterns of intron–exon structure distributions in tomato [ 5 ], grape [ 34 ], sugar beet [ 35 ], and rice [ 4 ] from those of the BTB members we studied in Paulownia . Thus, the differences and diversity in these structures emphasize that the evolutionary patterns between different species are complex and diverse.…”

“…MicroRNAs (miRNAs), a class of small non-coding RNAs, play significant roles in biotic and abiotic stressors by controlling their target genes [ 47 ]. According to studies on the targeting relationship between miRNAs and BTB genes, miRNA families are linked to development and stress target BTB genes [ 34 ]. By comparing the miRNA and transcriptome before and after PaWB, 74 pf-miRNAs targeting 42 PfBTB s were found.…”

Genome-Wide Identification and Expression Analysis of the Broad-Complex, Tramtrack, and Bric-à-Brac Domain-Containing Protein Gene Family in Potato

“…The present work focused on identifying and characterizing the BTB gene family across the genome of S. tuberosum. As per earlier studies, the number of BTBs identified were 77 in A. thaliana [4], 38 in Solanum lycopersicum [39], and 69 in Vitis vinifera [40]. We identified a total of 57 BTBs in the potato genome.…”