Genome-wide analysis and identification of the PEBP genes of Brassica juncea var. Tumida

Abstract

Background Phosphatidylethanolamine-binding protein (PEBP) is widely present in animals, plants, and microorganisms. Plant PEBP genes are mainly involved in flowering transition and nutritional growth. These genes have been studied in several plants; however, to the best of our knowledge, no studies have explored them in Brassica juncea var. tumida. This study identified and characterized the entire PEBP gene family of Brassica juncea var. tumida. Results A total of 21 PEBP genes were identified from Brassica juncea var. tumida. Through phylogenetic analysis, the 21 corresponding proteins were classified into the following four clusters: TERMINAL FLOWER 1 (TFL1)-like proteins (n = 8), MOTHER OF FT AND TFL1 (MFT)-like proteins (n = 5), FLOWERING LOCUS T (FT)-like proteins (n = 6), and ybhB-like proteins (n = 2). A total of 18 genes contained four exons and had similar gene structures in each subfamily except BjMFT1, BjPYBHB1, and Arabidopsis thaliana CENTRORADIALIS homolog of Brassica juncea var. tumida (BjATC1). In the analysis of conserved motif composition, the BjPEBP genes exhibited similar characteristics, except for BjFT3, BjMFT1, BjPYBHB1, BjPYBHB2, and BjATC1. The BjPEBP promoter includes multiple cis-acting elements such as the G-box and I-box elements that respond to light, ABRE and GARE-motif elements that respond to hormones, and MBSI and CAT-box elements that are associated with plant growth and development. Analysis of RNA-Seq data revealed that the expression of a few BjPEBP genes may be associated with the development of a tumorous stem. The results of qRT–PCR showed that BjTFL1 and BjPYBHB1 were highly expressed in the flower tissue, BjFT1 and BjATC1 were mainly expressed in the root, and BjMFT4 were highly detected in the stem. The results of yeast two-hybrid screening suggested that BjFT interacts with Bj14-3-3. These results indicate that BjFT is involved in flowering regulation. Conclusions To the best of our knowledge, this study is the first to perform a genome-wide analysis of PEBP genes family in Brassica juncea var. tumida. The findings of this study may help improve the yield and molecular breeding of Brassica juncea var. tumida.

Studying Salt-Induced Shifts in Gene Expression Patterns of Glucosinolate Transporters and Glucosinolate Accumulation in Two Contrasting Brassica Species

“…Regarding amphidiploids, the presence of twelve genes suggests these species inherited six genes from each of their parental species, corresponding to the GTR genes found in Arabidopsis [42]. This is in line with the previous research conducted on other gene families of B. juncea which showed that the allotetraploid Brassicas attained genes approximately three times more than Arabidopsis [72]. Similar observations of gene duplications have been reported in other polyploid crops, such as cotton and wheat [74,75].…”

“…The presence of cis-regulatory elements associated with signalling molecules like JA, SA, and related elements suggests a role for GTR genes in stress conditions, highlighting a degree of specificity. This observation reinforces the concept of neofunctionalization occurring after genome duplication and triplication during speciation and evolution [72].…”

“…Genome-wide studies of various gene families in Brassicaceae have consistently indicated their expansion compared with Arabidopsis. Notable examples are not limited to but include APX, NPR, DOF, shattering genes, SOD, and PEBP [68][69][70][71][72][73]. Regarding amphidiploids, the presence of twelve genes suggests these species inherited six genes from each of their parental species, corresponding to the GTR genes found in Arabidopsis [42].…”