Transcriptome-Based Identification, Characterization, Evolutionary Analysis, and Expression Pattern Analysis of the WRKY Gene Family and Salt Stress Response in Panax ginseng

Abstract

WRKY transcription factors are some of the most important transcription factors in planta, and they are involved in biological and abiotic stresses, growth and development, and biochemical processes. The WRKY gene family has been found in many higher plants, while little is known about WRKY-encoding genes in ginseng. As a traditional and important economic medicinal herb and health food, ginseng has been a model species for other related medicinal plants. Here, we analyze the WRKY transcript factor gene family in ginseng from a genetics and genomics perspective in the hope that this study can create a new avenue for understanding the role of PgWRKYs. By identifying and analyzing all candidate WRKY transcription factor family members based on the transcriptome of ginseng, a total of 118 PgWRKY genes was obtained following gene classification, the phylogenetic relationship, conserved domain structure, functional differentiation, and an expression activity analysis. A phylogenetic analysis revealed that the PgWRKYs were clustered into three groups: I, II, and III transcription factors. Members in group Ⅱ were further divided into five sub-groups: Ⅱa to Ⅱe. An expression analysis showed a trend of co-expression among most PgWRKY genes, forming an interaction network. The coding sequences were WRKYGQK; only two genes were WRKYGKK, and only one gene was WSKYGQK. Moreover, a salt stress treatment analysis of the response of PgWRKY39-01, PgWRKY062, and PgWRKY064 genes was investigated using RT-qPCR. After salt stress treatment, the expression of three PgWRKY genes was increased, indicating that PgWRKYs can participate in regulating the response to salt stresses in ginseng. These comprehensive data provide a reference for elucidating the functions of this transcription factor family in the growth, development, and salt stress response of ginseng.

Identification and Characterization of the BBX Gene Family in Bambusa pervariabilis × Dendrocalamopsis grandis and Their Potential Role under Adverse Environmental Stresses

“…In Arabidopsis thaliana, the corresponding numbers were thirteen, four, eight, and seven [10], while in B. pervariabilis × D. grandis, they were three, four, six, and eight. These findings imply that the BBX gene may have originated from a common ancestor in several species and independently spread following the divergence of dicotyledons and monocotyledons [36].…”

“…The GO database is a widely used tool for standardizing the functional classification of genes in transcriptome analyses [36]. Studies have shown that members of the BDBBX gene family exhibit different functions.…”

Genome-wide characterization, evolutionary analysis, and expression pattern analysis of the trihelix transcription factor family and gene expression analysis under MeJA treatment in Panax ginseng

“…Under normal conditions, transcription factors with binding function and can be to other proteins domain or DNA sequence promoter region to perform their specific functions [ 2 ]. Currently, the GRAS [ 3 , 4 ], AP2/ERF [ 5 ], MYB [ 6 ], WRKY [ 7 ], NF-Y [ 8 ], HD‑Zip [ 9 ], bHLH [ 10 ], and other specific transcription factor families have been bioinformatically analysed, and their functions have been verified in ginseng. The trihelix transcription factor had been functionally validated in many plants, but no in-depth reports or systematic studies about this gene family in ginseng.…”