Genome-wide identification and expression analysis of the plant-specific PLATZ gene family in Tartary buckwheat (Fagopyrum tataricum)

Abstract

Background Plant AT-rich sequence and zinc-binding (PLATZ) proteins belong to a novel class of plant-specific zinc-finger-dependent DNA-binding proteins that play essential roles in plant growth and development. Although the PLATZ gene family has been identified in several species, systematic identification and characterization of this gene family has not yet been carried out for Tartary buckwheat, which is an important medicinal and edible crop with high nutritional value. The recent completion of Tartary buckwheat genome sequencing has laid the foundation for this study. Results A total of 14 FtPLATZ proteins were identified in Tartary buckwheat and were classified into four phylogenetic groups. The gene structure and motif composition were similar within the same group, and evident distinctions among different groups were detected. Gene duplication, particularly segmental duplication, was the main driving force in the evolution of FtPLATZs. Synteny analysis revealed that Tartary buckwheat shares more orthologous PLATZ genes with dicotyledons, particularly soybean. In addition, the expression of FtPLATZs in different tissues and developmental stages of grains showed evident specificity and preference. FtPLATZ3 may be involved in the regulation of grain size, and FtPLATZ4 and FtPLATZ11 may participate in root development. Abundant and variable hormone-responsive cis-acting elements were distributed in the promoter regions of FtPLATZs, and almost all FtPLATZs were significantly regulated after exogenous hormone treatments, particularly methyl jasmonate treatment. Moreover, FtPLATZ6 was significantly upregulated under all exogenous hormone treatments, which may indicate that this gene plays a critical role in the hormone response of Tartary buckwheat. Conclusions This study lays a foundation for further exploration of the function of FtPLATZ proteins and their roles in the growth and development of Tartary buckwheat and contributes to the genetic improvement of Tartary buckwheat.

JmjC Domain-containing Histone Demethylase Gene Family in Chinese Cabbage: Genome-wide Identification and Expressional Profiling

“…suggesting that these genes might have the same regulatory mechanisms under drought and salt stress both in cotton and Chinese cabbage. And a similar phenomenon exists in Jatropha, and JcJMJ18 expression was significantly upregulated under salt stress [19]. Furthermore, >65.4% of BrJMJs expression were upregulated under drought stress, which is consistent with its results in wheat [38],…”

“…Gene duplication, a key driver of speciation [39], enables organisms to adapt to changing environments [19]. In plants, tandem and segmental replication are the most common causes of gene family expansion [40], with segmental replication occurring regularly in slower-evolving gene families [41].…”

“…In plants, JmjC-containing proteins mediate the epigenetic processes, including plant growth and development, floral transformation, and stress responses [17][18][19]. In A. thaliana, AtJMJ30 is responsible for regulating flowering time and root growth [20,21]; other JmjC family members, such as AtJMJ16 and AtJMJ17, are associated with leaf senescence and the drought response [22,23].…”