Genome-Wide Analysis of C2H2 Zinc-Finger Family Transcription Factors and Their Responses to Abiotic Stresses in Poplar (Populus trichocarpa)

Abstract

BackgroundC2H2 zinc-finger (C2H2-ZF) proteins are a large gene family in plants that participate in various aspects of normal plant growth and development, as well as in biotic and abiotic stress responses. To date, no overall analysis incorporating evolutionary history and expression profiling of the C2H2-ZF gene family in model tree species poplar (Populus trichocarpa) has been reported.Principal FindingsHere, we identified 109 full-length C2H2-ZF genes in P. trichocarpa, and classified them into four groups, based on phylogenetic analysis. The 109 C2H2-ZF genes were distributed unequally on 19 P. trichocarpa linkage groups (LGs), with 39 segmental duplication events, indicating that segmental duplication has been important in the expansion of the C2H2-ZF gene family. Promoter cis-element analysis indicated that most of the C2H2-ZF genes contain phytohormone or abiotic stress-related cis-elements. The expression patterns of C2H2-ZF genes, based on heatmap analysis, suggested that C2H2-ZF genes are involved in tissue and organ development, especially root and floral development. Expression analysis based on quantitative real-time reverse transcription polymerase chain reaction indicated that C2H2-ZF genes are significantly involved in drought, heat and salt response, possibly via different mechanisms.ConclusionsThis study provides a thorough overview of the P. trichocarpa C2H2-ZF gene family and presents a new perspective on the evolution of this gene family. In particular, some C2H2-ZF genes may be involved in environmental stress tolerance regulation. PtrZFP2, 19 and 95 showed high expression levels in leaves and/or roots under environmental stresses. Additionally, this study provided a solid foundation for studying the biological roles of C2H2-ZF genes in Populus growth and development. These results form the basis for further investigation of the roles of these candidate genes and for future genetic engineering and gene functional studies in Populus.

Comprehensive analysis of trihelix genes and their expression under biotic and abiotic stresses in Populus trichocarpa

“…Of the 56 trihelix genes, 39 had only one gene product, while the remaining 17 genes (30%) had multiple gene products, which could be attributed to alternative splicing according to the Phytozome V10.3 database. This percentage was similar to that of the C2H2 gene family (26%) in P. trichocarpa 17. Among these 17 genes, 15 encoded two possible cDNAs, while PtrGT24 and PtrGT37 each encoded three possible transcripts (Supplementary Table S1).…”

Comprehensive Genomic Analysis and Expression Profiling of the C2H2 Zinc Finger Protein Family under Abiotic Stresses in Cucumber (Cucumis sativus L.)

“…Many studies have shown that C2H2-ZFP genes respond to abiotic stress and their expression changes after different time points after stress treatment [15,47,56]. In our study, 16 genes were induced by at least one type of stress.…”

“…C2H2-ZFPs mainly participate in growth development and abiotic stress responses of plants as thoroughly studied in rice [16], durum wheat [17], and poplar plants [15,47]. However few studies have investigated C2H2-ZFP genes in cucumber.…”

C2H2 Zinc Finger Proteins: Master Regulators of Abiotic Stress Responses in Plants

“…Most C2H2 zinc finger proteins in plants contain the highly conserved sequence QALGGH in their zinc finger domains: such proteins are referred to as Q-type zinc finger proteins. Unlike proteins containing the QALGGH sequence, a class of C2H2type zinc finger proteins do not contain any conserved motifs in the zinc finger region are known as C-type proteins (Agarwal et al, 2007;Liu et al, 2015b).…”