Comprehensive analysis of bZIP transcription factors uncovers their roles during dimorphic floret differentiation and stress response in Cleistogenes songorica

Abstract

BackgroundTranscription factors act as important regulators of transcription networks. Basic leucine zipper (bZIP) transcription factors have been shown to be involved in multiple biological processes in plants. However, no information is available for the bZIP family in Cleistogenes songorica, which is an important xerophytic and allotetraploid grass in desert grasslands.ResultsIn this study, 86 CsbZIPs were identified in the allotetraploid C. songorica genome. For location analysis, CsbZIPs were distributed evenly across two subgenomes of C. songorica. Phylogenetic tree analysis among three species indicated that CsbZIPs were evolutionarily more closely related to OsbZIPs than AtbZIPs. Syntenic and phylogenetic analyses confirmed that the CsbZIPs were mainly expanded by whole-genome duplication events. Furthermore, it was determined that rice and C. songorica might have undergone purified selection during their long evolutionary history by calculating the Ks values and Ka/Ks ratios of orthologous gene pairs. By analysing the expression patterns of CsbZIPs in different tissues and under abiotic stresses, 21 CsbZIP genes were differentially expressed between chasmogamous (CH) and cleistogamous (CL) flowers, including two FLOWERING LOCUS D (FD) genes. In shoots and roots, 79.1 and 87.2% of the CsbZIP genes, respectively, displayed transcript changes under at least one stress treatment, such as heat, cold, drought and salt. Strikingly, 17 common CsbZIP genes showed differential expression under stress response and during CL flowering. Co-expression network, GO annotation and real-time quantitative reverse transcription PCR (qRT-PCR) analyses revealed a close relationship between CL flowering-associated genes and abiotic stress-related genes.ConclusionsBZIP TFs were comprehensively analysed and identified in allotetraploid C. songorica. Our results provide insights into the evolutionary history of the bZIP family in C. songorica and provide abiotic stress-responsive and CL-associated candidate CsbZIP genes for potential applications in the genetic improvement of plants.

Genome-Wide Analysis of the Role of NAC Family in Flower Development and Abiotic Stress Responses in Cleistogenes songorica

“…The Ks values peaked at 0.6–1.8 between C. songorica and rice ( Figure 3 a). The Ka/Ks ratios were primarily distributed at 0–0.36, with the maximum value being observed in the CsNAC059 - LOC_Os03g59730.1 pair (Ka/Ks = 0.62) ( Figure 3 b: Table S2 ), indicating that they undergo purifying selection during biological evolution between two species [ 37 ].…”

“…A total of 72.7% CsNAC duplicated gene was found between subgenome A and B in C. songorica , which was the same as the bZIP family (72.5%). In addition, a previous study indicated that C. songorica experienced a whole-genome duplication event during biological evolution [ 37 ]. These results suggested that whole-genome duplication events resulted in the expansion of the NAC family in C. songorica .…”

“…C. songorica was planted according to a previous report [ 37 ]. All seedlings were grown in a growing room at 26 ± 2 °C, under photosynthetically active radiation of 150 μmol m −2 s −1 , a 16 h photoperiod and 65% relative humidity.…”

QTL mapping for plant height and fruit branch number based on RIL population of upland cotton

“…Gh_ D13G0612 (AT5G23190) and Gh_D13G0806 (AT2G23180) in qFBN-c18-2 were annotated as cytochrome P450 genes, which may be involved in brassinosteroid (BR) biosynthesis (Wu et al 2016). Gh_D13G0732 (AT1G68640) in qFBN-c18-2 was annotated as bZIP transcription factor family protein, which may be involved in multiple biological processes in plants (Hu et al 2016;Lozano-Sotomayor et al 2016;Yan et al 2019). In general, these candidate genes for PH and FBN could play an important role in cell elongation, and tissue and organ differentiation and formation in plant development, but their specific functions need to be further verified.…”

Integrated analysis of co-expression, conserved genes and gene families reveal core regulatory network of heat stress response in Cleistogenes songorica, a xerophyte perennial desert plant

“…The 59 RNA-seq data under abiotic stresses including data from this article were used to co-expression analysis [40]. According to the result from each sample regarding the DEGs expression quantity, we removed the expression quantity from all samples that were < 1 and expressions that barely changed (DEGs variance was < 0.75).…”