Among major reactive oxygen species (ROS), hydrogen peroxide (H2O2) exhibits dual roles in plant metabolism. Low levels of H2O2 modulate many biological/physiological processes in plants; whereas, its high level can cause damage to cell structures, having severe consequences. Thus, steady-state level of cellular H2O2 must be tightly regulated. Glutathione peroxidases (GPX) and ascorbate peroxidase (APX) are two major ROS-scavenging enzymes which catalyze the reduction of H2O2 in order to prevent potential H2O2-derived cellular damage. Employing bioinformatics approaches, this study presents a comparative evaluation of both GPX and APX in 18 different plant species, and provides valuable insights into the nature and complex regulation of these enzymes. Herein, (a) potential GPX and APX genes/proteins from 18 different plant species were identified, (b) their exon/intron organization were analyzed, (c) detailed information about their physicochemical properties were provided, (d) conserved motif signatures of GPX and APX were identified, (e) their phylogenetic trees and 3D models were constructed, (f) protein-protein interaction networks were generated, and finally (g) GPX and APX gene expression profiles were analyzed. Study outcomes enlightened GPX and APX as major H2O2-scavenging enzymes at their structural and functional levels, which could be used in future studies in the current direction.

Members of the AP2/ERF transcription factor family play critical roles in plant development, biosynthesis of key metabolites, and stress response. A detailed study was performed to identify TtAP2s/ERFs in the durum wheat (Triticum turgidum ssp. durum) genome, which resulted in the identification of 271 genes distributed on chromosomes 1A-7B. By carrying 27 genes, chromosome 6A had the highest number of TtAP2s/ERFs. Furthermore, a duplication assay of TtAP2s/ERFs demonstrated that 70 duplicated gene pairs had undergone purifying selection. According to RNA-seq analysis, the highest expression levels in all tissues and in response to stimuli were associated with DRF and ERF subfamily genes. In addition, the results revealed that TtAP2/ERF genes have tissue-specific expression patterns, and most TtAP2/ERF genes were significantly induced in the root tissue. Additionally, 13 TtAP2/ERF genes (six ERFs, three DREBs, two DRFs, one AP2, and one RAV) were selected for further analysis via qRT-PCR of their potential in coping with drought and salinity stresses. The TtAP2/ERF genes belonging to the DREB subfamily were markedly induced under both drought-stress and salinity-stress conditions. Furthermore, docking simulations revealed several residues in the pocket sites of the proteins associated with the stress response, which may be useful in future site-directed mutagenesis studies to increase the stress tolerance of durum wheat. This study could provide valuable insights for further evolutionary and functional assays of this important gene family in durum wheat.

Brachypodium distachyon (brachypodium) is a small grass with the biological and genomic attributes necessary to serve as a model system for all grasses including small grains and grasses being developed as energy crops (e.g., switchgrass and Miscanthus ). To add natural variation to the toolkit available to plant biologists using brachypodium as a model system, it is imperative to establish extensive, well-characterized germplasm collections. The objectives of this study were to collect brachypodium accessions from throughout Turkey and then characterize the molecular (nuclear and organelle genome), morphological, and cytological variation within the collection. We collected 164 lines from 45 diverse geographic regions of Turkey and created 146 inbred lines. The majority of this material (116 of 146 inbred lines) was diploid. The similarity matrix for the diploid lines based on AFLP analysis indicated extensive diversity, with genetic distances ranging from 0.05 to 0.78. Organelle genome diversity, on the other hand, was low both among and within the lines used in this study. The geographic distribution of genotypes was not significantly correlated with either nuclear or organelle genome variation for the genotypes studied. Phenotypic characterization of the lines showed extensive variation in flowering time (7–22 weeks), seed production (4–193 seeds/plant), and biomass (15–77 g). Chromosome morphology of the collected brachypodium accessions varied from submetacentric to metacentric, except for chromosome 5, which was acrocentric. The diverse brachypodium lines developed in this study will allow experimental approaches dependent upon natural variation to be applied to this new model grass. These results will also help efforts to have a better understanding of complex large genomes (i.e., wheat, barley, and switchgrass).