Genome-wide identification, new classification, expression analysis and screening of drought & heat resistance related candidates in the RING zinc finger gene family of bread wheat (Triticum aestivum L.).

BACKGROUND: RING (Really Interesting New Gene) zinc finger (RING-zf) proteins belong to an important subclass of zinc fingers superfamily, which play versatile roles during various developmental stages and in abiotic stress responses. Based on the conserved cysteine and histidine residues, the RING-zf domains are classified into RING-HC (C3HC4), RING-H2 (C3H2C3), RING-v, RING-D, RING-S/T, RING-G, and RING-C2. However, little is known about the function of the RING-zfs of wheat. RESULTS: In this study, 129 (93.5%) of 138 members were found in nucleus, indicating TaRING-zf were primarily engaged in the degradation of transcription factors and other nuclear-localized proteins. 138 TaRING-zf domains can be divided into four canonical or modified types (RING-H2, RING-HC, RING-D, and RING-M). The RING-M was newly identified in T. aestivum, and might represent the intermediate other states between RING-zf domain and other modified domains. The consensus sequence of the RING-M domain can be described as M-X2-R-X14-Cys-X1-H-X2-Cys-X2-Cys-X10-Cys-X2-Cys. Further interspecies collinearity analyses showed that TaRING-zfs were more closely related to the genes in Poaceae. According to the public transcriptome data, most of the TaRING-zfs were expressed at different 15 stages of plant growth, development, and some of them exhibited specific responses to drought/heat stress. Moreover, 4 RING-HC (TraesCS2A02G526800.1, TraesCS4A02G290600.1, TraesCS4B02G023600.1 and TraesCS4D02G021200.1) and 2 RING-H2 (TraesCS3A02G288900.1 and TraesCS4A02G174600.1) were significantly expressed at different development stages and under drought stress. These findings provide valuable reference data for further study of their physiological functions in wheat varieties. CONCLUSIONS: Taken together, the characterization and classifications of the TaRING-zf family were extensively studied and some new features about it were revealed. This study could provide some valuable targets for further studies on their functions in growth and development, and abiotic stress responses in wheat.

The specific DNA barcodes based on chloroplast genes for species identification of Theaceae plants.

More than 600 species in over 40 genera have been identified in family Theaceae worldwide. The accurate identification of Theaceae plants can ensure the market economic order, and it plays a vital role in achieving the sustainable utilization of germplasm resources. DNA barcoding, one of the most potential species identification technologies at present, has advanced in the rapid, accurate and repetitive discrimination of species. In this study, matK + ndhF + ycf1 was observed as the optimal combined candidate gene sequence of DNA barcodes by analyzing genetic information of four single chloroplast DNA sequences, including matK, rbcL, ndhF and ycf1, as well as six combined gene sequences. Subsequently, the experiments were performed on phylogenetic analysis based on genetic distance to study the phylogenetic relationship of Theaceae plants and evaluate the species identification accuracy of matK + ndhF + ycf1. Lastly, the species-specific DNA barcodes were designed by searching the variable sites (one type of single nucleotide polymorphism sites) for the accurate identification of Camellia amplexicaulis, Franklinia alatamaha, Gordonia brandegeei and Stewartia micrantha. The previous methods of screening and testing candidate gene sequences were optimized, and innovation was made in the above methods. The process of making visual DNA barcodes was standardized. Besides, DNA barcoding technology increased the accuracy of species identification and DNA barcoding was analyzed in accordance with the theories of population genetics (e.g., neutral theory of molecular evolution). The results of the study will lay a basis for the identification and protection of Theaceae species and germplasm resources. Supplementary Information: The online version contains supplementary material available at 10.1007/s12298-022-01175-7.