Genome-wide characterization and expression profiling of Eucalyptus grandis HD-Zip gene family in response to salt and temperature stress

Abstract

Background The HD-Zip transcription factors are unique to plants and play an essential role in plant growth, development and stress responses. The HD-Zip transcription factor family consists of a highly conserved homeodomain (HD) and a leucine zipper domain (LZ) domain. Although the HD-Zip gene family has been extensively studied in many plant species, a systematic study of the Eucalyptus HD-Zip family has not been reported until today. Here, we systematically identified 40 HD-Zip genes in Eucalyptus (Eucalyptus grandis). Besides, we comprehensively analyzed the HD-Zips of Eucalyptus by studying the homology, conserved protein regions, gene structure, 3D structure of the protein, location of the genes on the chromosomes and the expression level of the genes in different tissues. Results The HD-Zip family in Eucalyptus has four subfamilies, which is consistent with other plants such as Arabidopsis and rice. Moreover, genes that are in the same group tend to have similar exon-intron structures, motifs, and protein structures. Under salt stress and temperature stress, the Eucalyptus HD-Zip transcription factors show a differential expression pattern. Conclusions Our findings reveal the response of HD-Zip transcription factors under salt and temperature stresses, laying a foundation for future analysis of Eucalyptus HD-Zip transcription factors.

Evolutionary Analysis of the Steroidogenic Acute Regulatory Protein-Related Lipid Transfer Domain and Its Response to Salt Stress In Vitis Vinifera

“…Moreover, some differences in physical and chemical properties are observed in different groups. These results are consistent with those in previous studies (Schrick et al 2004;Hill et al 2016;Zhang et al 2020). The analysis of the tertiary structure shows that eight major functional structural proteins, namely, MLN64 (Soccio et al 2003;Murcia et al 2006) Various abiotic stresses are related to the expansion of some genes because of tandem and segmental duplication events (Cannon et al 2004;Lynch et al 2000;Raes et al 2003;Otto et al 2002;Duarte et al 2006;Wang et al 2010;Finet et al 2013).…”

“…Prior studies that have highlighted the importance of the HD-Zip transcription factor family (Ding et al 2017;Chen et al 2017;Zhang et al 2020). However, a few studies have explored the HD-Zip III and the HD-Zip IV subfamily members containing the START domain proteins on plant salt stress.…”

“…This result suggests that the HD-Zip IV has a potential role in the defense environment, and HD-Zip IV is in uenced by ethylene (Li et al 2017b). The members of HD-Zip I and HD-Zip are reported to be related to salt stresses in Eucalyptus (Zhang et al 2020). EgHD-Zip27 from the HD-Zip II subfamily and EgHD-Zip37 from the HD-Zip I subfamily play an essential role in coping with salt stress (Zhang et al 2020), but the members of HD-Zip III and HD-Zip IV with salt stress are not mentioned.…”

“…A functional study on the GL2, a member of the HD-Zip START domain family, has found that the START domain is required for the GL2 transcription factor activity (Schrick et al 2014). HD-Zip III subfamily possesses the START domain, HD-START-associated domain, and Me-Glu-Lys-Hi-Leu-Ala (MEKHLA) domain, whereas the HD-Zip IV lacks the MEKHLA domain (Williams et al 2005;Zhang et al 2020). HD-Zip IV genes are expressed explicitly in the outer cell and epidermal and subepidermal cells of multiple species during biotic and abiotic stresses (Ingram et al 2000;Nakamura et al 2006).…”

Systematic Analysis of HD-ZIP Transcription Factors in Sesame Genome and Gene Expression Profiling of SiHD-ZIP Class I Entailing Drought Stress Responses at Early Seedling Stage

“…In-silico identification of SiHD-ZIP proteins HD-ZIP is a plant-specific TF family known for its roles in plant growth, development and responses to light and stress [39]. So far, HD-ZIP is a widely characterized TF family throughout plant kingdom such as Arabidopsis ( 48) [14], rice (48) [40], maize (55) [26], wheat ( 46) [22], potato (43) [39], tomato (51) [41], medicago (52) [42], foxtail millet (47) [20], tea plant (33) [8], grape (31) [43], cassava (57) [11], soybean (88) [44], Chinese cabbage (113) [45], poplar (63) [46], pear (52) [47], peach (33) [48], plum blossom (32) [49] and eucalyptus (40) [50]. In the given study, total 61 sesame HD-ZIP proteins, encoded by comparatively smaller number of genes (44) have been identified, based on sequence homology search (A. thaliana) and domains assignment rules by HMM (Supplementary Table 1).…”