Transcriptome-wide identification of walnut PP2C family genes in response to external stimulus

Abstract

Walnut is an important economic tree species while confronting with global environmental stress, resulting in decline in quality and yield. Therefore, it is urgent to elucidate the molecular mechanism for the regulation of walnut response to adversity. The protein phosphatase 2C (PP2C) gene family participates in cellular processes in eukaryotes through reversible phosphorylation of proteins and signal transduction regulation. However, the stress response function of PP2C genes was far to be clarified. Therefore, to understand the stress response mechanism of walnut tree, in this study, a total of 41 PP2C genes with complete ORFs were identified from Juglans regia, whose basic bio-information and expression patterns in response to multiple stresses and ABA were confirmed. The results showed that the ORFs of JrPP2Cs were 495 ~ 3231 bp in length, the predicted JrPP2C proteins contained 164 to 1076 amino acids and the molecular weights were 18,581.96 ~ 118,853.34 Da, the pI was 4.55 ~ 9.58. These JrPP2C genes were unevenly distributed on 14 chromosomes, among which Chr11 and Chr13 contained the most genes. Phylogenetic analysis found that these JrPP2C proteins were classed into 9 subfamilies, among which group F covered most JrPP2Cs. The JrPP2Cs in the same subfamily exhibited similarities in the composition of conserved domains, amino acid sequences of motifs and exon/intron organization in DNA sequences. Each JrPP2C includes 4 ~ 10 motifs and each motif contained 15 ~ 37 amino acids. Among the motifs, motif1, motif2, motif3 and motif8 were most abundant. Most of the JrPP2C genes diversely response to osmotic, cadmium, and Colletotrichum gloeosporioide stress as well as ABA treatments, among which JrPP2C28, JrPP2C17, JrPP2C09, JrPP2C36 were more obvious and deserves further attention. All these results indicated that JrPP2C genes play potential vital roles in plant response to multiple stimulus, and are possibly involved in ABA-dependent signaling pathway.

Genome-Wide Identification of the CBF Gene Family and ICE Transcription Factors in Walnuts and Expression Profiles under Cold Conditions

“…The previous studies showed that the conserved domains in transcription factors (TFs) might be related to gene functions, and the cis -acting elements play roles in the regulation of genes and post-transcriptional modification; similar results have also been found in other plant studies [ 28 , 37 , 39 ]. All CBF proteins contained only one domain, AP2, indicating that they play key roles in plant growth, development, and stress, which is consistent with the previous studies [ 54 , 55 ].…”

“…Cis -acting elements are well-known participants in the control of gene expression [ 37 , 38 , 48 ]. In our study, many cis -acting elements associated with responsiveness to light and phytohormones were identified in the upstream CBF and ICE promoter regions ( Figure 4 ), which suggests that both CBF and ICE proteins might be associated with photosynthetic and hormone responses and regulations.…”

“…Climate change may affect the growth of woody tree species in their distribution region, as low temperatures affect plant development and growth in wild walnuts [ 23 , 30 ]. The developments in whole genome sequencing in walnut and woody species have revealed evidence of cold and chilling stress [ 28 , 31 , 32 , 33 , 34 ] and the genome-wide identification of gene families related to stress studies in Juglans species [ 35 , 36 , 37 , 38 ]. CBF and ICE1, as important transcription factors in response to cold stress, may enhance the cold resistance of plants under low-temperature conditions by regulating the essential functional genes [ 39 , 40 , 41 ].…”

Genome-Wide Identification and Expression Analysis of BnPP2C Gene Family in Response to Multiple Stresses in Ramie (Boehmeria nivea L.)

“…After identification of the ramie PP2C gene family, 63 members of the BnPP2C family were mapped on the chromosomes by TBtools and renamed according to the chromosome number and the order of the position of each gene on the chromosome (BnPP2C1-BnPP2C63). The analysis showed that the 62 BnPP2C genes assembled were unevenly distributed on the 14 chromosomes of ramie (Figure 3), with most BnPP2Cs anchored in Chr1 (8). Only two BnPP2Cs in each were anchored in Chr5, Ch10 and Chr12.…”

“…The PP2C families have been reported in many plant species, such as Arabidopsis thaliana (80) [5], wheat (Triticum aestivum) (257) [6], cucumber (Cucumis sativus) (56) [7], walnut (Juglans regia) (44) [8], etc. Phylogenetic analysis classified the 80 AtPP2C genes in Arabidopsis into 13 subfamilies (A-L), while the other seven were not involved in the grouping.…”