Genome-wide Identification and Evolution of the PP2C Gene Family in Eight Rosaceae Species and Expression Analysis Under Stress in Pyrus bretschneideri

Wang, Guo‐Ming; Sun, Xun; Guo, Zhi-Hua; Joldersma, Dirk; Guo, Liu; Qiao, Xin; Qi, Kaijie; Gu, Chao; Zhang, Shaoling

doi:10.3389/fgene.2021.770014

Cited by 17 publications

(12 citation statements)

References 67 publications

(99 reference statements)

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“…JrVHAG1 was induced by CdCl 2 and further confirmed that its Cd-responsive function is also achieved through the ABA signal pathway [54]. PbrPP2C10, PbrPP2C11, PbrPP2C15, and PbrPP2C18 were up-regulated by exogenous ABA, as a presumption that PbrPP2C is related to ABA [37]. Therefore, based on the performance of JrPP2Cs under different stress and ABA in this study and other previous reports, we believe that the response of walnut PP2C family genes to stress is related to ABA signal.…”

Section: Discussionmentioning

confidence: 55%

“…In order to reveal the adversity adaptation mechanism of walnuts then to provide a basis for walnut cultivation and management to ensure the yield and quality, in this study, 41 walnut PP2C genes those may have potential functions in stress response were identified (Table 1). The sequence characteristics (ORF length, amino acid number, molecular weight, and pI) of JrPP2Cs (Table 1) were ranged similarly as other species, for instance, the molecular weights of PP2C proteins from Pyrus bretschneideri, tomoto and current walnut were 7.5 ~ 243 [37], 6.7 ~ 120 [26], and 18.6 ~ 119 kDa, respectively. In terms of evolutionary relationship, the 41 JrPP2C proteins shared a high similarity with the members of PP2C family of Arabidopsis and poplar, and could be classified into eleven subfamilies with reference to the classification in Arabidopsis [38], and wild soybean [39] (Fig.…”

Section: Discussionmentioning

confidence: 78%

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

et al. 2022

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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.

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Section: Discussionmentioning

confidence: 55%

Section: Discussionmentioning

confidence: 78%

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

et al. 2022

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“…Fifty-six FvPP2C and 228 FaPP2C genes were identified by homology comparison ( Supplementary Tables S1 and S2 ). Obviously, the amount of FvPP2C in woodland strawberry was much less than that in A. thaliana (80) [ 29 ], rice (78) [ 29 ], wheat (95) [ 49 ], apple (128) [ 50 ], and peach (74) [ 50 ], while the amount of FaPP2C in pineapple strawberry was higher. In addition, 56 CsPP2Cs were identified in cucumber, which was consistent with woodland strawberry.…”

Section: Discussionmentioning

confidence: 99%

“…The PP2C gene family members in most plants such as A. thaliana [ 29 ], rice [ 29 ], wheat [ 50 ] and cucumber [ 51 ] were divided into 13 subfamilies by systematic cluster analysis. In this study, the PP2C genes of A. thaliana , woodland, and pineapple strawberries were divided into 11 subfamilies ( Figure 1 ).…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Identification and Abiotic Stress Response Analysis of PP2C Gene Family in Woodland and Pineapple Strawberries

Guo

Liu

et al. 2023

IJMS

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Protein phosphatase 2C (PP2C) is a negative regulator of serine/threonine residue protein phosphatase and plays an important role in abscisic acid (ABA) and abiotic-stress-mediated signaling pathways in plants. The genome complexity of woodland strawberry and pineapple strawberry is different due to the difference in chromosome ploidy. This study conducted a genome-wide investigation of the FvPP2C (Fragaria vesca) and FaPP2C (Fragaria ananassa) gene family. Fifty-six FvPP2C genes and 228 FaPP2C genes were identified from the woodland strawberry and pineapple strawberry genomes, respectively. FvPP2Cs were distributed on seven chromosomes, and FaPP2Cs were distributed on 28 chromosomes. The size of the FaPP2C gene family was significantly different from that of the FvPP2C gene family, but both FaPP2Cs and FvPP2Cs were localized in the nucleus, cytoplasm, and chloroplast. Phylogenetic analysis revealed that 56 FvPP2Cs and 228 FaPP2Cs could be divided into 11 subfamilies. Collinearity analysis showed that both FvPP2Cs and FaPP2Cs had fragment duplication, and the whole genome duplication was the main cause of PP2C gene abundance in pineapple strawberry. FvPP2Cs mainly underwent purification selection, and there were both purification selection and positive selection effects in the evolution of FaPP2Cs. Cis-acting element analysis found that the PP2C family genes of woodland and pineapple strawberries mainly contained light responsive elements, hormone responsive elements, defense and stress responsive elements, and growth and development-related elements. The results of quantitative real-time PCR (qRT-PCR) showed that the FvPP2C genes showed different expression patterns under ABA, salt, and drought treatment. The expression level of FvPP2C18 was upregulated after stress treatment, which may play a positive regulatory role in ABA signaling and abiotic stress response mechanisms. This study lays a foundation for further investigation on the function of the PP2C gene family.

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“…The PP2C genes encode crucial signaling molecules in developmental processes, phytohormone signaling, and stress responses in Arabidopsis spp., maize, and members of the Rosaceae family (Kerk et al, 2002;Wei and Pan 2014;Guo et al, 2021). However, characterization of the chestnut PP2C gene family was yet to be undertaken, despite the availability of the chestnut genome sequence.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide identification, evolutionary, and expression analyses of the PP2C gene family in Castanea mollissima Blume.

Shang

Wang

et al. 2022

Preprint

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Chestnut (Castanea mollissima Bl.) is an economically important tree species that is primarily utilized for nut and timber production. The protein phosphatase 2C (PP2C) gene family contributes largely to stress responses and developmental processes in several plants. However, the classification, characteristics, and functions of chestnut PP2C genes are unknown. Here, we provide comprehensive analyses and expression profiles of PP2C genes in the chestnut genome. A total of 68 genes were identified, whose protein length (PL), molecular weights (MW) and isoelectric points (IP) are 186 ~ 1079 amino acids, 20.31 ~ 119.40 kDa, and 4.66 ~ 9.30, respectively. They are randomly distributed on 12 chromosomes. These genes formed 12 phylogenetic clusters. Most CmPP2C (PP2C in chestnut) proteins within a subgroup had similar compositions of amino acid sequences of motifs, conserved domains, and exon/introns, according to phylogenetic analyses. The expression profile analysis revealed both significant CmPP2C expression levels in leaves and seeds, and the clear involvement of CmPP2C22 in seed development and multiple abiotic stresses. These findings indicate that CmPP2C genes play potential vital roles in chestnut response to multiple abiotic stresses and provide new insights into the function of CmPP2C genes.

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Genome-wide Identification and Evolution of the PP2C Gene Family in Eight Rosaceae Species and Expression Analysis Under Stress in Pyrus bretschneideri

Cited by 17 publications

References 67 publications

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

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

Genome-Wide Identification and Abiotic Stress Response Analysis of PP2C Gene Family in Woodland and Pineapple Strawberries

Genome-wide identification, evolutionary, and expression analyses of the PP2C gene family in Castanea mollissima Blume.

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