Pervasive duplication, biased molecular evolution and comprehensive functional analysis of the PP2C family in Glycine max

Fan, Kai; Chen, Yunrui; Mao, Zhijun; Yao, Fang; Li, Zhaowei; Lin, Weiwei; Zhang, Yongqiang; Liu, Jianping; Huang, Jinwen

doi:10.1186/s12864-020-06877-4

Cited by 7 publications

(6 citation statements)

References 59 publications

(78 reference statements)

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“…2, 5B), indicating the functional similarity and specificity of these JrPP2C genes. Moreover, the gene and protein structural features of JrPP2Cs were similar to those of PP2C in Glycine max [44], Gossypium hirsutum [45], Brassica rapa [46] and Brachypodium distachyon [47]. Soybean PP2Cs could control plant growth and development [44].…”

Section: Discussionmentioning

confidence: 83%

“…Moreover, the gene and protein structural features of JrPP2Cs were similar to those of PP2C in Glycine max [44], Gossypium hirsutum [45], Brassica rapa [46] and Brachypodium distachyon [47]. Soybean PP2Cs could control plant growth and development [44]. Cotton PP2C gene family plays critical role in organ and fiber development, as well as abiotic stress tolerance [45].…”

Section: Discussionmentioning

confidence: 93%

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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: 83%

Section: Discussionmentioning

confidence: 93%

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

et al. 2022

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“…Compared to previous studies [ 28 ], the latest version of GFF3 annotation file was used to determine PP2C and SnRK2 genes of Williams 82, which would be more accurate to reveal the structure and function of the two gene families. In addition, Zhang et al and Fan et al both only observed expression patterns of these genes at different tissues, and neither elaborated the mechanic networks under drought stress related to the ABA signaling pathway [ 29 , 34 ]. In this study, we focus on the abundance of PP2C-A and SnRK2 members under ABA and drought treatments.…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Identification, Expression and Interaction Analysis of GmSnRK2 and Type A PP2C Genes in Response to Abscisic Acid Treatment and Drought Stress in Soybean Plant

Shen

Nan

Jiang

et al. 2022

IJMS

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As a typical ancient tetraploid, soybean (Glycine max) is an important oil crop species and plays a crucial role in supplying edible oil, plant protein and animal fodder worldwide. As global warming intensifies, the yield of soybean in the field is often strongly restricted by drought stress. SNF1-related protein kinase 2 (SnRK2) and type A protein phosphatase 2C (PP2C-A) family members are core components of the abscisic acid (ABA) signal transduction pathway in plants and have been suggested to play important roles in increasing plant tolerance to drought stress, but genetic information supporting this idea is still lacking in soybean. Here, we cloned the GmSnRK2s and GmPP2C-A family genes from the reference genome of Williams 82 soybean. The results showed that the expression patterns of GmSnRK2s and GmPP2C-As are spatiotemporally distinct. The expression of GmSnRK2s in response to ABA and drought signals is not strictly the same as that of Arabidopsis SnRK2 homologous genes. Moreover, our results indicated that the duplicate pairs of GmSnRK2s and GmPP2C-As have similar expression patterns, cis-elements and relationships. GmSnRK2.2 may have a distinct function in the drought-mediated ABA signaling pathway. Furthermore, the results of yeast two-hybrid (Y2H) assays between GmSnRK2s and GmPP2C-As revealed that GmSnRK2.17, GmSnRK2.18, GmSnRK2.22, GmPP2C5, GmPP2C7, GmPP2C10 and GmPP2C17 may play central roles in the crosstalk among ABA signals in response to drought stress. Furthermore, GmPP2C-As and GmSnRKs were targeted by miRNA and validated by degradome sequencing, which may play multiple roles in the crosstalk between ABA and drought signals and other stress signals. Taken together, these results indicate that GmSnRK2s and GmPP2C-As may play a variety of roles in the drought-mediated ABA signaling pathway.

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“…The conserved motifs of the KUP family in G. hirsutum, G. barbadense, G. arboretum, and G. raimondii were identified with MEME (http://meme-suite.org/tools/meme) (Bailey et al, 2009). Parameters were set on the basis of values that were previously used to analyze putative motifs (Fan et al, 2019;Fan et al, 2020). The identified motifs were further annotated by using CDD (Marchler-Bauer et al, 2015).…”

Section: Structural and Promoter Analysismentioning

confidence: 99%

Molecular Evolution and Expansion of the KUP Family in the Allopolyploid Cotton Species Gossypium hirsutum and Gossypium barbadense

et al. 2020

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The comprehensive analysis of gene family evolution will elucidate the origin and evolution of gene families. The K+ uptake (KUP) gene family plays important roles in K+ uptake and transport, plant growth and development, and abiotic stress responses. However, the current understanding of the KUP family in cotton is limited. In this study, 51 and 53 KUPs were identified in Gossypium barbadense and Gossypium hirsutum , respectively. These KUPs were divided into five KUP subfamilies, with subfamily 2 containing three groups. Different subfamilies had different member numbers, conserved motifs, gene structures, regulatory elements, and gene expansion and loss rates. A paleohexaploidization event caused the expansion of GhKUP and GbKUP in cotton, and duplication events in G. hirsutum and G. barbadense have happened in a common ancestor of Gossypium . Meanwhile, the KUP members of the two allopolyploid subgenomes of G. hirsutum and G. barbadense exhibited unequal gene proportions, gene structural diversity, uneven chromosomal distributions, asymmetric expansion rates, and biased gene loss rates. In addition, the KUP families of G. hirsutum and G. barbadense displayed evolutionary conservation and divergence. Taken together, these results illustrated the molecular evolution and expansion of the KUP family in allopolyploid cotton species.

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Pervasive duplication, biased molecular evolution and comprehensive functional analysis of the PP2C family in Glycine max

Cited by 7 publications

References 59 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, Expression and Interaction Analysis of GmSnRK2 and Type A PP2C Genes in Response to Abscisic Acid Treatment and Drought Stress in Soybean Plant

Molecular Evolution and Expansion of the KUP Family in the Allopolyploid Cotton Species Gossypium hirsutum and Gossypium barbadense

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