Genome-wide identification and expression analysis of the phosphatase 2A family in rubber tree (Hevea brasiliensis)

Chao, Jinquan; Huang, Zhejun; Yang, Shuguang; Deng, Xianwen; Tian, Weimin

doi:10.1371/journal.pone.0228219

Cited by 4 publications

(2 citation statements)

References 37 publications

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“…The gene position of PtrGASAs and chromosome size were obtained from Phytozome 12.0 and visualized by the TBtools (South China Agricultural University, Guangzhou, China). The cis-acting elements of promoters were predicted using PlantCARE (http://bioinformatics.psb.ugent.be/webtools/plantcare/html/, accessed on 5 September 2021) and classified by reference [73][74][75] ). The gene structure map of GASA genes was drawn by using the gene structure visualization server GSDS2.0 (http://gsds.gao-lab.org/, accessed on 11 September 2021).…”

Section: Identification Of Gasa Family Genes In P Trichocarpa and P Euphraticamentioning

confidence: 99%

Genome-Wide Comprehensive Analysis of the GASA Gene Family in Populus

Han

Jiao

Niu

et al. 2021

IJMS

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Gibberellic acid-stimulated Arabidopsis (GASA) proteins, as cysteine-rich peptides (CRPs), play roles in development and reproduction and biotic and abiotic stresses. Although the GASA gene family has been identified in plants, the knowledge about GASAs in Populus euphratica, the woody model plant for studying abiotic stress, remains limited. Here, we referenced the well-sequenced Populus trichocarpa genome, and identified the GASAs in the whole genome of P. euphratica and P. trichocarpa. 21 candidate genes in P. trichocarpa and 19 candidate genes in P. euphratica were identified and categorized into three subfamilies by phylogenetic analysis. Most GASAs with signal peptides were located extracellularly. The GASA genes in Populus have experienced multiple gene duplication events, especially in the subfamily A. The evolution of the subfamily A, with the largest number of members, can be attributed to whole-genome duplication (WGD) and tandem duplication (TD). Collinearity analysis showed that WGD genes played a leading role in the evolution of GASA genes subfamily B. The expression patterns of P. trichocarpa and P. euphratica were investigated using the PlantGenIE database and the real-time quantitative PCR (qRT-PCR), respectively. GASA genes in P. trichocarpa and P. euphratica were mainly expressed in young tissues and organs, and almost rarely expressed in mature leaves. GASA genes in P. euphratica leaves were also widely involved in hormone responses and drought stress responses. GUS activity assay showed that PeuGASA15 was widely present in various organs of the plant, especially in vascular bundles, and was induced by auxin and inhibited by mannitol dramatically. In summary, this present study provides a theoretical foundation for further research on the function of GASA genes in P. euphratica.

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Section: Identification Of Gasa Family Genes In P Trichocarpa and P Euphraticamentioning

confidence: 99%

Genome-Wide Comprehensive Analysis of the GASA Gene Family in Populus

Han

Jiao

Niu

et al. 2021

IJMS

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“…A transcript similar to protein phosphatase 2C (PP2C) was one of the 20 hubs in cluster c171. Chao et al (2020), in a genome-wide identification and expression analysis of the phosphatase 2A family in rubber trees, identified cis-acting elements related to the low temperature responsiveness (LTR) category. Under non-stress conditions, PP2C proteins negatively regulate the ABA-mediated signaling pathway by inactivating ABA-responsive genes.…”

Section: Identification Of Key Elements Within Cold Response-associat...mentioning

confidence: 99%

A deeper cascade of mechanisms involved in cold resistance inHevea brasiliensis

Silva

Bajay

Aono

et al. 2021

Preprint

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Hevea brasiliensis, a tropical tree species from the Amazon rainforest, is the main source of natural rubber worldwide. Due to the high pressure of fungal diseases in hot, humid regions, rubber plantations have been moved to “escape areas”, which are dryer and have lower temperatures during the winter. Here, we combined gene expression data of a primary (GT1) and a secondary (RRIM600) young rubber tree clones, which present different cold tolerance strategies, to analyze rubber tree gene expression regulation during 24 h of cold exposure (10°C). Together with traditional differential expression approaches, a RNA sequencing (RNA-seq) gene coexpression network (GCN) comprising 27,220 genes was established in which the genes were grouped into 832 clusters. In the GCN, most of the rubber tree molecular responses to cold stress were grouped in 26 clusters, which were divided into three GCN modules: a downregulated group comprising 12 clusters and two upregulated groups comprising eleven and three clusters. Considering the three modules identified, the general Hevea response to short-term cold exposure involved downregulation of gibberellin (GA) signaling, complex regulation of jasmonic acid (JA) stress responses and programmed cell death (PCD) and upregulation of ethylene responsive genes. The hub genes of the cold-responsive modules were subsequently identified and analyzed. As a result of the GCN strategy applied in this study, we could not only access individual DEGs related to the Hevea cold response, but also provide insights into a deeper cascade of associated mechanisms involved in the response to cold stress in young rubber trees. Our results may represent the genetic stress responses of the species, developed during its evolution, since the varieties chosen for this work are genotypes that were selected during the early years of rubber tree domestication. The understanding of H. brasiliensis cold response mechanisms can greatly improve the breeding strategies for this crop, which has a narrow genetic base, is impacted by climate change and is the only source for large-scale rubber production.

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Walnut phosphatase 2A proteins interact with basic leucine zipper protein JrVIP1 to regulate osmotic stress response <i>via</i> calcium signaling

He,

Chen,

et al. 2024

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Genome-wide identification and expression analysis of the phosphatase 2A family in rubber tree (Hevea brasiliensis)

Cited by 4 publications

References 37 publications

Genome-Wide Comprehensive Analysis of the GASA Gene Family in Populus

Genome-Wide Comprehensive Analysis of the GASA Gene Family in Populus

A deeper cascade of mechanisms involved in cold resistance inHevea brasiliensis

Walnut phosphatase 2A proteins interact with basic leucine zipper protein JrVIP1 to regulate osmotic stress response <i>via</i> calcium signaling

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