Genome-wide identification and characterization of the apple (Malus domestica) HECT ubiquitin-protein ligase family and expression analysis of their responsiveness to abiotic stresses

Xu, Jianing; Xing, Shanshan; Cui, Hongyuan; Chen, Xuesen; Wang, Xiaoyun

doi:10.1007/s00438-015-1129-0

Cited by 24 publications

(21 citation statements)

References 50 publications

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“…Meng et al [19] analyzed 365 plant HECT genes, including 19 HECT genes from the soybean genome (2 n = 4 x = 40), and divided them into seven phylogenetic groups. Xu et al [20] identified 13 HECT genes from the apple genome (2 n = 2 x = 34) and divided them into four phylogenetic groups, consistent with those of A. thaliana .…”

Section: Introductionmentioning

confidence: 99%

Comprehensive Genomic Survey, Characterization and Expression Analysis of the HECT Gene Family in Brassica rapa L. and Brassica oleracea L.

Álam

Cui

Batool

et al. 2019

Genes

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The HECT-domain protein family is one of the most important classes of E3 ligases. While the roles of this family in human diseases have been intensively studied, the information for plant HECTs is limited. In the present study, we performed the identification of HECT genes in Brassica rapa and Brassica oleracea, followed by analysis of phylogeny, gene structure, additional domains, putative cis-regulatory elements, chromosomal location, synteny, and expression. Ten and 13 HECT genes were respectively identified in B. rapa and B. oleracea and then resolved into seven groups along with their Arabidopsis orthologs by phylogenetic analysis. This classification is well supported by analyses of gene structure, motif composition within the HECT domain and additional protein domains. Ka/Ks ratio analysis showed that these HECT genes primarily underwent purifying selection with varied selection pressures resulting in different rates of evolution. RNA-Seq data analysis showed that the overwhelming majority of them were constitutively expressed in all tested tissues. qRT-PCR based expression analysis of the 10 B. rapa HECT genes under salt and drought stress conditions showed that all of them were responsive to the two stress treatments, which was consistent with their promoter sequence analysis revealing the presence of an important number of phytohormone-responsive and stress-related cis-regulatory elements. Our study provides useful information and lays the foundation for further functional determination of each HECT gene across the Brassica species.

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Section: Introductionmentioning

confidence: 99%

Comprehensive Genomic Survey, Characterization and Expression Analysis of the HECT Gene Family in Brassica rapa L. and Brassica oleracea L.

Álam

Cui

Batool

et al. 2019

Genes

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“…F-box proteins often mediate the mechanism of ubiquitination and degradation of stress-related proteins which may be positive or negative regulatory proteins. The F-box gene directly or indirectly affects plant hormone signal transduction pathway and affects resistance of plants to saline and alkaline conditions, especially the ABA signal pathway [ 51 , 52 ]. In this study, the expression of dehydrin DHN3 was upregulated and probable F-box protein At5g04010 was downregulated (electronic supplementary material, table S3), indicating that these two genes may be involved in the response of L. perenne roots to saline stress.…”

Section: Discussionmentioning

confidence: 99%

Growth, physiological and transcriptomic analysis of the perennial ryegrassLolium perennein response to saline stress

Guo

Zhu³

et al. 2020

R. Soc. open sci.

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Salinization of soil is a global environmental concern. To bioremediate or use saline-alkali lands, most studies focused on screening of halophytes and breeding of saline-tolerant non-halophyte vegetables. Seldom studies investigated effects of salinity on general landscape plants, which are important for landscape construction in urban areas. In the present study, effects of salinity on seed germination and seedling growth of the perennial ryegrass Lolium perenne were investigated. The final seed germination rate was not affected at salinity up to 6.4‰. Partial seedlings wilted in all saline treatments and the mortality of L. perenne was positively correlated with salinity. Treatments with salinity equal to or lower than 1.6‰ did not affect length and dry weight of shoot and root. These results suggested that L. perenne could be sowed and then grow well in low-salinity areas. To explore the underlying physiological mechanisms, contents of photosynthetic pigments and antioxidant indices were determined. The results showed that contents of chlorophyll a , b and carotenoid significantly decreased in all saline treatments, in comparison to the control. Similarly, activities of superoxide dismutase and peroxidase decreased and contents of glutathione and malondialdehyde increased in saline treatments. Additionally, transcriptome analysis identified 792 differentially expressed genes (DEGs) in L. perenne shoots between 6.4‰ saline treatment and the control. Compared with the control, genes in relation to iron transportation and amino acid metabolism were downregulated, but genes participating in energy metabolism were upregulated. These changes would inhibit toxicity of ion accumulation and provide more energy for plants to resist saline stress.

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“…This protein complex plays an important role for unneeded protein degradation during the cell cycle. It has been found that several publications have reported that these proteins respond to salt stress [71,84,85,86,87,88,89]. Thus, it is crucial to investigate this degradation process as a pathway system in which OsFBL23 and OsFBL16 are involved.…”

Section: Discussionmentioning

confidence: 99%

Two-State Co-Expression Network Analysis to Identify Genes Related to Salt Tolerance in Thai Rice

Suratanee

Chokrathok

Chutimanukul

et al. 2018

Genes

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Khao Dawk Mali 105 (KDML105) rice is one of the most important crops of Thailand. It is a challenging task to identify the genes responding to salinity in KDML105 rice. The analysis of the gene co-expression network has been widely performed to prioritize significant genes, in order to select the key genes in a specific condition. In this work, we analyzed the two-state co-expression networks of KDML105 rice under salt-stress and normal grown conditions. The clustering coefficient was applied to both networks and exhibited significantly different structures between the salt-stress state network and the original (normal-grown) network. With higher clustering coefficients, the genes that responded to the salt stress formed a dense cluster. To prioritize and select the genes responding to the salinity, we investigated genes with small partners under normal conditions that were highly expressed and were co-working with many more partners under salt-stress conditions. The results showed that the genes responding to the abiotic stimulus and relating to the generation of the precursor metabolites and energy were the great candidates, as salt tolerant marker genes. In conclusion, in the case of the complexity of the environmental conditions, gaining more information in order to deal with the co-expression network provides better candidates for further analysis.

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Genome-wide identification and characterization of the apple (Malus domestica) HECT ubiquitin-protein ligase family and expression analysis of their responsiveness to abiotic stresses

Cited by 24 publications

References 50 publications

Comprehensive Genomic Survey, Characterization and Expression Analysis of the HECT Gene Family in Brassica rapa L. and Brassica oleracea L.

Comprehensive Genomic Survey, Characterization and Expression Analysis of the HECT Gene Family in Brassica rapa L. and Brassica oleracea L.

Growth, physiological and transcriptomic analysis of the perennial ryegrassLolium perennein response to saline stress

Two-State Co-Expression Network Analysis to Identify Genes Related to Salt Tolerance in Thai Rice

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