Patterns of Gene Duplication and Their Contribution to Expansion of Gene Families in Grapevine

Wang, Nian; Xiang, Yue; Fang, Linchuan; Wang, Yajie; Xin, H. P.; Li, Shaohua

doi:10.1007/s11105-013-0556-5

Cited by 41 publications

(33 citation statements)

References 48 publications

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“…The large proportion of duplicated genes in the TIFY family revealed that WGD made a large contribution to the generation of the TIFY gene family. Although the duplicated TIFY genes may have a common ancestor, their functions and expression patterns were complex, since duplicated genes can undergo substantial changes in their structures and/or regulatory mechanisms to assume novel roles [62,63]. For example, in the duplicated gene pair of BoJAZ1/BoJAZ19 identified in this work, BoJAZ1 has five exons with 241 amino acid residues, while BoJAZ19 has three exons with 292 amino acid residues, and their expression levels were different in various cabbage tissues.…”

Section: Discussionmentioning

confidence: 84%

“…Gene duplication, including tandem, segmental, and whole genome duplication, plays an important role in the evolution of various species and contributes to the expansion of gene families [61,62]. Previous whole genome identification found a total of 1825 gene clusters containing 4365 tandemly duplicated in B. oleracea, and there were similar numbers in B. rapa (5181) and A. thaliana (4170) [34].…”

Section: Discussionmentioning

confidence: 99%

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Genome-Wide Identification, Expression Profile of the TIFY Gene Family in Brassica oleracea var. capitata, and Their Divergent Response to Various Pathogen Infections and Phytohormone Treatments

Liu

Zhao

Yang

et al. 2020

Genes

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TIFY, a plant-specific gene family with the conserved motif TIF[F/Y]XG, plays important roles in various plant biological processes. Here, a total of 36 TIFY genes were identified in the Brassica oleracea genome and classified into JAZ (22 genes), TIFY (7 genes), ZML (5 genes), and PPD (2 genes) subfamilies based on their conserved motifs, which were distributed unevenly across nine chromosomes with different lengths (339–1077 bp) and exon numbers (1–8). Following phylogenetic analysis with A. thaliana and B. rapa TIFY proteins, ten clades were obtained. The expression of these TIFY genes was organ-specific, with thirteen JAZ genes and two PPD genes showing the highest expression in roots and leaves, respectively. More importantly, the JAZs showed divergent responses to various pathogen infections and different phytohormone treatments. Compared with the susceptible line, most JAZs were activated after Plasmodiophora brassicae infection, while there were both induced and inhibited JAZs after Fusarium oxysporum or Xanthomonas campestris infection in the resistance line, indicating their probably distinct roles in disease resistance or susceptibility. Further, the JAZs were all upregulated after MeJA treatment, but were mostly downregulated after SA/ET treatment. In summary, these results contribute to our understanding of the TIFY gene family, revealing that JAZs may play crucial and divergent roles in phytohormone crosstalk and plant defense.

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Section: Discussionmentioning

confidence: 84%

Section: Discussionmentioning

confidence: 99%

Genome-Wide Identification, Expression Profile of the TIFY Gene Family in Brassica oleracea var. capitata, and Their Divergent Response to Various Pathogen Infections and Phytohormone Treatments

Liu

Zhao

Yang

et al. 2020

Genes

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“…The duplication pattern of a gene usually reveals how the gene was generated, how its function evolved and what roles it may played in plant growth and development (Wang et al, 2013). WGD is predicted to produce new genomic regions based on an ancestral genome, and this event occurs once or several times over many (sometimes hundreds of) millions of years (Wang et al, 2011).…”

Section: Discussionmentioning

confidence: 99%

“…This indicates that the functions of members of a gene family are indispensable for plant growth and development in a given species. In addition, genes in families that were mainly produced by WGD usually evolve slowly (Wang et al, 2013; Soltis and Soltis, 2016). In this study, we found that 19 of the 24 TIFY genes were produced by WGD.…”

Section: Discussionmentioning

confidence: 99%

Identification of TIFY Family Genes and Analysis of Their Expression Profiles in Response to Phytohormone Treatments and Melampsora larici-populina Infection in Poplar

Xia

Cao

et al. 2017

Front. Plant Sci.

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The TIFY domain contains approximately 36 conserved amino acids that form the core motif TIF[F/Y]XG, and they were reported to play important roles in plant growth, tissue development and defense regulation. Moreover, more and more evidence has shown that some members of the TIFY gene family perform their functions by modulating plant hormone signaling pathways. Poplar trees are found worldwide, and they comprise approximately 30 species. Benefit from the importance of poplar and its advanced platform, this tree is considered to be the model perennial plant. Here, we conducted a genome-wide identification of TIFY genes in poplar, and 24 TIFY genes were found. These 24 TIFY genes were assigned to different subfamilies according to the presence or absence of domains and motifs that they harbored. Careful analyses of their locations, structures, evolution and duplication patterns revealed an overview of this gene family in poplar. The expression profiles of these 24 TIFY genes were then analyzed in different tissues using publicly available expression data; their expression profiles following different JA/SA treatments and infection with leaf rust pathogen were also carefully examined by qRT-PCR assays. Based on their expression profiles, the functions of a number of TIFY genes could be predicted. By performing this study, we have provided valuable information for further functional characterisation of TIFY genes in poplar and candidate genes for the improvement of poplar disease resistance.

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“…VvWRKY02 and VvWRKY57 were duplicated gene pairs according to a whole genome analysis of grapevine gene duplications [46]. This might suggest an origin of group IV from subgroups IId + IIe.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide identification of WRKY family genes and their response to cold stress in Vitis vinifera

et al. 2014

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BackgroundWRKY transcription factors are one of the largest families of transcriptional regulators in plants. WRKY genes are not only found to play significant roles in biotic and abiotic stress response, but also regulate growth and development. Grapevine (Vitis vinifera) production is largely limited by stressful climate conditions such as cold stress and the role of WRKY genes in the survival of grapevine under these conditions remains unknown.ResultsWe identified a total of 59 VvWRKYs from the V. vinifera genome, belonging to four subgroups according to conserved WRKY domains and zinc-finger structure. The majority of VvWRKYs were expressed in more than one tissue among the 7 tissues examined which included young leaves, mature leaves, tendril, stem apex, root, young fruits and ripe fruits. Publicly available microarray data suggested that a subset of VvWRKYs was activated in response to diverse stresses. Quantitative real-time PCR (qRT-PCR) results demonstrated that the expression levels of 36 VvWRKYs are changed following cold exposure. Comparative analysis was performed on data from publicly available microarray experiments, previous global transcriptome analysis studies, and qRT-PCR. We identified 15 VvWRKYs in at least two of these databases which may relate to cold stress. Among them, the transcription of three genes can be induced by exogenous ABA application, suggesting that they can be involved in an ABA-dependent signaling pathway in response to cold stress.ConclusionsWe identified 59 VvWRKYs from the V. vinifera genome and 15 of them showed cold stress-induced expression patterns. These genes represented candidate genes for future functional analysis of VvWRKYs involved in the low temperature-related signal pathways in grape.

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Patterns of Gene Duplication and Their Contribution to Expansion of Gene Families in Grapevine

Cited by 41 publications

References 48 publications

Genome-Wide Identification, Expression Profile of the TIFY Gene Family in Brassica oleracea var. capitata, and Their Divergent Response to Various Pathogen Infections and Phytohormone Treatments

Genome-Wide Identification, Expression Profile of the TIFY Gene Family in Brassica oleracea var. capitata, and Their Divergent Response to Various Pathogen Infections and Phytohormone Treatments

Identification of TIFY Family Genes and Analysis of Their Expression Profiles in Response to Phytohormone Treatments and Melampsora larici-populina Infection in Poplar

Genome-wide identification of WRKY family genes and their response to cold stress in Vitis vinifera

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