Genome-wide identification of <i>CBF</i> genes and their responses to cold acclimation in <i>Taraxacum kok-saghyz</i>

Zhang, Haifeng; Gong, Yongyong; Sun, Ping; Chen, Sixue; Ma, Chunquan

doi:10.7717/peerj.13429

Cited by 8 publications

(11 citation statements)

References 59 publications

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“…All ApseCBFs, most AcyanCBFs, and AtruCBFs were single-exon structures, while AcyanCBF1, AcyanCBF2, AtruCBF2, AtruCBF6 contained one intron (Figure 2c). The results showed that most members of the CBF family in three Acer species were intron deletion genes, which were consistent with CBFs in Taraxacum koksaghyz [15]. The loss of introns might shorten the time required for gene transcription to translation, thereby accelerating gene expression and functional protein production to adapt to the changes of the plant and environment [35].…”

Section: Discussionsupporting

confidence: 63%

“…According to the phylogenetic tree analysis, the results showed that the CBF family members of the three species of Acer, P. trichocarpa, and A. thaliana did not form a separate cluster of evolutionary branches, indicating that there was a certain degree of homology between the CBF gene families of several species. At the same time, the CBF gene family may have undergone great differentiation in evolu-tion (Figure 1) [15]. Although CBF homologs from A. thaliana, A. pseudosieboldianum, and A. yangbiense were clustered in the same group, they were divided into separate subgroups, indicating that the duplications of CBFs in eudicot plants were independent events, and the duplication and divergence occurred after speciation [33].…”

Section: Discussionmentioning

confidence: 99%

“…Among them, the DREB group consists of six subgroups, of which the A1 subgroup consists of the CBF/DREB1 transcription factors [13]. Studies have performed the genome-wide analysis of CBF/DREB1 genes in several plant species, such as Lolium perenne [14], Taraxacum kok-saghyz [15], Camellia sinensis [16], Eucalyptus grandis [17], Brassica rapa [18] and so on. In previous studies, cold treatment (4 • C) induced the expression of LpCBF3 in Lolium perenne [14], the LeCBF1 gene in Lycopersicon esculentum, and the CpCBF1 and CpCBF2 in Carica papaya were also found to be cold-inducible [19,20].…”

Section: Introductionmentioning

confidence: 99%

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Identification and Analysis of the CBF Gene Family in Three Species of Acer under Cold Stress

Zhao

Han

Cai

et al. 2023

IJMS

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The C-Repeat Binding Factor (CBF) gene family has been identified and characterized in multiple plant species, and it plays a crucial role in responding to low temperatures. Presently, only a few studies on tree species demonstrate the mechanisms and potential functions of CBFs associated with cold resistance, while our study is a novel report on the multi-aspect differences of CBFs among three tree species, compared to previous studies. In this study, genome-wide identification and analysis of the CBF gene family in Acer truncatum, Acer pseudosieboldianum, and Acer yangbiense were performed. The results revealed that 16 CBF genes (five ApseCBFs, four AcyanCBFs, and seven AtruCBFs) were unevenly distributed across the chromosomes, and most CBF genes were mapped on chromosome 2 (Chr2) and chromosome 11 (Chr11). The analysis of phylogenetic relationships, gene structure, and conserved motif showed that 16 CBF genes could be clustered into three subgroups; they all contained Motif 1 and Motif 5, and most of them only spanned one exon. The cis-acting elements analysis showed that some CBF genes might be involved in hormone and abiotic stress responsiveness. In addition, CBF genes exhibited tissue expression specificity. High expressions of ApseCBF1, ApseCBF3, AtruCBF1, AtruCBF4, AtruCBF6, AtruCBF7, and ApseCBF3, ApseCBF4, ApseCBF5 were detected on exposure to low temperature for 3 h and 24 h. Low expressions of AtruCBF2, AtruCBF6, AtruCBF7 were detected under cold stress for 24 h, and AtruCBF3 and AtruCBF5 were always down-regulated under cold conditions. Taken together, comprehensive analysis will enhance our understanding of the potential functions of the CBF genes on cold resistance, thereby providing a reference for the introduction of Acer species in our country.

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Section: Discussionsupporting

confidence: 63%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Identification and Analysis of the CBF Gene Family in Three Species of Acer under Cold Stress

Zhao

Han

Cai

et al. 2023

IJMS

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“…The members of the CBF and ICE gene families are associated with the size of the genome and the effects of plant evolution [ 28 ]. This is in contrast to the number of CBF family members in annual plants; for example, there are 4 in A. thaliana , 12 in Lolium perenne [ 48 ], 14 in lettuce [ 47 ], 32 in the biennial herb Brassica oleracea [ 54 ], and 24 in the perennial herbs Taraxacum kok [ 55 ]. In the perennial woody plants, there are some reports of the presence of CBF members in whole genomes; for instance, in three Acer species, a total of five, four, and seven CBFs were identified in Acer truncatum , Acer pseudosieboldianum , and Acer yangbiense , respectively [ 8 ].…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Identification of the CBF Gene Family and ICE Transcription Factors in Walnuts and Expression Profiles under Cold Conditions

Zhou,

Ma,

Liu

et al. 2023

IJMS

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Cold stress impacts woody tree growth and perennial production, especially when the temperature rapidly changes in late spring. To address this issue, we conducted the genome-wide identification of two important transcription factors (TFs), CBF (C-repeat binding factors) and ICE (inducers of CBF expression), in three walnut (Juglans) genomes. Although the CBF and ICE gene families have been identified in many crops, very little systematic analysis of these genes has been carried out in J. regia and J. sigillata. In this study, we identified a total of 16 CBF and 12 ICE genes in three Juglans genomes using bioinformatics analysis. Both CBF and ICE had conserved domains, motifs, and gene structures, which suggests that these two TFs were evolutionarily conserved. Most ICE genes are located at both ends of the chromosomes. The promoter cis-regulatory elements of CBF and ICE genes are largely involved in light and phytohormone responses. Based on 36 RNA sequencing of leaves from four walnut cultivars (‘Zijing’, ‘Lvling’, ‘Hongren’, and ‘Liao1’) under three temperature conditions (8 °C, 22 °C, and 5 °C) conditions in late spring, we found that the ICE genes were expressed more highly than CBFs. Both CBF and ICE proteins interacted with cold-related proteins, and many putative miRNAs had interactions with these two TFs. These results determined that CBF1 and ICE1 play important roles in the tolerance of walnut leaves to rapid temperature changes. Our results provide a useful resource on the function of the CBF and ICE genes related to cold tolerance in walnuts.

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“…Recently, it was also found that low-temperature-induced CBF interacts with PIF3 to enhance the stability of PHYB, which in turn enhances the low-temperature tolerance of Arabidopsis [25]. CBF homologs in rice, tomato, wheat, barley, and maize have been identified and demonstrated that their transcripts are induced by low temperature [26], and PtCBF1, PtCBF2, PtCBF3, and PtCBF4 gene expression levels are upregulated in poplar leaves under low-temperature conditions [27].…”

Section: The Cbf-dependent Signaling Pathwaymentioning

confidence: 99%

Low-Temperature Signaling Pathways and Their Signaling Factors in Plant

Li¹,

Liu²,

Hao³

et al. 2023

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Low temperature as abiotic stress adversely impacts plant growth and development, and limits the ecological distribution of plants as well. Throughout their long evolutionary history, plants have developed a range of complicated and precise molecular regulatory mechanisms to deal with low-temperature stress, involving the activation of signal transduction pathways and the regulation of related genes. In this review, we provide a systematic summary of the most recent research findings regarding three hypotheses of cellular perception of low-temperature signals and two major intracellular low-temperature signaling pathways, including CBF-dependent signaling pathways and CBF-independent signaling pathways. Focus is placed on the functions of each component of the ICE-CBF-COR signaling cascade as well as their interrelationships. This review concludes that although some progress has been made in the identification, function, and mechanism of low-temperature response genes, their roles in the low-temperature regulatory network and molecular mechanisms still need to be studied in detail, which will be of great significance for improving the low-temperature tolerance of plants and adapting to climate change.

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Genome-wide identification of CBF genes and their responses to cold acclimation in Taraxacum kok-saghyz

Cited by 8 publications

References 59 publications

Identification and Analysis of the CBF Gene Family in Three Species of Acer under Cold Stress

Identification and Analysis of the CBF Gene Family in Three Species of Acer under Cold Stress

Genome-Wide Identification of the CBF Gene Family and ICE Transcription Factors in Walnuts and Expression Profiles under Cold Conditions

Low-Temperature Signaling Pathways and Their Signaling Factors in Plant

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