Functional characterization of genes with daily expression patterns in common wheat

Kiseleva, A. A.; Bragina, M. K.; Muterko, Aleksandr F; Салина, Е. А.

doi:10.1007/s11103-022-01262-z

Cited by 5 publications

(4 citation statements)

References 73 publications

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“…To have an insight of the potential biological roles of the TCP genes, we performed Gene ontology analysis using A. thaliana TCP protein sequences ( Figure 6 ). We observed that many processes were assigned to the biological processes (BP), mainly involved in growth and development, concurring with previous findings ( İlhan et al, 2018 ; Kiseleva et al, 2022 ). A fewer processes in molecular function (MF), also had significant fold changes, and most of them were involved in DNA binding, supporting previous findings that TCPs are involved in DNA binding ( Kosugi and Ohashi, 2002 ; He et al, 2021 ).…”

Section: Biological Functionssupporting

confidence: 92%

Genomic survey of TCP transcription factors in plants: Phylogenomics, evolution and their biology

Zhou

Hwarari

et al. 2022

Front. Genet.

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The TEOSINTE BRANCHED1 (TBI1), CYCLOIDEA (CYC), and PROLIFERATING CELL NUCLEAR ANTIGEN FACTORS (PCF1 and PCF2) proteins truncated as TCP transcription factors carry conserved basic-helix-loop-helix (bHLH) structure, related to DNA binding functions. Evolutionary history of the TCP genes has shown their presence in early land plants. In this paper, we performed a comparative discussion on the current knowledge of the TCP Transcription Factors in lower and higher plants: their evolutionary history based on the phylogenetics of 849 TCP proteins from 37 plant species, duplication events, and biochemical roles in some of the plants species. Phylogenetics investigations confirmed the classification of TCP TFs into Class I (the PCF1/2), and Class II (the C- clade) factors; the Class II factors were further divided into the CIN- and CYC/TB1- subclade. A trace in the evolution of the TCP Factors revealed an absence of the CYC/TB1subclade in lower plants, and an independent evolution of the CYC/TB1subclade in both eudicot and monocot species. 54% of the total duplication events analyzed were biased towards the dispersed duplication, and we concluded that dispersed duplication events contributed to the expansion of the TCP gene family. Analysis in the TCP factors functional roles confirmed their involvement in various biochemical processes which mainly included promoting cell proliferation in leaves in Class I TCPs, and cell division during plant development in Class II TCP Factors. Apart from growth and development, the TCP Factors were also shown to regulate hormonal and stress response pathways. Although this paper does not exhaust the present knowledge of the TCP Transcription Factors, it provides a base for further exploration of the gene family.

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Section: Biological Functionssupporting

confidence: 92%

Genomic survey of TCP transcription factors in plants: Phylogenomics, evolution and their biology

Zhou

Hwarari

et al. 2022

Front. Genet.

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“…These algorithms are widely used to assess the transcript stability of candidate reference genes in various species [32][33][34][35]. The use of reference genes in expression analysis has greatly facilitated our understanding of the important information related to gene functions and complex biological processes in plants, such as the signaling and metabolic pathways that underlie developmental and cellular processes [36][37][38][39].…”

Section: Introductionmentioning

confidence: 99%

Selection and Validation of Optimal RT-qPCR Reference Genes for the Normalization of Gene Expression under Different Experimental Conditions in Lindera megaphylla

Liu

Chen

et al. 2023

Plants

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Lindera megaphylla, a broad-leaved evergreen that is used as a landscape ornamental plant and medicinal plant, is an ecologically important and dominant tree species. However, little is known about the molecular mechanisms of its growth, development, and metabolism. The selection of suitable reference genes is critical for molecular biological analyses. To date, no research on reference genes as a foundation for gene expression analysis has been undertaken in L. megaphylla. In this study, 14 candidate genes were selected from the transcriptome database of L. megaphylla for RT-qPCR assay under different conditions. Results showed that helicase-15 and UBC28 were most stable in different tissues of seedlings and adult trees. For different leaf developmental stages, the best combination of reference genes was ACT7 and UBC36. UBC36 and TCTP were the best under cold treatment, while PAB2 and CYP20-2 were the best under heat treatment. Finally, a RT-qPCR assay of LmNAC83 and LmERF60 genes were used to further verify the reliability of selected reference genes above. This work is the first to select and evaluate the stability of reference genes for the normalization of gene expression analysis in L. megaphylla and will provide an important foundation for future genetic studies of this species.

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“…With the research on circadian clock genes and output pathways, it is critical to decode the function and regulation of genes from the diurnal dynamics throughout the day. The combination of transcriptome sequencing technology and time‐series experimental design makes it possible to examine global transcriptional changes in response to the circadian clock and environmental cues (Desai et al, 2021; Kiseleva et al, 2022; Wang et al, 2021; Weng et al, 2019; Yi et al, 2022). Previous analyses have established comprehensive molecular mechanisms under a certain day length (e.g., 12/12 h day/night) (Filichkin et al, 2011; Hotta et al, 2013; Xu et al, 2011) or under constant light conditions (Hudson, 2010; Muller et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

Diurnal transcriptome dynamics reveal the photoperiod response of Pyrus

Liu

Wang

et al. 2023

Physiologia Plantarum

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Photoperiod provides a key environmental signal that controls plant growth. Plants have evolved an integrated mechanism for sensing photoperiods with internal clocks to orchestrate physiological events. This mechanism has been identified to enable timely plant growth and improve fitness. Although the components and pathways underlying photoperiod regulation have been described in many species, diurnal patterns of gene expression at the genome‐wide level under different photoperiods are rarely reported in perennial fruit trees. To explore the global gene expression in response to photoperiod, pear plants were cultured under long‐day (LD) and short‐day (SD) conditions. A time‐series transcriptomic study was implemented using LD and SD samples collected at 4 h intervals over 2 days. We identified 13,677 rhythmic genes, of which 7639 were identified under LD and 10,557 under SD conditions. Additionally, 4674 genes were differentially expressed in response to photoperiod change. We also characterized the candidate homologs of clock‐associated genes in pear. Clock genes were involved in the regulation of many processes throughout the day, including photosynthesis, stress response, hormone dynamics, and secondary metabolism. Strikingly, genes within photosynthesis‐related pathways were enriched in both the rhythmic and differential expression analyses. Several key candidate genes were identified to be associated with regulating photosynthesis and improving productivity under different photoperiods. The results suggest that temporal variation in gene expression should not be ignored in pear gene function research. Overall, our work expands the understanding of photoperiod regulation of plant growth, particularly by extending the research to non‐model trees.

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Functional characterization of genes with daily expression patterns in common wheat

Cited by 5 publications

References 73 publications

Genomic survey of TCP transcription factors in plants: Phylogenomics, evolution and their biology

Genomic survey of TCP transcription factors in plants: Phylogenomics, evolution and their biology

Selection and Validation of Optimal RT-qPCR Reference Genes for the Normalization of Gene Expression under Different Experimental Conditions in Lindera megaphylla

Diurnal transcriptome dynamics reveal the photoperiod response of Pyrus

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