Genome-wide identification of members of the TCP gene family in switchgrass (Panicum virgatum L.) and analysis of their expression

Zheng, Aiping; Sun, Fengli; Cheng, Tingting; Wang, Yongfeng; Xie, Kunliang; Zhang, Chao; Xi, Yajun

doi:10.1016/j.gene.2019.03.059

Cited by 16 publications

(15 citation statements)

References 44 publications

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“…Gene families, consisting of multiple genes that share similar structures and functions, act in important roles for a given organism. Now, all kinds of gene families have been found in eukaryotes, such as bHLH [1], TCP [2], and Prx [3]. Among all gene families, SPL (squamosa promoter binding protein, SBP) is a plant-specific family that is widely distributed in green plants.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide identification, phylogeny and expression analysis of the SPL gene family in wheat

Zhu

Liu

et al. 2020

BMC Plant Biol

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Background Members of the plant-specific SPL gene family (squamosa promoter-binding protein -like) contain the SBP conserved domain and are involved in the regulation of plant growth and development, including the development of plant flowers and plant epidermal hair, the plant stress response, and the synthesis of secondary metabolites. This family has been identified in various plants. However, there is no systematic analysis of the SPL gene family at the genome-wide level of wheat. Results In this study, 56 putative TaSPL genes were identified using the comparative genomics method; we renamed them TaSPL001 - TaSPL056 on their chromosomal distribution. According to the un-rooted neighbor joining phylogenetic tree, gene structure and motif analyses, the 56 TaSPL genes were divided into 8 subgroups. A total of 81 TaSPL gene pairs were designated as arising from duplication events and 64 interacting protein branches were identified as involve in the protein interaction network. The expression patterns of 21 randomly selected TaSPL genes in different tissues (roots, stems, leaves and inflorescence) and under 4 treatments (abscisic acid, gibberellin, drought and salt) were detected by quantitative real-time polymerase chain reaction (qRT-PCR). Conclusions The wheat genome contains 56 TaSPL genes and those in same subfamily share similar gene structure and motifs. TaSPL gene expansion occurred through segmental duplication events. Combining the results of transcriptional and qRT-PCR analyses, most of these TaSPL genes were found to regulate inflorescence and spike development. Additionally, we found that 13 TaSPLs were upregulated by abscisic acid, indicating that TaSPL genes play a positive role in the abscisic acid-mediated pathway of the seedling stage. This study provides comprehensive information on the SPL gene family of wheat and lays a solid foundation for elucidating the biological functions of TaSPLs and improvement of wheat yield.

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Section: Introductionmentioning

confidence: 99%

Genome-wide identification, phylogeny and expression analysis of the SPL gene family in wheat

Zhu

Liu

et al. 2020

BMC Plant Biol

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“…( Xu et al, 2014 ), Cucumis sativus L. ( Wei et al, 2014 ), Solanum tuberosum L. ( Bao et al, 2019 ; Wang et al, 2019b ), Solanum lycopersicum L. ( Parapunova et al, 2014 ), Populus euphratica Oliv. ( Ma et al, 2016 ), Z. mays ( Chai et al, 2017 ), and Panicum virgatum L. ( Zheng et al, 2019 ). Despite the wide-ranging identification of TCPs, just a few of them have been intensively studied.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification of TCP Transcription Factors Family in Sweet Potato Reveals Significant Roles of miR319-Targeted TCPs in Leaf Anatomical Morphology

Ren

Zhang

et al. 2021

Front. Plant Sci.

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Plant-specific TCP transcription factors play vital roles in the controlling of growth, development, and the stress response processes. Extensive researches have been carried out in numerous species, however, there hasn’t been any information available about TCP genes in sweet potato (Ipomoea batatas L.). In this study, a genome-wide analysis of TCP genes was carried out to explore the evolution and function in sweet potato. Altogether, 18 IbTCPs were identified and cloned. The expression profiles of the IbTCPs differed dramatically in different organs or different stages of leaf development. Furthermore, four CIN-clade IbTCP genes contained miR319-binding sites. Blocking IbmiR319 significantly increased the expression level of IbTCP11/17 and resulted in a decreased photosynthetic rate due to the change in leaf submicroscopic structure, indicating the significance of IbmiR319-targeted IbTCPs in leaf anatomical morphology. A systematic analyzation on the characterization of the IbTCPs together with the primary functions in leaf anatomical morphology were conducted to afford a basis for further study of the IbmiR319/IbTCP module in association with leaf anatomical morphology in sweet potato.

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“…To date, genome-wide identification of the TCP family members has been identified and characterized in many dicots and monocots plants, such as A. thaliana (Li, 2015), Solanum lycopersicum (Parapunova et al, 2014), Malus domestica (Xu et al, 2014), Citrullus lanatus (Shi et al, 2016), Nicotiana tabacum (Chen et al, 2016), Fragaria vesca (Wei et al, 2016), Glycine max (Feng et al, 2018), Gossypium barbadense (Zheng et al, 2018), Vitis vinifera (Leng et al, 2019), Solanum tuberosum (Bao et al, 2019), Phyllostachys edulis (Liu et al, 2018), Z. mays (Ding et al, 2019), Panicum virgatum (Zheng et al, 2019), Hordeum vulgare subsp. vulgare (Gao et al, 2021), and so on.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification and Comparative Analysis of the Teosinte Branched 1/Cycloidea/Proliferating Cell Factors 1/2 Transcription Factors Related to Anti-cancer Drug Camptothecin Biosynthesis in Ophiorrhiza pumila

et al. 2021

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Ophiorrhiza pumila (O. pumila; Op) is a medicinal herbaceous plant, which can accumulate camptothecin (CPT). CPT and its derivatives are widely used as chemotherapeutic drugs for treating malignant tumors. Its biosynthesis pathway has been attracted significant attention. Teosinte branched 1/cycloidea/proliferating cell factors 1/2 (TCP) transcription factors (TFs) regulate a variety of physiological processes, while TCP TFs are involved in the regulation of CPT biosynthesis remain unclear. In this study, a systematic analysis of the TCP TFs family in O. pumila was performed. A total of 16 O. pumila TCP (OpTCP) genes were identified and categorized into two subgroups based on their phylogenetic relationships with those in Arabidopsis thaliana. Tissue-specific expression patterns revealed that nine OpTCP genes showed the highest expression levels in leaves, while the other seven OpTCPs showed a higher expression level in the stems. Co-expression, phylogeny analysis, and dual-luciferase (Dual-LUC) assay revealed that OpTCP15 potentially plays important role in CPT and its precursor biosynthesis. In addition, the subcellular localization experiment of candidate OpTCP genes showed that they are all localized in the nucleus. Our study lays a foundation for further functional characterization of the candidate OpTCP genes involved in CPT biosynthesis regulation and provides new strategies for increasing CPT production.

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Genome-wide identification of members of the TCP gene family in switchgrass (Panicum virgatum L.) and analysis of their expression

Cited by 16 publications

References 44 publications

Genome-wide identification, phylogeny and expression analysis of the SPL gene family in wheat

Genome-wide identification, phylogeny and expression analysis of the SPL gene family in wheat

Genome-Wide Identification of TCP Transcription Factors Family in Sweet Potato Reveals Significant Roles of miR319-Targeted TCPs in Leaf Anatomical Morphology

Genome-Wide Identification and Comparative Analysis of the Teosinte Branched 1/Cycloidea/Proliferating Cell Factors 1/2 Transcription Factors Related to Anti-cancer Drug Camptothecin Biosynthesis in Ophiorrhiza pumila

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