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Genome-wide Analysis and Characterization of Eucalyptus grandis TCP Transcription Factors

Year 2023, Volume: 29 Issue: 2, 413 - 426, 31.03.2023

Emre İlhan Ayşe Gül Kasapoğlu Selman Muslu Ahmed Sidar Aygören Murat Aydın

https://doi.org/10.15832/ankutbd.1104949
Cited By: 2

Abstract

Teosinte branched/Cycloidea/Proliferating cell factors (TCPs), a small transcription gene family, serve in developmental processes such as branching, flowering, and growth of plants. In this study, the TCP transcription gene family of eucalyptus, which is considered important for its medicinal and industrial uses, was bioinformatically investigated. A total of 16 Eucalyptus grandis TCP (Egra-TCP) genes were found to be distributed on chromosomes 1, 2, 4, 6, 7, 9, 10 and 11. Several segmentally-duplicated gene couples including Egra-TCP-7/Egra-TCP-11, -13 and -16, Egra-TCP-6/Egra-TCP-12 and -15, Egra-TCP-12/Egra-TCP-15 and Egra-TCP-11/Egra-TCP-13 were discovered. Egra-TCPs were divided into three main clades based on phylogenetic analysis, motif, and gene structure. While Egra-TCP-10 has the highest molecular weight with 47.19 kDa, the lowest was Egra-TCP-1 with 21.68 kDa. Twelve Egra-TCP genes were found to have no introns, while the Egra-TCP-7, -15, and -16 genes had a single intron. The orthologous relationships among E. grandis/Arabidopsis thaliana and E. grandis/Vitis vinifera were identified through a synteny analysis. Digital gene expression profiles of Egra-TCP genes in tissues such as xylem, phloem, shoot tips, young and mature leaf revealed a high expression pattern. The findings of this study contributes to existing knowledge in the biotechnology field by providing contributing to our understanding of the molecular basis of the TCP gene family in the eucalyptus plant.

Keywords

bHLH domain CYC/TB1 clade Digital gene expression Phylogenetic analysis TCP transcription factors

Thanks

This study was presented at the International Conference on Food, Agriculture and Animal Sciences (ICOFAAS 2018) and published in the Abstract Book as an abstract.

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Year 2023, Volume: 29 Issue: 2, 413 - 426, 31.03.2023

Emre İlhan Ayşe Gül Kasapoğlu Selman Muslu Ahmed Sidar Aygören Murat Aydın

https://doi.org/10.15832/ankutbd.1104949
Cited By: 2

Abstract

References

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  • Aygören A S, Muslu S, Isıyel M, Öner B M, Kasapoğlu A G, Aydınyurt R, Yaprak E, Uçar S, İlhan E & Aydın M (2022). Genome-Wide Analysis and Characterization of the VPE Gene Family under Salt and Drought Stress in Common Bean Genotypes. European Journal of Science and Technology, Ejosat Special Issue 2022 (ICAENS) 553-560. doi.org/10.31590/ejosat.1083440
  • Bailey T L, Williams N, Misleh C & Li W W (2006). MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Research 34: W369-W373. doi.org/10.1093/nar/gkl198
  • Cao P B, Le T, Chu H D, Le L, L, T, Aza, S, La V, Tran T & Vu X (2021). Genome-wide Analysis of Aldehyde Dehydrogenase (ALDH) Gene Superfamily in Eucalyptus grandis by Using Bioinformatics Methods. Asian Journal of Plant Sciences 20(2): 210-219. doi.org/10.3923/ajps.2021.210.219
  • Chen C, Chen H, Zhang Y, Thomas H R, Frank M H, He Y & Xia R (2020). TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data. Mol Plant 13(8): 1194-1202. doi.org/10.1016/j.molp.2020.06.009
  • Chen L, Chen Y Q, Ding A M, Chen H, Xia F, Wang W F & Sun Y H (2016). Genome-wide analysis of TCP family in tobacco. Genet Mol Res 15(2): doi.org/10.4238/gmr.15027728.
  • Citerne H L, Le Guilloux M, Sannier J, Nadot S & Damerval C (2013). Combining Phylogenetic and Syntenic Analyses for Understanding the Evolution of TCP ECE Genes in Eudicots. PLoS One 8(9): e74803. doi.org/10.1371/journal.pone.0074803
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  • Feng K, Hao J N, Liu J X, Huang W, Wang G L, Xu Z S, Huang Y & Xiong A S (2019). Genome-wide identification, classification, and expression analysis of TCP transcription factors in carrot. Canadian Journal of Plant Science 99(4): 525-535. doi.org/10.1139/cjps-2018-0232
  • Feng Z J, Xu S C, Liu N, Zhang G W, Hu Q Z & Gong Y M (2018). Soybean TCP transcription factors: Evolution, classification, protein interaction and stress and hormone responsiveness. Plant Physiol Biochem 127: 129-142. doi.org/10.1016/j.plaphy.2018.03.020
  • Francis A, Dhaka N, Bakshi M, Jung K H, Sharma M K & Sharma R (2016). Comparative phylogenomic analysis provides insights into TCP gene functions in Sorghum. Sci Rep 6:38488. Erratum in: Sci Rep 2017;7:45801. doi.org/10.1038/srep38488
  • He J, He X, Chang P, Jiang H, Gong D & Sun Q (2020). Genome-wide identification and characterization of TCP family genes in Brassica juncea var. tumida. PeerJ 8: e9130. doi.org/10.7717/peerj.9130
  • Horton P, Park K J, Obayashi T, Fujita N, Harada H, Adams-Collier C J & Nakai K (2007). WoLF PSORT: protein localization predictor. Nucleic Acids Res 35: W585-W587. doi.org/10.1093/nar/gkm259
  • Hu B, Jin J, Guo A Y, Zhang H, Luo J C & Gao G (2015). GSDS 2.0: an upgraded gene feature visualization server. Bioinformatics 31(8): 1296-1297. doi.org/10.1093/bioinformatics/btu817
  • Huo, N, Zhang S, Zhu T, Dong L, Wang Y, Mohr T, Hu T, Liu Z, Dvorak J, Luo M C, Wang D, Lee J Y,Altenbach S & Gu Y Q (2018). Gene duplication and evolution dynamics in the homeologous regions harboring multiple prolamin and resistance gene families in hexaploid wheat. Front Plant Sci 9: 673. doi.org/10.3389/fpls.2018.00673
  • İlhan E (2018). Genome-wide analysis of Eucalyptus grandis YABBY transcription factors. Turkish Journal of Agricultural Research 5(2): 158-166. doi.org/10.19159/tutad.408654
  • Ilhan E, Buyuk I & Inal B (2018). Transcriptome - Scale characterization of salt responsive bean TCP transcription factors. Gene 642: 64-73. doi.org/10.1016/j.gene.2017.11.021
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Details

Primary Language English
Journal Section Research Article
Authors

Emre İlhan 0000-0002-8404-7900

Ayşe Gül Kasapoğlu 0000-0002-6447-4921

Selman Muslu 0000-0003-4777-0726

Ahmed Sidar Aygören 0000-0002-6264-9935

Murat Aydın 0000-0003-1091-0609

Publication Date March 31, 2023
Submission Date April 24, 2022
Acceptance Date August 17, 2022
Published in Issue Year 2023 Volume: 29 Issue: 2

Cite

APA İlhan, E., Kasapoğlu, A. G., Muslu, S., Aygören, A. S., et al. (2023). Genome-wide Analysis and Characterization of Eucalyptus grandis TCP Transcription Factors. Journal of Agricultural Sciences, 29(2), 413-426. https://doi.org/10.15832/ankutbd.1104949

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