Genome-wide identification and expression analysis of the RcYABBYs reveals their potential functions in rose (Rosa chinensis Jacq.)

References

• Buttar, Z. A., Yang, Y., Sharif, R., Nan Wu, S., Xie, Y., & Wang, C., et al (2020). Genome wide identification, characterization, and expression analysis of YABBY-gene family in WHEAT (Triticum aestivum L.). Agronomy, 10, 1189. doi:10.3390/agronomy10081189
   Google Scholar
• Chen, -Y.-Y., Hsiao, -Y.-Y., Chang, S.-B., Zhang, D., Lan, S.-R., Liu, Z.-J., & Tsai, W.-C. (2020). Genome-wide identification of yabby genes in orchidaceae and their expression patterns in Phalaenopsis orchid. Genes (Basel), 11, 955. doi:10.3390/genes11090955
   Web of Science ®Google Scholar
• Chung, Y., Zhu, Y., M-f, W., Simonini, S., Kuhn, A., Armenta-Medina, A., … Wagner, D. (2019). Auxin response factors promote organogenesis by chromatin-mediated repression of the pluripotency gene SHOOTMERISTEMLESS. Nat Commun, 10, 886. doi:10.1038/s41467-019-08861-3
   PubMed Web of Science ®Google Scholar
• De Vega, D., Holden, N., Hedley, P.E., Morris, J., Luna, E., … Newton, A. (2021). Chitosan primes plant defence mechanisms against Botrytis cinerea, including expression of Avr9/Cf-9 rapidly elicited genes. Plant, Cell … Environment, 44, 290–303. doi:10.1111/pce.13921
   PubMed Web of Science ®Google Scholar
• Fan, J., Xie, Y., Zhang, Z., … Chen, L. (2018). Melatonin: A multifunctional factor in plants. Int J Mol Sci, 19, 1528. doi:10.3390/ijms19051528
   Web of Science ®Google Scholar
• Filyushin, M., Slugina, M., Shchennikova, A.V., … Kochieva, E.Z. (2017). YABBY3-orthologous genes in wild tomato species: Structure, variability, and expression. Acta Naturae, 9, 101–109. doi:10.32607/2075-8251-2017-9-4-101-109
   PubMed Web of Science ®Google Scholar
• Franco-Zorrilla, J.M., López-Vidriero, I., … Carrasco, J.L. (2014). DNA-binding specificities of plant transcription factors and their potential to define target genes. Proceedings of the National Academy of Science, 111, 2367–2372. doi:10.1073/pnas.1316278111
   PubMed Web of Science ®Google Scholar
• Gasteiger, E., Hoogland, C., Gattiker, A., Duvaud, S., Wilkins, M. R., Appel, R. D., … Bairoch, A. In Walker, J. M. (eds) (2005). Protein identification and analysis tools on the ExPASy server. Proteomics Protoc Handbooks, 571–607. Humana Press. doi:10.1385/1-59259-890-0:571
   Google Scholar
• Higo, K., Ugawa, Y., Iwamoto, M., & Korenaga, T. (1999). Plant cis-acting regulatory DNA elements (PLACE) database: 1999. Nucleic Acids Research, 27, 297–300. doi:10.1093/nar/27.1.297
   PubMed Web of Science ®Google Scholar
• Hu, B., Jin, J., Guo, A.Y., Zhang, H., Luo, J., & Gao, G. (2015). GSDS 2.0: An upgraded gene feature visualization server. Bioinformatics, 31, 1296–1297. doi:10.1093/bioinformatics/btu817
   PubMed Web of Science ®Google Scholar
• Hussain, S., Nanda, S., Zhang, J., Rehmani, M.I.A., Suleman, M., Li, G., & Hou, H. (2021). Auxin and cytokinin interplay during Leaf Morphogenesis and Phyllotaxy. Plants, 10, 1732. doi:10.3390/plants10081732
   Google Scholar
• Jiangtao, C., Yingzhen, K., & Qian, W. (2015). MapGene2Chrom, a tool to draw gene physical map based on Perl and SVG languages. Yi Chuan, 37, 91–97. doi:10.16288/j.yczz.2015.01.013
   PubMedGoogle Scholar
• Jung, S., Lee, T., Cheng, C.-H., Buble, K., Zheng, P., Yu, J., … Main, D. (2019). 15 years of GDR: New data and functionality in the Genome Database for Rosaceae. Nucleic Acids Research, 47, D1137–D1145. doi:10.1093/nar/gky1000
   PubMed Web of Science ®Google Scholar
• Kayani, S.I., Shen, Q., & Ma, Y. (2019). The YABBY family transcription factor AaYABBY5 directly targets cytochrome P450 Monooxygenase (CYP71AV1) and double-bond reductase 2 (DBR2) involved in artemisinin biosynthesis in Artemisia Annua. Front Plant Sci, 10. doi:10.3389/fpls.2019.01084
   PubMed Web of Science ®Google Scholar
• Lescot, M., Déhais, P., Thijs, G., Marchal, Y., Van de Peer, Y., Rouzé, P., and Rombauts, S., (2002). PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Research, 30(1), 325–327. doi:10.1073/pnas.1316278111
   PubMed Web of Science ®Google Scholar
• Li, C., Dong, N., Shen, L., Lu, M., Zhai, J., Zhao, Y., Chen, L., Wan, Z., Liu, Z., Ren, H., & Wu, S., (2022). Genome-wide identification and expression profile of YABBY genes in Averrhoa carambola. Peer J, 9, e12558. https://doi.org/10.7717/peerj.12558
   PubMed Web of Science ®Google Scholar
• Li, C., Fang, Q., Zhang, W., Li, Y., Zhang, J., Chen, S., Yin, Z., Li, W., Liu, W., Yi, Z., Mu, Z., and Du, J., (2021). Genome-wide identification of the CCCH gene family in rose (Rosa chinensis Jacq.) reveals its potential functions, Biotechnology & Biotechnological Equipment, 35(1), 517–526, doi:10.1080/13102818.2021.1901609
   Web of Science ®Google Scholar
• Li, Z., Li, G., Cai, M., Priyadarshani, S.V.G.N., Aslam, M., Zhou, Q., … Qin, Y. (2019). Genome-wide analysis of the YABBY transcription factor family in pineapple and functional identification of AcYABBY4 involvement in salt stress. International Journal of Molecular Sciences, 20, 5863. doi:10.3390/ijms20235863
   Web of Science ®Google Scholar
• Liu, X., Li, D., Zhang, S., Xu, Y., & Zhang, Z. (2019). Genome-wide characterization of the rose (Rosa chinensis) WRKY family and role of RcWRKY41 in gray mold resistance. BMC Plant Biology, 19, 522. doi:10.1186/s12870-019-2139-6
   PubMed Web of Science ®Google Scholar
• Liu, X., Liao, X.-Y., Zheng, Y., Zhu, M.-J., Yu, X., Jiang, Y.-T., … Lan, S. (2020). Genome-wide identification of the YABBY gene family in seven species of magnoliids and expression analysis in Litsea. Plants, 10, 21. doi:10.3390/plants10010021
   Google Scholar
• Liu, J., Wu, S., & Sun, J. (2021a). Genome-wide analysis reveals widespread roles for RcREM genes in floral organ development in Rosa chinensis. Genomics, 113, 3881–3894. doi:10.1016/j.ygeno.2021.09.017
   PubMed Web of Science ®Google Scholar
• Livak, K.J., & Schmittgen, T.D. (2001). Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method. Methods, 25, 402–408. doi:10.1006/meth.2001.1262
   PubMed Web of Science ®Google Scholar
• Ma, R., Huang, B., Huang, Z., & Zhang, Z. (2021). Genome-wide identification and analysis of the YABBY gene family in Moso Bamboo (Phyllostachys edulis (Carrière) J. Houz). J. Houz). PeerJ, 9, e11780. doi:10.7717/peerj.11780
   PubMed Web of Science ®Google Scholar
• Madeira, F., Park, Y.M., Lee, J., Buso, N., Gur, T., Madhusoodanan, N., … Lopez, R. (2019). The EMBL-EBI search and sequence analysis tools APIs in 2019. Nucleic Acids Res, 47, W636–W641. doi:10.1093/nar/gkz268
   PubMed Web of Science ®Google Scholar
• Nan, H., Ludlow, R.A., Lu, M., & An, H. (2021). Genome-wide analysis of dof genes and their response to abiotic stress in rose (Rosa chinensis). Front Genet, 12. doi:10.3389/fgene.2021.538733
   Google Scholar
• Nanda, S., Rout, E., & Joshi, R.K. (2016). Curcuma longa mitogen-activated protein kinase 6 (ClMPK6) stimulates the defense response pathway and enhances the resistance to necrotrophic fungal infection. Plant Molecular Biology Reporter, 34, 886–898. doi:10.1007/s11105-015-0972-9
   Web of Science ®Google Scholar
• Nasim, J. (2016). MEME SUITE: Tools for motif discovery and searching. Plant Syst Evol, 302, 202–208. doi:10.1006/jmbi.1990.9999
   Google Scholar
• Nawaz, K., Chaudhary, R., Sarwar, A., Ahmad, B., Gul, A., Hano, C., Abbasi, B. H.,Anjum, & S., (2020). Melatonin as Master Regulator in Plant Growth, Development and Stress Alleviator for Sustainable Agricultural Production. Current Status and Future Perspectives. Sustainability, 13(1), 294. https://doi.org/10.3390/su13010294
   Google Scholar
• Romanova, M.A., Maksimova, A.I., Pawlowski, K., & Voitsekhovskaja, O.V. (2021). YABBY genes in the development and evolution of land plants. Int J Mol Sci, 22, 4139. doi:10.3390/ijms22084139
   PubMed Web of Science ®Google Scholar
• Tamura, K., Stecher, G., Kumar, S., & Battistuzzi, F.U. (2021). MEGA11: Molecular evolutionary genetics analysis version 11. Molecular Biology and Evolution, 38, 3022–3027. doi:10.1093/molbev/msab120
   PubMed Web of Science ®Google Scholar
• Wan, S., Mak, M.W., & Kung, S.Y. (2012). MGOASVM: Multi-label protein subcellular localization based on gene ontology and support vector machines. BMC Bioinformatics, 13. doi:10.1186/1471-2105-13-290
   Web of Science ®Google Scholar
• Wheeler, T.J., & Eddy, S.R. (2013). Nhmmer: DNA homology search with profile HMMs. Bioinformatics, 29, 2487–2489. doi:10.1093/bioinformatics/btt403
   PubMed Web of Science ®Google Scholar
• Wójcik, A.M., Wójcikowska, B., & Gaj, M.D. (2020). Current perspectives on the auxin-mediated genetic network that controls the induction of somatic embryogenesis in plants. Int J Mol Sci, 21, 1333. doi:10.3390/ijms21041333
   Web of Science ®Google Scholar
• Wu, M.-F., Yamaguchi, N., Xiao, J., Bargmann, B., Estelle, M., Sang, Y., & Wagner, D. (2015). Auxin-regulated chromatin switch directs acquisition of flower primordium founder fate. eLife Elife 4, 4. doi:10.7554/eLife.09269
   Web of Science ®Google Scholar
• Zhang, T., Li, C., Li, D., Liu, Y., & Yang, X. (2020). Roles of YABBY transcription factors in the modulation of morphogenesis, development, and phytohormone and stress responses in plants. Journal of Plant Research, 133, 751–763. doi:10.1007/s10265-020-01227-7
   PubMed Web of Science ®Google Scholar
• Zhang, S., Wang, L., & Sun, X. (2019). Genome-wide analysis of the YABBY gene family in grapevine and functional characterization of VvYABBY4. Front Plant Sci, 10. doi:10.3389/fpls.2019.01207
   Web of Science ®Google Scholar
• Zhao, Y., Liu, C., Ge, D., Yan, M., Ren, Y., Huang, X., & Yuan, Z. (2020). Genome-wide identification and expression of YABBY genes family during flower development in Punica granatum L. Gene, 752, 144784. doi:10.1016/j.gene.2020.144784
   PubMed Web of Science ®Google Scholar
• Zhao, S.-P., Lu, D., & T-f, Y. (2017). Genome-wide analysis of the YABBY family in soybean and functional identification of GmYABBY10 involvement in high salt and drought stresses. Plant Physiol Biochem, 119, 132–146. doi:10.1016/j.plaphy.2017.08.026
   PubMed Web of Science ®Google Scholar