Genome-wide identification, phylogenetic analysis, and expression profiling of the BBX family genes in pear

References

• Almada, R., Cabrera, N., Casaretto, J.A., Ruiz-Lara, S., & González Villanueva, E. (2009). VvCO and VvCOL1, two CONSTANS homologous genes, are regulated during flower induction and dormancy in grapevine buds. Plant Cell Reports, 28, 1193–1203. doi:10.1007/s00299-009-0720-4 ​
   PubMed Web of Science ®Google Scholar
• Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W., & Lipman, D.J. (1997). Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Research, 25, 3389–3402. doi:10.1093/nar/25.17.3389
   PubMed Web of Science ®Google Scholar
• An, H., Roussot, C., Suárez-López, P., Corbesier, L., Vincent, C., Piñeiro, M., … Coupland, G. (2004). CONSTANS acts in the phloem to regulate a systemic signal that induces photoperiodic flowering of Arabidopsis. Development, 131, 3615–3626. doi:10.1242/dev.01231
   PubMed Web of Science ®Google Scholar
• Bateman, A. (2004). The Pfam protein families database. Nucleic Acids Research, 32, 138D–141. doi:10.1093/nar/gkh121 ​
   PubMed Web of Science ®Google Scholar
• Campoli, C., Drosse, B., Searle, I., Coupland, G., & Korff, M.V. (2012). Functional characterisation of HvCO1, the barley (Hordeum vulgare) flowering time ortholog of CONSTANS. The Plant Journal, 69, 868–880. doi:10.1111/tpj.2012.69.issue-5
   PubMed Web of Science ®Google Scholar
• Cao, Y.P., Han, Y.H., Li, D.H., Lin, Y., & Cai, Y.P. (2016). MYB transcription factors in chinese pear (Pyrus bretschneideri Rehd.): Genome-wide identification, classification, and expression profiling during fruit development. Frontiers in Plant Science, 7, 577. doi:10.3389/fpls.2016.00577
   PubMed Web of Science ®Google Scholar
• Chang, C.J., Li, Y.H., Chen, L.T., Chen, W.C., Hsieh, W.P., Shin, J., … Wu, S.H. (2008). LZF1, a HY5-regulated transcriptional factor, functions in Arabidopsis de-etiolation. Plant Journal, 54, 205–219. doi:10.1111/j.1365-313X.2008.03401.x
   PubMed Web of Science ®Google Scholar
• Chen, J., Chen, J.Y., Wang, J.N., Kuang, J.F., Shan, W., & Lu, W.J. (2012). Molecular characterization and expression profiles of MaCOL1, a CONSTANS-like gene in banana fruit. Gene, 496, 110–117. doi:10.1016/j.gene.2012.01.008
   PubMed Web of Science ®Google Scholar
• Chen, J., Yin, H., Gu, J., Li, L., Liu, Z., Jiang, X., … Wu, J. (2014). Genomic characterization, phylogenetic comparison and differential expression of the cyclic nucleotide-gated channels gene family in pear (Pyrus bretchneideri Rehd.). Genomics, 105, 39–52. doi:10.1016/j.ygeno.2014.11.006
   PubMed Web of Science ®Google Scholar
• Cheng, X.F., & Wang, Z.Y. (2005). Overexpression of COL9, a CONSTANS-LIKE gene, delays flowering by reducing expression of CO and FT in Arabidopsis thaliana. Plant Journal, 43, 758–768. doi:10.1111/j.1365-313X.2005.02491.x
   PubMed Web of Science ®Google Scholar
• Chia, T.Y., Müller, A., Jung, C., & Mutasa-Göttgens, E.S. (2008). Sugar beet contains a large CONSTANS-LIKE gene family including a CO homologue that is independent of the early-bolting (B) gene locus. Journal of Experimental Botany, 59, 2735 Exper. doi:10.1093/jxb/ern129
   Web of Science ®Google Scholar
• Chu, Z.N., Wang, X., Li, Y., Yu, H.Y., Li, J.H., Lu, Y.G., & Youyang, B. (2016). Genomic organization, phylogenetic and expression analysis of the B-BOX gene family in tomato. Frontiers in Plant Science, 7, 1552. doi:10.3389/fpls.2016.01552
   PubMed Web of Science ®Google Scholar
• Conesa, A., Gotz, S., Garcia-Gomez, J.M., Terol, J., Talon, M., & Robles, M. (2005). Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics, 21, 3674–3676. doi:10.1093/bioinformatics/bti610
   PubMed Web of Science ®Google Scholar
• Crocco, C.D., & Botto, J.F. (2013). BBX proteins in green plants: Insights into their evolution, structure, feature and functional diversification. Gene, 531, 44–52. doi:10.1016/j.gene.2013.08.037
   PubMed Web of Science ®Google Scholar
• Crocco, C.D., Holm, M., Yanovsky, M.J., & Botto, J.F. (2010). AtBBX21 and COP1 genetically interact in the regulation of shade avoidance. The Plant Journal, 64, 551–562. doi:10.1111/tpj.2010.64.issue-4
   PubMed Web of Science ®Google Scholar
• Crocco, C.D., Holm, M., Yanovsky, M.J., & Botto, J.F. (2011). Function of B-BOX under shade. Plant Signaling & Behavior, 6, 101–104. doi:10.4161/psb.6.1.14185
   PubMedGoogle Scholar
• Crooks, G.E., Hon, G., Chandonia, J.M., & Brenner, S.E. (2004). WebLogo: A sequence logo generator. Genome Research, 14, 1188–1190. doi:10.1101/gr.849004
   PubMed Web of Science ®Google Scholar
• Datta, S., Hettiarachchi, C., Johansson, H., & Holm, M. (2007). Salt tolerance HOMOLOG2, a B-box protein in Arabidopsis that activates transcription and positively regulates light-mediated development. The Plant Cell, 19, 3242–3255. doi:10.1105/tpc.107.054791
   PubMed Web of Science ®Google Scholar
• Datta, S., Hettiarachchi, G.H., Deng, X.W., & Holm, M. (2006). Arabidopsis CONSTANS-LIKE3 is a positive regulator of red light signaling and root growth. The Plant Cell, 18, 70–84. doi:10.1105/tpc.105.038182
   PubMed Web of Science ®Google Scholar
• Datta, S., Johansson, H., Hettiarachchi, C., Irigoyen, M.L., Desai, M., Rubio, V., & Holm, M. (2008). LZF1/SALT TOLERANCE HOMOLOG3, an Arabidopsis B-box protein involved in light-dependent development and gene expression, undergoes COP1-mediated ubiquitination. The Plant Cell, 20, 2324–2338. doi:10.1105/tpc.108.061747
   PubMed Web of Science ®Google Scholar
• Dou, J.Q., Cheng, L.J., Xu, F.H., Zhang, J.H., & Tong, Z.K. (2015). Cloning and expression analysis of a B-box-type protein gene BlCOL13 in Betula luminifera. Acta Horticulturae Sinica, 42, 1367–1377.
   Google Scholar
• Fan, X.Y., Sun, Y., Cao, D.M., Bai, M.Y., Luo, X.M., Yang, H.J., … Wang, Z.Y. (2012). BZS1, a B-box protein, promotes photomorphogenesis downstream of both brassinosteroid and light signaling pathways. Molecular Plant, 5, 591–600. doi:10.1093/mp/sss041
   PubMed Web of Science ®Google Scholar
• Gangappa, S.N., & Botto, J.F. (2014). The BBX family of plant transcription factors. Trends in Plant Science, 19, 460–470. doi:10.1016/j.tplants.2014.01.010
   PubMed Web of Science ®Google Scholar
• Gangappa, S.N., Crocco, C.D., Johansson, H., Datta, S., Hettiarachchi, C., Holm, M., & Botto, J.F. (2013). The Arabidopsis B-BOX Protein BBX25 Interacts with HY5, Negatively Regulating BBX22 Expression to Suppress Seedling Photomorphogenesis. The Plant Cell, 25, 1243–1257. doi:10.1105/tpc.113.109751
   PubMed Web of Science ®Google Scholar
• Gasteiger, E., Gattiker, A., Hoogland, C., Ivanyi, I., Appel, R.D., & Bairoch, A. (2003). ExPASy: The proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Research, 31, 3784–3788. doi:10.1093/nar/gkg563
   PubMed Web of Science ®Google Scholar
• Gong, W., Shen, Y.P., Ma, L.G., Pan, Y., Du, Y.L., Wang, D.H., … Zhu, Y.X. (2004). Genome-wide ORFeome cloning and analysis of Arabidopsis transcription factor genes. Plant Physiology, 135, 773–782. doi:10.1104/pp.104.042176
   PubMed Web of Science ®Google Scholar
• Griffiths, S., Dunford, R.P., Coupland, G., & Laurie, D.A. (2003). The evolution of CONSTANS-like gene families in barley, rice, and Arabidopsis. Plant Physiology, 131, 1855–1867. doi:10.1104/pp.102.016188
   PubMed Web of Science ®Google Scholar
• Guo, A.Y., Zhu, Q.H., Chen, X., & Luo, J.C. (2007). GSDS: A gene structure display server. Hereditas, 29, 1023–1026. doi:10.1360/yc-007-1023
   PubMedGoogle Scholar
• Hassidim, M., Harir, Y., Yakir, E., Kron, I., & Green, R.M. (2009). Over-expression of CONSTANS-LIKE 5 can induce flowering in short-day grown Arabidopsis. Planta, 230, 481–491. doi:10.1007/s00425-009-0958-7
   PubMed Web of Science ®Google Scholar
• Holtan, H.E., Bandong, S., Marion, C.M., Adam, L., Tiwari, S., Shen, Y., … Khanna, R. (2011). BBX32, an Arabidopsis b-box protein, functions in light signaling by suppressing hy5-regulated gene expression and interacting with STH2/BBX21. Plant Physiology, 156, 2109–2123. doi:10.1104/pp.111.177139
   PubMed Web of Science ®Google Scholar
• Huang, J.Y., Zhao, X.B., Weng, X.Y., Wang, L., & Xie, W.B. (2012). The Rice B-Box zinc finger gene family: Genomic identification, characterization, expression profiling and diurnal analysis. Plos One, 7, e48242. doi:10.1371/journal.pone.0048242
   PubMed Web of Science ®Google Scholar
• Huang, X.S., Li, K.Q., Xu, X.Y., Yao, Z.H., Jin, C., & Zhang, S.L. (2015). Genome-wide analysis of WRKY transcription factors in white pear (Pyrus bretschneideri) reveals evolution and patterns under drought stress. BMC Genomics, 16, 1104. doi:10.1186/s12864-015-2233-6
   PubMed Web of Science ®Google Scholar
• Imtiaz, M., Yang, Y.J., Liu, R.X., Xu, Y.J., Khan, M.A., Wei, Q., … Hong, B. (2015). Identifcation and functional characterization of the BBX24 promoter and gene from chrysanthemum in Arabidopsis. Plant Molecular Biology, 89, 1–19. doi:10.1007/s11103-015-0347-5
   PubMed Web of Science ®Google Scholar
• Indorf, M., Cordero, J., Neuhaus, G., & Rodríguez-Franco, M. (2007). Salt tolerance (STO), a stress-related protein, has a major role in light signalling. Plant Journal, 51, 563–574. doi:10.1111/j.1365-313X.2007.03162.x
   PubMed Web of Science ®Google Scholar
• Jeanmougin, F., Thompson, J.D., Gouy, M., Higgins, D.G., & Gibson, T.J. (1998). Multiple sequence alignment with Clustal X. Trends in Biochemical Sciences, 23, 403–405. doi:10.1016/S0968-0004(98)01285-7
   PubMed Web of Science ®Google Scholar
• Khanna, R., Kronmiller, B., Maszle, D.R., Coupland, G., Holm, M., Mizuno, T., & Wu, S.-H. (2009). The Arabidopsis B-box zinc finger family. The Plant Cell, 21, 3416–3420. doi:10.1105/tpc.109.069088
   PubMed Web of Science ®Google Scholar
• Kielbowicz-Matuk, A., Rey, P., & Rorat, T. (2014). Interplay between circadian rhythm, time of the day and osmotic stress constraints in the regulation of the expression of a Solanum Double B-box gene. Annals of Botany, 113, 831–842. doi:10.1093/aob/mct303
   PubMed Web of Science ®Google Scholar
• Kim, S.-K., Yun, C.-H., Lee, J.H., Jang, Y.H., Park, H.-Y., & Kim, J.-K. (2008). OsCO3, a CONSTANS-LIKE gene, controls flowering by negatively regulating the expression of FT-like genes under SD conditions in rice. Planta, 228, 355–365. doi:10.1007/s00425-008-0742-0
   PubMed Web of Science ®Google Scholar
• Klug, A., & Schwabe, J.W. (1995). Protein motifs 5. Zinc fingers. Faseb Journal, 9, 597–604.
   PubMed Web of Science ®Google Scholar
• Kumagai, T., Ito, S., Nakamichi, N., Niwa, Y., Murakami, M., Yamashino, T., & Mizuno, T. (2008). The common function of a novel subfamily of B-Box zinc finger proteins with reference to circadian-associated events in Arabidopsis thaliana. Bioscience Biotechnology and Biochemistry, 72, 1539–1549. doi:10.1271/bbb.80041
   PubMed Web of Science ®Google Scholar
• Lee, Y.S., Jeong, D.H., Lee, D.Y., Yi, J., Ryu, C.H., Kim, S.L., … An, G. (2010). OsCOL4 is a constitutive flowering repressor upstream of Ehd1 and downstream of OsphyB. Plant Journal, 63, 18–30.
   PubMed Web of Science ®Google Scholar
• Lescot, M., Déhais, P., Thijs, G., Marchal, K., Moreau, Y., Van de Peer, Y., … 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, 325–327. doi:10.1093/nar/30.1.325
   PubMed Web of Science ®Google Scholar
• Letunic, I., Doerks, T., & Bork, P. (2012). SMART 7: Recent updates to the protein domain annotation resource. Nucleic Acids Research, 40, 302–305. doi:10.1093/nar/gkr931
   PubMed Web of Science ®Google Scholar
• Li, J.-M., Zheng, D.-M., Li, L.-T., Qiao, X., Wei, S.-W., Bai, B., … Wu, J. (2015). Genome-wide function, evolutionary characterization and expression analysis of sugar transporter family genes in pear (Pyrus bretschneideri Rehd). Plant Cell Physiology, 56, 1721–1737. doi:10.1093/pcp/pcv090
   PubMed Web of Science ®Google Scholar
• Li, M., Li, L.T., Dunwell, J.M., Qiao, X., Liu, X., & Zhang, S.L. (2014). Characterization of the lipoxygenase(LOX) gene family in the Chinese white pear (Pyrusbretschneideri) and comparison with other members of the Rosaceae. BMC Genomics, 15, 444. doi:10.1186/1471-2164-15-444
   PubMed Web of Science ®Google Scholar
• Li, X.L., Xue, C., Li, J.M., Qiao, X., Li, L.T., Yu, L.A., … Wu, J. (2016). Genome-wide identification, evolution and functional divergence of MYB transcription factors in chinese white pear (Pyrus bretschneideri). Plant Cell Physiology, 57, 824–847. doi:10.1093/pcp/pcw029
   PubMed Web of Science ®Google Scholar
• Lippuner, V., Cyert, M.S., & Gasser, C.S. (1996). Two classes of plant cDNA clones differentially complement yeast calcineurin mutants and increase salt tolerance of wild-type yeast. Journal of Biological Chemistry, 271, 12859–12866. doi:10.1074/jbc.271.22.12859
   PubMed Web of Science ®Google Scholar
• Nagaoka, S., & Takano, T. (2003). Salt tolerance-related protein STO binds to a Myb transcription factor homologue and confers salt tolerance in Arabidopsis. Journal of Experimental Botany, 54, 2231–2237. doi:10.1093/jxb/erg241
   PubMed Web of Science ®Google Scholar
• Park, H.-Y., Lee, S.-Y., Seok, H.-Y., Kim, S.-H., Sung, Z.R., & Moon, Y.-H. (2011). EMF1 interacts with EIP1, EIP6 or EIP9 involved in the regulation of flowering time in Arabidopsis. Plant Cell Physiology, 52, 1376–1388. doi:10.1093/pcp/pcr084
   PubMed Web of Science ®Google Scholar
• Putterill, J., Robson, F., Lee, K., Simon, R., & Coupland, G. (1995). The CONSTANS gene of Arabidopsis promotes flowering and encodes a protein showing similarities to zinc finger transcription factors. Cell, 80, 847–857. doi:10.1016/0092-8674(95)90288-0
   PubMed Web of Science ®Google Scholar
• Qiao, X., Li, M., Li, L.T., Yin, H., Wu, J.Y., & Zhang, S.L. (2015). Genome-wide identification and comparative analysis of the heat shock transcription factor family in Chinese white pear (Pyrus bretschneideri) and five other Rosaceae species. BMC Plant Biology, 15, 12. doi:10.1186/s12870-014-0401-5
   PubMed Web of Science ®Google Scholar
• Robson, F., Costa, M.M., Hepworth, S.R., Vizir, I., Pin˜eiro, M., Reeves, P.H., & Putterill, J. (2001). Functional importance of conserved domains in the flowering-time gene CONSTANS demonstrated by analysis of mutant alleles and transgenic plants. The Plant Journal, 28, 619–631. doi:10.1046/j.1365-313x.2001.01163.x
   PubMed Web of Science ®Google Scholar
• Samach, A., Onouchi, H., Gold, S.E., Ditta, G.S., Schwarz-Sommer, Z., Yanofsky, M.F., & Coupland, G. (2000). Distinct roles of CONSTANS target genes in reproductive development of Arabidopsis. Science, 288, 1613–1616. doi:10.1126/science.288.5471.1613
   PubMed Web of Science ®Google Scholar
• Schmittgen, T.D., & Livak, K.J. (2008). Analyzing real-time PCR data by the comparative CT method. Nature Protocols, 3, 1101–1108. doi:10.1038/nprot.2008.73
   PubMed Web of Science ®Google Scholar
• Schultz, J., Milpetz, F., Bork, P., & Ponting, C.P. (1998). Smart, a simple modular architecture research tool: Identification of signaling domains. Proceedings of the National Academy of Sciences of the United States of America, 95, 5857–5864.
   PubMed Web of Science ®Google Scholar
• Takuhara, Y., Kobayashi, M., & Suzuki, S. (2011). Low-temperature-induced transcription factors in grapevine enhance cold tolerance in transgenic Arabidopsis plants. Journal of Plant Physiology, 168, 967–975. doi:10.1016/j.jplph.2010.11.008
   PubMed Web of Science ®Google Scholar
• Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., & Kumar, S. (2011). MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution, 28, 2731–2739. doi:10.1093/molbev/msr121
   PubMed Web of Science ®Google Scholar
• Valverde, F., Mouradov, A., Soppe, W., Ravenscroft, D., Samach, A., & Coupland, G. (2004). Photoreceptor regulation of CONSTANS protein in photoperiodic flowering. Science, 303, 1003–1006. doi:10.1126/science.1091761
   PubMed Web of Science ®Google Scholar
• Wang, C.-Q., Sarmast, M.K., Jiang, J.S., & Dehesh, K. (2015). The transcriptional regulator BBX19 promotes hypocotyl growth by facilitating COP1-mediated early flowering3 degradation in Arabidopsis. The Plant Cell, 27, 1128–1139. doi:10.1105/tpc.15.00044
   PubMed Web of Science ®Google Scholar
• Wang, Q.M., Tu, X.J., Zhang, J.H., Chen, X.B., & Rao, L.Q. (2013). Heat stress-induced BBX18 negatively regulates the thermotolerance in Arabidopsis. Molecular Biology Reports, 40, 2679–2688. doi:10.1007/s11033-012-2354-9
   PubMed Web of Science ®Google Scholar
• Weng, X., Wang, L., Wang, J., Hu, Y., Du, H., Xu, C., … Zhang, Q. (2014). Grain number, plant height, and heading date7 is a central regulator of growth, development, and stress response. Plant Physiology, 164, 735–747. doi:10.1104/pp.113.231308
   PubMed Web of Science ®Google Scholar
• Winter, D., Vinegar, B., Nahal, H., Ammar, R., Wilson, G.V., & Provart, N.J. (2007). An “Electronic Fluorescent Pictograph” browser for exploring and analyzing large-scale biological data sets. Plos One, 2, e718. doi:10.1371/journal.pone.0000718
   PubMed Web of Science ®Google Scholar
• Wu, J., Wang, Z.W., Shi, Z.B., Zhang, S., Ming, R., Zhu, S.L., … Zhang, S.L. (2013). The genome of the pear (Pyrus bretschneideri Rehd.). Genome Research, 23, 396–408. doi:10.1101/gr.144311.112
   PubMed Web of Science ®Google Scholar
• Yang, Y.J., Ma, C., Xu, Y.J., Wei, Q., Imtiaz, M., Lan, H.B., … Gao, J.P. (2014). A Zinc finger protein regulates flowering time and abiotic stress tolerance in Chrysanthemum by modulating gibberellins biosynthesis. The Plant Cell, 26, 2038–2054. doi:10.1105/tpc.114.124867
   PubMed Web of Science ®Google Scholar
• Yano, M., Katayose, Y., Ashikari, M., Yamanouchi, U., Monna, L., Fuse, T., … Sasaki, T. (2000). Hd1, a major photoperiod sensitivity quantitative trait locus in rice, is closely related to the Arabidopsis flowering time gene CONSTANS. The Plant Cell, 12, 2473–2484. doi:10.1105/tpc.12.12.2473
   PubMed Web of Science ®Google Scholar
• Ye, J., Fang, L., Zheng, H.K., Zhang, Y., Chen, J., Zhang, Z.J., … Wang, J. (2006). WEGO: A web tool for plotting GO annotations. Nucleic Acids Research, 34, W293–W297. doi:10.1093/nar/gkl031
   PubMed Web of Science ®Google Scholar