New insights into the evolution of the SBP-box family and expression analysis of genes in the growth and development of Brassica juncea

References

• Gong Z, Xiong L, Shi H, et al. Plant abiotic stress response and nutrient use efficiency. Sci China Life Sci. 2020;63(5):635–674.
   PubMed Web of Science ®Google Scholar
• Jin J, Tian F, Yang D, et al. PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants. Nucleic Acids Res. 2017;45(D1):D1040–D1045.
   PubMed Web of Science ®Google Scholar
• Riechmann JL, Heard J, Martin G, et al. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science. 2000;290(5499):2105–2110.
   PubMed Web of Science ®Google Scholar
• Goff SA, Ricke D, Lan TH, et al. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science. 2002;296(5565):92–100.
   PubMed Web of Science ®Google Scholar
• Birkenbihl RP, Jach G, Saedler H, et al. Functional dissection of the plant-specific SBP-domain: overlap of the DNA-binding and nuclear localization domains. J Mol Biol. 2005;352(3):585–596.
   PubMed Web of Science ®Google Scholar
• Yamasaki K, Kigawa T, Inoue M, et al. A novel zinc-binding motif revealed by solution structures of DNA-binding domains of Arabidopsis SBP-family transcription factors. J Mol Biol. 2004;337(1):49–63.
   PubMed Web of Science ®Google Scholar
• Klein J, Saedler H, Huijser P. A new family of DNA binding proteins includes putative transcriptional regulators of the Antirrhinum majus floral meristem identity gene SQUAMOSA. Mol Gen Genet. 1996;250(1):7–16.
   PubMedGoogle Scholar
• Riese M, Hohmann S, Saedler H, et al. Comparative analysis of the SBP-box gene families in P. patens and seed plants. Gene. 2007;401(1–2):28–37.
   PubMed Web of Science ®Google Scholar
• Xie K, Wu C, Xiong L. Genomic organization, differential expression, and interaction of SQUAMOSA promoter-binding-like transcription factors and microRNA156 in rice. Plant Physiol. 2006;142(1):280–293.
   PubMed Web of Science ®Google Scholar
• Li J, Hou H, Li X, et al. Genome-wide identification and analysis of the SBP-box family genes in apple (Malus × domestica Borkh.). Plant Physiol Biochem. 2013;70:100–114.
   PubMed Web of Science ®Google Scholar
• Zhou Q, Zhang S, Chen F, et al. Genome-wide identification and characterization of the SBP-box gene family in Petunia. BMC Genomics. 2018;19(1):193.
   PubMed Web of Science ®Google Scholar
• Cai C, Guo W, Zhang B. Genome-wide identification and characterization of SPL transcription factor family and their evolution and expression profiling analysis in cotton. Sci Rep. 2018;8(1):762.
   PubMed Web of Science ®Google Scholar
• Manning K, Tör M, Poole M, et al. A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening. Nat Genet. 2006;38(8):948–952.
   PubMed Web of Science ®Google Scholar
• Jung JH, Lee HJ, Ryu JY, et al. SPL3/4/5 integrate developmental aging and photoperiodic signals into the FT-FD module in Arabidopsis flowering. Mol Plant. 2016;9(12):1647–1659.
   PubMed Web of Science ®Google Scholar
• Song S, Zhou H, Sheng S, et al. Genome-wide organization and expression profiling of the SBP-box gene family in Chinese jujube (Ziziphus jujuba Mill.). Int J Mol Sci. 2017;18(8):1734.
   Web of Science ®Google Scholar
• Han YC, Gao HY, Chen HJ, et al. The involvement of papaya CpSBP1 in modulating fruit softening and carotenoid accumulation by repressing CpPME1/2 and CpPDS4. Sci Hortic. 2019;256:108582.
   Web of Science ®Google Scholar
• Wei J, Wang C, Jiang J, et al. Cloning and expression analysis of BplSPL2, a novel SBP-box gene from Betula Platyphylla. Biotechnol Biotechnol Equip. 2010;24(2):1824–1827.
   Web of Science ®Google Scholar
• Chao LM, Liu YQ, Chen DY, et al. Arabidopsis transcription factors SPL1 and SPL12 confer plant thermotolerance at reproductive stage. Mol Plant. 2017;10(5):735–748.
   PubMed Web of Science ®Google Scholar
• Zhang HX, Jin JH, He YM, et al. Genome-wide identification and analysis of the SBP-Box family genes under phytophthora capsici stress in pepper (Capsicum annuum L.). Front Plant Sci. 2016;7:504.
   PubMed Web of Science ®Google Scholar
• Kropat J, Tottey S, Birkenbihl RP, et al. A regulator of nutritional copper signaling in Chlamydomonas is an SBP domain protein that recognizes the GTAC core of copper response element. Proc Natl Acad Sci USA. 2005;102(51):18730–18735.
   PubMed Web of Science ®Google Scholar
• Zhang Y, Schwarz S, Saedler H, et al. SPL8, a local regulator in a subset of gibberellin-mediated developmental processes in Arabidopsis. Plant Mol Biol. 2007;63(3):429–439.
   PubMed Web of Science ®Google Scholar
• Xu M, Hu T, Zhao J, et al. Developmental Functions of miR156-Regulated SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) Genes in Arabidopsis thaliana. PLoS Genet. 2016;12(8):e1006263.
   PubMed Web of Science ®Google Scholar
• Ferreira e Silva GF, Silva EM, Azevedo Mda S, et al. microRNA156-targeted SPL/SBP box transcription factors regulate tomato ovary and fruit development. Plant J. 2014;78(4):604–618.
   PubMed Web of Science ®Google Scholar
• Kelly PJ, Bones A, Rossiter JT. Sub-cellular immunolocalization of the glucosinolate sinigrin in seedlings of Brassica juncea. Planta. 1998;206(3):370–377.
   PubMed Web of Science ®Google Scholar
• Weng PF, Wu ZF, Shen XQ, et al. A new cleaner production technique of pickle mustard tuber at low salinity by lactic acid bacteria. J Food Process Eng. 2011;34(4):1144–1155.
   Web of Science ®Google Scholar
• Shi H, Wang LL, Sun LT, et al. Cell division and endoreduplication play important roles in stem swelling of tuber mustard (Brassica juncea Coss. var. tumida Tsen et Lee). Plant Biol (Stuttg). 2012;14(6):956–963.
   PubMed Web of Science ®Google Scholar
• Sun Q, Zhou G, Cai Y, et al. Transcriptome analysis of stem development in the tumourous stem mustard Brassica juncea var. tumida Tsen et Lee by RNA sequencing. BMC Plant Biol. 2012;12:53.
   PubMed Web of Science ®Google Scholar
• Altschul SF, Madden TL, Schäffer AA, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25(17):3389–3402.
   PubMed Web of Science ®Google Scholar
• Gasteiger E, Gattiker A, Hoogland C, et al. ExPASy: the proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res. 2003;31(13):3784–3788.
   PubMed Web of Science ®Google Scholar
• Kumar S, Nei M, Dudley J, et al. MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinformatics. 2008;9(4):299–306.
   PubMed Web of Science ®Google Scholar
• Chen C, Chen H, Zhang Y, et al. TBtools - an integrative toolkit developed for interactive analyses of big biological data. Mol Plant. 2020. doi: 10.1016/j.molp.2020.06.009
   Web of Science ®Google Scholar
• Bailey TL, Boden M, Buske FA, et al. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 2009;37(Web Server issue):W202–W208.
   PubMed Web of Science ®Google Scholar
• Wang Y, Tang H, Debarry JD, et al. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res. 2012;40(7):e49.
   PubMed Web of Science ®Google Scholar
• Lescot M, Dehais P, Thijs G, et al. PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res. 2002;30(1):325–327.
   PubMed Web of Science ®Google Scholar
• Conesa A, Gotz S, Garcia-Gomez JM, et al. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics. 2005;21(18):3674–3676.
   PubMed Web of Science ®Google Scholar
• Li MY, Xie FJ, He Q, et al. Expression analysis of XTH in stem swelling of stem mustard and selection of reference genes. Genes. 2020;11(1):113.
   Web of Science ®Google Scholar
• Pfaffl MW. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res. 2001;29(9):e45.
   PubMed Web of Science ®Google Scholar
• Rose AB. The effect of intron location on intron-mediated enhancement of gene expression in Arabidopsis. Plant J. 2004;40(5):744–751.
   PubMed Web of Science ®Google Scholar
• Kong H, Landherr LL, Frohlich MW, et al. Patterns of gene duplication in the plant SKP1 gene family in angiosperms: evidence for multiple mechanisms of rapid gene birth. Plant J. 2007;50(5):873–885.
   PubMed Web of Science ®Google Scholar
• Semon M, Wolfe KH. Consequences of genome duplication. Curr Opin Genet Dev. 2007;17(6):505–512.
   PubMed Web of Science ®Google Scholar
• Yamasaki H, Hayashi M, Fukazawa M, et al. SQUAMOSA promoter binding protein-like7 is a central regulator for copper homeostasis in Arabidopsis. Plant Cell. 2009;21(1):347–361.
   PubMed Web of Science ®Google Scholar
• Wu G, Park MY, Conway SR, et al. The sequential action of miR156 and miR172 regulates developmental timing in Arabidopsis. Cell. 2009;138(4):750–759.
   PubMed Web of Science ®Google Scholar
• Kavas M, Kızıldoğan AK, Abanoz B. Comparative genome-wide phylogenetic and expression analysis of SBP genes from potato (Solanum tuberosum). Comput Biol Chem. 2017;67:131–140.
   PubMed Web of Science ®Google Scholar
• Nagaharu U. Genome analysis in Brassica with special reference to the experimental formation of B. napus and peculiar mode of fertilization. J Jpn Bot. 1935;7:389–452.
   Google Scholar
• Panjabi P, Jagannath A, Bisht NC, et al. Comparative mapping of Brassica juncea and Arabidopsis thaliana using intron polymorphism (IP) markers: homoeologous relationships, diversification and evolution of the A, B and C Brassica genomes. BMC Genomics. 2008;9:113.
   PubMed Web of Science ®Google Scholar
• Li M, Zhao SZ, Zhao CZ, et al. Cloning and characterization of SPL-family genes in the peanut (Arachis hypogaea L.). Genet Mol Res. 2016;15(1).
   Web of Science ®Google Scholar
• Hou H, Li J, Gao M, et al. Genomic organization, phylogenetic comparison and differential expression of the SBP-Box family genes in grape. PLoS One. 2013;8(3):e59358.
   PubMed Web of Science ®Google Scholar
• Zhang L, Wu B, Zhao D, et al. Genome-wide analysis and molecular dissection of the SPL gene family in Salvia miltiorrhiza. J Integr Plant Biol. 2014;56(1):38–50.
   PubMed Web of Science ®Google Scholar
• Glazebrook J. Contrasting mechanisms of defense against biotrophic and necrotrophic pathogens. Annu Rev Phytopathol. 2005;43:205–227.
   PubMed Web of Science ®Google Scholar
• Okabe Y, Yamaoka T, Ariizumi T, et al. Aberrant stamen development is associated with parthenocarpic fruit set through up-regulation of gibberellin biosynthesis in tomato. Plant Cell Physiol. 2019;60(1):38–51.
   PubMed Web of Science ®Google Scholar
• Huang WJ, Wang YR, Li X, et al. Biosynthesis and regulation of salicylic acid and N-Hydroxypipecolic acid in plant immunity. Mol Plant. 2020;13(1):31–41.
   PubMed Web of Science ®Google Scholar
• Tan HW, Song XM, Duan WK, et al. Genome-wide analysis of the SBP-box gene family in Chinese cabbage (Brassica rapa subsp. pekinensis). Genome. 2015;58(11):463–477.
   PubMed Web of Science ®Google Scholar
• Pan F, Wang Y, Liu H, et al. Genome-wide identification and expression analysis of SBP-like transcription factor genes in Moso Bamboo (Phyllostachys edulis). BMC Genomics. 2017;18(1):486.
   PubMed Web of Science ®Google Scholar
• Unte US, Sorensen AM, Pesaresi P, et al. SPL8, an SBP-box gene that affects pollen sac development in Arabidopsis. Plant Cell. 2003;15(4):1009–1019.
   PubMed Web of Science ®Google Scholar