| [1] |
Shuai B, Reynaga-Pena CG, Springer PS. 2002. The Lateral Organ Boundaries gene defines a novel, plant-specific gene family. Plant Physiology 129:747−61 doi: 10.1104/pp.010926 |
| [2] |
Matsumura Y, Iwakawa H, Machida Y, Machida C. 2009. Characterization of genes in the ASYMMETRIC LEAVES2/LATERAL ORGAN BOUNDARIES (AS2/LOB) family in Arabidopsis thaliana, and functional and molecular comparisons between AS2 and other family members. The Plant Journal 58:525−37 doi: 10.1111/j.1365-313X.2009.03797.x |
| [3] |
Majer C, Hochholdinger F. 2011. Defining the boundaries: structure and function of LOB domain proteins. Trends Plant Science 16:47−52 doi: 10.1016/j.tplants.2010.09.009 |
| [4] |
Chanderbali AS, He F, Soltis PS, Soltis DE. 2015. Out of the water: origin and diversification of the LBD gene family. Molecular Biology and Evolution 32:1996−2000 doi: 10.1093/molbev/msv080 |
| [5] |
Yang Y, Yu X, Wu P. 2006. Comparison and evolution analysis of two rice subspecies LATERAL ORGAN BOUNDARIES domain gene family and their evolutionary characterization from Arabidopsis. Molecular Phylogenetics and Evolution 39:248−62 doi: 10.1016/j.ympev.2005.09.016 |
| [6] |
Zhang Y, Zhang S, Zheng C. 2014. Genome-wide analysis of LATERAL ORGAN BOUNDARIES domain gene family in Zea mays. Journal of Genetics 93:79−91 doi: 10.1007/s12041-014-0342-7 |
| [7] |
Gupta K, Gupta S. 2021. Molecular and in silico characterization of tomato LBD transcription factors reveals their role in fruit development and stress responses. Plant Gene 27:100309 doi: 10.1016/j.plgene.2021.100309 |
| [8] |
Cao H, Liu C, Liu C, Zhao Y, Xu R. 2016. Genomewide analysis of the lateral organ boundaries domain gene family in Vitis vinifera. Journal of Genetics 95:515−26 doi: 10.1007/s12041-016-0660-z |
| [9] |
Wang X, Zhang S, Su L, Liu X, Hao Y. 2013. A genome-wide analysis of the LBD (LATERAL ORGAN BOUNDARIES domain) gene family in Malus domestica with a functional characterization of MdLBD11. PLoS One 8:e57044 doi: 10.1371/journal.pone.0057044 |
| [10] |
Zhu Q, Guo A, Gao G, Zhong Y, Xu M, et al. 2007. DPTF: a database of poplar transcription factors. Bioinformatics 23:1307−8 doi: 10.1093/bioinformatics/btm113 |
| [11] |
Lu Q, Shao F, Macmillan C, Wilson IW, van der Merwe K, et al. 2018. Genomewide analysis of the lateral organ boundaries domain gene family in Eucalyptus grandis reveals members that differentially impact secondary growth. Plant Biotechnology Journal 16:124−36 doi: 10.1111/pbi.12754 |
| [12] |
Fan M, Xu C, Xu K, Hu Y. 2012. LATERAL ORGAN BOUNDARIES DOMAIN transcription factors direct callus formation in Arabidopsis regeneration. Cell Research 22:1169−80 doi: 10.1038/cr.2012.63 |
| [13] |
Okushima Y, Fukaki H, Onoda M, Theologis A, Tasaka M. 2007. ARF7 and ARF19 regulate lateral root formation via direct activation of LBD/ASL genes in Arabidopsis. The Plant Cell 19:118−30 doi: 10.1105/tpc.106.047761 |
| [14] |
Uchida N, Townsley B, Chung KH, Sinha N. 2007. Regulation of SHOOT MERISTEMLESS genes via an upstream-conserved noncoding sequence coordinates leaf development. Proceedings of the National Academy of Sciences of the United States of America 104:15953−58 doi: 10.1073/pnas.0707577104 |
| [15] |
Xu L, Xu Y, Dong A, Sun Y, Pi L, et al. 2003. Novel as1 and as2 defects in leaf adaxial-abaxial polarity reveal the requirement for ASYMMETRIC LEAVES1 and 2 and ERECTA functions in specifying leaf adaxial identity. Development 130:4097−107 doi: 10.1242/dev.00622 |
| [16] |
Xu B, Li Z, Zhu Y, Wang H, Ma H, et al. 2008. Arabidopsis genes AS1, AS2, and JAG negatively regulate boundary-specifying genes to promote sepal and petal development. Plant Physiology 146:566−75 doi: 10.1104/pp.107.113787 |
| [17] |
Borghi L, Bureau M, Simon R. 2007. Arabidopsis JAGGED LATERAL ORGANS is expressed in boundaries and coordinates KNOX and PIN activity. The Plant Cell 19:1795−808 doi: 10.1105/tpc.106.047159 |
| [18] |
Soyano T, Thitamadee S, Machida Y, Chua NH. 2008. ASYMMETRIC LEAVES2-LIKE19/LATERAL ORGAN BOUNDARIES DOMAIN30 and ASL20/LBD18 regulate tracheary element differentiation in Arabidopsis. The Plant Cell 20:3359−73 doi: 10.1105/tpc.108.061796 |
| [19] |
Rubin G, Tohge T, Matsuda F, Saito K, Scheible WR. 2009. Members of the LBD family of transcription factors repress anthocyanin synthesis and affect additional nitrogen responses in Arabidopsis. The Plant Cell 21:3567−84 doi: 10.1105/tpc.109.067041 |
| [20] |
Li H, Liu X, An J, Hao Y, Wang X, et al. 2017. Cloning and elucidation of the functional role of apple MdLBD13 in anthocyanin biosynthesis and nitrate assimilation. Plant Cell, Tissue and Organ Culture (PCTOC) 130:47−59 doi: 10.1007/s11240-017-1203-x |
| [21] |
Yordanov YS, Regan S, Busov V. 2010. Members of the LATERAL ORGAN BOUNDARIES DOMAIN transcription factor family are involved in the regulation of secondary growth in Populus. The Plant Cell 22:3662−77 doi: 10.1105/tpc.110.078634 |
| [22] |
Omary M, Gil-Yarom N, Yahav C, Steiner E, Hendelman A, et al. 2022. A conserved superlocus regulates above- and below-ground root initiation. Science 375:eabf4368 doi: 10.1126/science.abf4368 |
| [23] |
Ba L, Kuang J, Chen J, Lu W. 2016. MaJAZ1 attenuates the MaLBD5-mediated transcriptional activation of jasmonate biosynthesis gene MaAOC2 in regulating cold tolerance of banana fruit. Journal of Agricultural and Food Chemistry 64:738−45 doi: 10.1021/acs.jafc.5b05005 |
| [24] |
Lamesch P, Berardini TZ, Li D, Swarbreck D, Wilks C, et al. 2012. The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Research 40:D1202−D1210 doi: 10.1093/nar/gkr1090 |
| [25] |
Goodstein DM, Shu S, Howson R, Neupane R, Hayes RD, et al. 2012. Phytozome: a comparative platform for green plant genomics. Nucleic Acids Research 40:D1178−D1186 doi: 10.1093/nar/gkr944 |
| [26] |
Jung S, Lee T, Cheng CH, Buble K, Zheng P, et al. 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 |
| [27] |
Finn RD, Coggill P, Eberhardt RY, Eddy SR, Mistry J, et al. 2016. The Pfam protein families database: towards a more sustainable future. Nucleic Acids Research 44:D279−D285 doi: 10.1093/nar/gkv1344 |
| [28] |
Ponting CP, Schultz J, Milpetz F, Bork P. 1999. SMART: identification and annotation of domains from signalling and extracellular protein sequences. Nucleic Acids Research 27:229−32 doi: 10.1093/nar/27.1.229 |
| [29] |
Marchler-Bauer A, Bo Y, Han L, He J, Lanczycki CJ, et al. 2017. CDD/SPARCLE: functional classification of proteins via subfamily domain architectures. Nucleic Acids Research 45:D200−D203 doi: 10.1093/nar/gkw1129 |
| [30] |
Wilkins MR, Gasteiger E, Bairoch A, Sanchez JC, Williams KL, et al. 1999. Protein identification and analysis tools in the ExPASy server. In 2-D Proteome Analysis Protocols, ed. Link AJ. Vol. 112. NJ: Humana Totowa. pp. 531–52. https://doi.org/10.1385/1-59259-584-7:531 |
| [31] |
Bailey TL, Williams N, Misleh C, Li WW. 2006. MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Research 34:W369−W373 doi: 10.1093/nar/gkl198 |
| [32] |
Chen C, Chen H, Zhang Y, Thomas HR, Frank MH, et al. 2020. TBtools: an integrative toolkit developed for interactive analyses of big biological data. Molecular Plant 13:1194−202 doi: 10.1016/j.molp.2020.06.009 |
| [33] |
Wang Y, Tang H, DeBarry JD, Tan X, Li J, et al. 2012. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Research 40:e49 doi: 10.1093/nar/gkr1293 |
| [34] |
Lescot M, Déhais P, Thijs G, Marchal K, Moreau Y, et al. 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 30:325−27 doi: 10.1093/nar/30.1.325 |
| [35] |
Zhang Q, Chen W, Sun L, Zhao F, Huang B, et al. 2012. The genome of Prunus mume. Nature Communications 3:1318 doi: 10.1038/ncomms2290 |
| [36] |
Zhang M, Cheng W, Yuan X, Wang J, Cheng T, et al. 2022. Integrated transcriptome and small RNA sequencing in revealing miRNA-mediated regulatory network of floral bud break in Prunus mume. Frontiers in Plant Science 13:931454 doi: 10.3389/fpls.2022.931454 |
| [37] |
Zhang T, Qiao Q, Du X, Zhang X, Hou Y, et al. 2022. Cultivated hawthorn (Crataegus pinnatifida var. major) genome sheds light on the evolution of Maleae (apple tribe). Journal of Integrative Plant Biology 64:1487−501 doi: 10.1111/jipb.13318 |
| [38] |
Zhang L, Hu J, Han X, Li J, Gao Y, et al. 2019. A high-quality apple genome assembly reveals the association of a retrotransposon and red fruit colour. Nature Communications 10:1494 doi: 10.1038/s41467-019-09518-x |
| [39] |
Zhang Y, Li Z, Ma B, Hou Q, Wan X. 2020. Phylogeny and functions of LOB domain proteins in plants. International Journal of Molecular Sciences 21:2278 doi: 10.3390/ijms21072278 |
| [40] |
Cannon SB, Mitra A, Baumgarten A, Young ND, May G. 2004. The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana. BMC Plant Biology 4:10 doi: 10.1186/1471-2229-4-10 |
| [41] |
Huang B, Huang Z, Ma R, Ramakrishnan M, Chen J, et al. 2021. Genome-wide identification and expression analysis of LBD transcription factor genes in Moso bamboo (Phyllostachys edulis). BMC Plant Biology 21:296 doi: 10.1186/s12870-021-03078-3 |
| [42] |
Tian Y, Han X, Qu Y, Zhang Y, Rong H, et al. 2022. Genome-wide identification of the Ginkgo (Ginkgo biloba L.) LBD transcription factor gene and characterization of its expression. International Journal of Molecular Sciences 23:5474 doi: 10.3390/ijms23105474 |
| [43] |
Ye L, Wang X, Lyu M, Siligato R, Eswaran G, et al. 2021. Cytokinins initiate secondary growth in the Arabidopsis root through a set of LBD genes. Current Biology 31:3365−3373.e7 doi: 10.1016/j.cub.2021.05.036 |
| [44] |
Cho C, Jeon E, Pandey SK, Ha SH, Kim J. 2019. LBD13 positively regulates lateral root formation in Arabidopsis. Planta 249:1251−58 doi: 10.1007/s00425-018-03087-x |
| [45] |
Goh T, Toyokura K, Yamaguchi N, Okamoto Y, Uehara T, et al. 2019. Lateral root initiation requires the sequential induction of transcription factors LBD16 and PUCHI in Arabidopsis thaliana. New Phytologist 224:749−60 doi: 10.1111/nph.16065 |
| [46] |
Berckmans B, Vassileva V, Schmid SPC, Maes S, Parizot B, et al. 2011. Auxin-dependent cell cycle reactivation through transcriptional regulation of Arabidopsis E2Fa by lateral organ boundary proteins. The Plant Cell 23:3671−83 doi: 10.1105/tpc.111.088377 |
| [47] |
Li C, Zhu S, Zhang H, Chen L, Cai M, et al. 2017. OsLBD37 and OsLBD38, two class II type LBD proteins, are involved in the regulation of heading date by controlling the expression of Ehd1 in rice. Biochemical and Biophysical Research Communications 486:720−25 doi: 10.1016/j.bbrc.2017.03.104 |
| [48] |
Teng RM, Yang N, Liu CF, Chen Y, Wang YX, et al. 2022. CsLBD37, a LBD/ASL transcription factor, affects nitrate response and flowering of tea plant. Scientia Horticulturae 306:111457 doi: 10.1016/j.scienta.2022.111457 |
| [49] |
Zhuo X, Zheng T, Li S, Zhang Z, Zhang M, et al. 2021. Identification of the PmWEEP locus controlling weeping traits in Prunus mume through an integrated genome-wide association study and quantitative trait locus mapping. Horticulture Research 8:131 doi: 10.1038/s41438-021-00573-4 |