[1]

Dye BT, Schulman BA. 2007. Structural mechanisms underlying posttranslational modification by ubiquitin-like proteins. Annual Review of Biophysics and Biomolecular Structure 36:131−50

doi: 10.1146/annurev.biophys.36.040306.132820
[2]

Ciechanover A. 1998. The ubiquitin-proteasome pathway: on protein death and cell life. The EMBO journal 17:7151−60

doi: 10.1093/emboj/17.24.7151
[3]

Moon J, Parry G, Estelle M. 2004. The ubiquitin-proteasome pathway and plant development. The Plant Cell 16:3181−95

doi: 10.1105/tpc.104.161220
[4]

Smalle J, Vierstra RD. 2004. The ubiquitin 26S proteasome proteolytic pathway. Annual Review of Plant Biology 55:555−90

doi: 10.1146/annurev.arplant.55.031903.141801
[5]

Harper JW, Burton JL, Solomon MJ. 2002. The anaphase-promoting complex: it's not just for mitosis any more. Genes & Development 16:2179−206

doi: 10.1101/gad.1013102
[6]

Jackson PK, Eldridge AG, Freed E, Furstenthal L, Hsu JY, et al. 2000. The lore of the RINGs: substrate recognition and catalysis by ubiquitin ligases. Trends in Cell Biology 10:429−39

doi: 10.1016/S0962-8924(00)01834-1
[7]

Aravind L, Koonin EV. 2000. The U box is a modified RING finger - a common domain in ubiquitination. Current Biology 10:PR132−R134

doi: 10.1016/S0960-9822(00)00398-5
[8]

Ohi MD, Vander kooi CW, Rosenberg JA, Chazin WJ, Gould KL. 2003. Structural insights into the U-box, a domain associated with multi-ubiquitination. Nature Structural & Molecular Biology 10:250−55

doi: 10.1038/nsb906
[9]

Azevedo C, Santos-Rosa MJ, Shirasu K. 2001. The U-box protein family in plants. Trends in Plant Science 6:354−58

doi: 10.1016/S1360-1385(01)01960-4
[10]

Meacham GC, Patterson C, Zhang W, Younger JM, Cyr DM. 2001. The Hsc70 co-chaperone CHIP targets immature CFTR for proteasomal degradation. Nature Cell Biology 3:100−5

doi: 10.1038/35050509
[11]

Stone SL, Anderson EM, Mullen RT, Goring DR. 2003. ARC1 is an E3 ubiquitin ligase and promotes the ubiquitination of proteins during the rejection of self-incompatible Brassica pollen. The Plant Cell 15:885−98

doi: 10.1105/tpc.009845
[12]

Koegl M, Hoppe T, Schlenker S, Ulrich HD, Mayer TU, et al. 1999. A novel ubiquitination factor, E4, is involved in multiubiquitin chain assembly. Cell 96:635−44

doi: 10.1016/S0092-8674(00)80574-7
[13]

Hatakeyama S, Yada M, Matsumoto M, Ishida N, Nakayama KI. 2001. U box proteins as a new family of ubiquitin-protein ligases. Journal of Biological Chemistry 276:33111−20

doi: 10.1074/jbc.M102755200
[14]

Patterson C. 2002. A new gun in town: The U box is a ubiquitin ligase domain. Science's STKE 2002:pe4

doi: 10.1126/stke.2002.116.pe4
[15]

Wiborg J, O'shea C, Skriver K. 2008. Biochemical function of typical and variant Arabidopsis thaliana U-box E3 ubiquitin-protein ligases. Biochemical Journal 413:447−57

doi: 10.1042/BJ20071568
[16]

Zeng LR, Park CH, Venu RC, Gough J, Wang GL. 2008. Classification, expression pattern, and E3 ligase activity assay of rice U-Box-containing proteins. Molecular Plant 1:800−15

doi: 10.1093/mp/ssn044
[17]

Luo Q, Li Y, Wang W, Fei X, Deng X. 2015. Genome-wide survey and expression analysis of Chlamydomonas reinhardtii U-box E3 ubiquitin ligases (CrPUBs) reveal a functional lipid metabolism module. PLoS One 10:e0122600

doi: 10.1371/journal.pone.0122600
[18]

Wang C, Duan W, Riquicho AR, Jing Z, Liu T, et al. 2015. Genome-wide survey and expression analysis of the PUB family in Chinese cabbage (Brassica rapa ssp pekinesis). Molecular Genetics and Genomics 290:2241−60

doi: 10.1007/s00438-015-1075-x
[19]

Wang N, Liu Y, Cong Y, Wang T, Zhong X. 2016. Genome-wide identification of soybean U-box E3 ubiquitin ligases and roles of GmPUB8 in negative regulation of drought stress response in Arabidopsis. Plant and Cell Physiology 57:1189−209

doi: 10.1093/pcp/pcw068
[20]

Andersen P, Kragelund BB, Olsen AN, Larsen FH, Chua NH, et al. 2004. Structure and biochemical function of a prototypical Arabidopsis U-box domain. Journal of Biological Chemistry 279:40053−61

doi: 10.1074/jbc.M405057200
[21]

Mudgil Y, Shiu SH, Stone SL, Salt JN, Goring DR. 2004. A large complement of the predicted Arabidopsis ARM repeat proteins are members of the U-box E3 ubiquitin ligase family. Plant Physiology 134:59−66

doi: 10.1104/pp.103.029553
[22]

Yee D, Goring DR. 2009. The diversity of plant U-box E3 ubiquitin ligases: from upstream activators to downstream target substrates. Journal of Experimental Botany 60:1109−21

doi: 10.1093/jxb/ern369
[23]

Cho SK, Chung HS, Ryu MY, Park MJ, Lee MM, et al. 2006. Heterologous expression and molecular and cellular characterization of CaPUB1 encoding a hot pepper U-box E3 ubiquitin ligase homolog. Plant Physiology 142:1664−82

doi: 10.1104/pp.106.087965
[24]

Cho SK, Ryu MY, Song C, Kwak JM, Kim WT. 2008. Arabidopsis PUB22 and PUB23 are homologous U-box E3 ubiquitin ligases that play combinatory roles in response to drought stress. The Plant Cell 20:1899−914

doi: 10.1105/tpc.108.060699
[25]

Liu Y, Wu Y, Huang X, Sun J, Xie Q. 2011. AtPUB19, a U-box E3 ubiquitin ligase, negatively regulates abscisic acid and drought responses in Arabidopsis thaliana. Molecular Plant 4:938−46

doi: 10.1093/mp/ssr030
[26]

Raab S, Drechsel G, Zarepour M, Hartung W, Koshiba T, et al. 2009. Identification of a novel E3 ubiquitin ligase that is required for suppression of premature senescence in Arabidopsis. The Plant Journal 59:39−51

doi: 10.1111/j.1365-313X.2009.03846.x
[27]

Salt JN, Yoshioka K, Moeder W, Goring DR. 2011. Altered germination and subcellular localization patterns for PUB44/SAUL1 in response to stress and phytohormone treatments. PLoS One 6:e21321

doi: 10.1371/journal.pone.0021321
[28]

Park JJ, Yi J, Yoon J, Cho LH, Ping J, et al. 2011. OsPUB15, an E3 ubiquitin ligase, functions to reduce cellular oxidative stress during seedling establishment. The Plant Journal 65:194−205

doi: 10.1111/j.1365-313X.2010.04416.x
[29]

Sato S, Tabata S, Hirakawa H, Asamizu E, Shirasawa K, et al. 2012. The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485:635−41

doi: 10.1038/nature11119
[30]

Bai YL, Kissoudis C, Yan Z, Visser RGF, van der Linden G. 2018. Plant behaviour under combined stress: tomato responses to combined salinity and pathogen stress. The Plant Journal 93:781−93

doi: 10.1111/tpj.13800
[31]

Moin M, Bakshi A, Madhav MS, Kirti PB. 2019. Comprehensive expression profiling reveals the possible involvement of Cullins in developmental and stress regulation in rice. Environmental and Experimental Botany 160:101−11

doi: 10.1016/j.envexpbot.2019.01.008
[32]

Khan N, Fatima F, Haider MS, Shazadee H, Liu Z, et al. 2019. Genome-wide identification and expression profiling of the polygalacturonase (PG) and pectin methylesterase (PME) genes in grapevine (Vitis vinifera L). International Journal of Molecular Sciences 20:3180

doi: 10.3390/ijms20133180
[33]

Dai Q, Geng L, Lu M, Jin W, Nan X, et al. 2017. Comparative transcriptome analysis of the different tissues between the cultivated and wild tomato. PLoS One 12:e0172411

doi: 10.1371/journal.pone.0172411
[34]

Pattison RJ, Csukasi F, Zheng Y, Fei Z, van der Knaap E, et al. 2015. Comprehensive tissue-specific transcriptome analysis reveals distinct regulatory programs during early tomato fruit development. Plant Physiology 168:1684−701

doi: 10.1104/pp.15.00287
[35]

Lu S, Wang J, Chitsaz F, Derbyshire MK, Geer RC, et al. 2020. CDD/SPARCLE: the conserved domain database in 2020. Nucleic Acids Research 48:D265−D268

doi: 10.1093/nar/gkz991
[36]

Han Y, Ding T, Su B, Jiang H. 2016. Genome-wide identification, characterization and expression analysis of the chalcone synthase family in maize. International Journal of Molecular Sciences 17:161

doi: 10.3390/ijms17020161
[37]

Moore RC, Purugganan MD. 2003. The early stages of duplicate gene evolution. Proceedings of the National Academy of Sciences of the United States of America 100:15682−87

doi: 10.1073/pnas.2535513100
[38]

Gilbert W, de Souza SJ, Long MY. 1997. Origin of genes. Proceedings of the National Academy of Sciences 94:7698−703

doi: 10.1073/pnas.94.15.7698
[39]

Long M, Langley CH. 1993. Natural selection and the origin of jingwei, a chimeric processed functional gene in Drosophila. Science 260:91−95

doi: 10.1126/science.7682012
[40]

Cao Y, Han Y, Meng D, Li D, Jin Q, et al. 2016. Structural, evolutionary, and functional analysis of the Class III peroxidase gene family in Chinese pear (Pyrus bretschneideri). Frontier in Plant Science 7:1874

doi: 10.3389/fpls.2016.01874
[41]

Khan N, Ke H, Hu CM, Naseri E, Haider MS. 2019. Genome-wide identification, evolution, and transcriptional profiling of PP2C gene family in Brassica rapa. BioMed Research International 2019:2965035

doi: 10.1155/2019/2965035
[42]

Stebbins GL. 1950. Variation and evolution in plants. pp 644. London: Oxford University Press . pp 643−44.

[43]

Lynch M, Conery JS. 2000. The evolutionary fate and consequences of duplicate genes. Science 290:1151−55

doi: 10.1126/science.290.5494.1151
[44]

Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, et al. 2010. Genome sequence of the palaeopolyploid soybean. Nature 463:178−83

doi: 10.1038/nature08670
[45]

Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, et al. 2009. The B73 maize genome: complexity, diversity, and dynamics. Science 326:1112−15

doi: 10.1126/science.117853
[46]

Aderemi F, Wuraola A. 2006. Effects of dietary replacement of maize with malted or unmalted sorghum on the performance of weaner rabbits. African Journal of Food, Agriculture, Nutrition and Development 10:4032−46

doi: 10.4314/ajfand.v10i9.62886
[47]

Maere S, de Bodt S, Raes J, Casneuf T, van Montagu M, et al. 2005. Modeling gene and genome duplications in eukaryotes. Proceedings of the National Academy of Sciences of the United States of America 102:5454−59

doi: 10.1073/pnas.0501102102
[48]

Birchler JA, Veitia RA. 2007. The gene balance hypothesis: from classical genetics to modern genomics. The Plant Cell 19:395−402

doi: 10.1105/tpc.106.049338
[49]

Goodstein DM, Shu SQ, Howson R, Neupane R, Hayes RD, et al. 2011. Phytozome: a comparative platform for green plant genomics. Nucleic Acids Research 40:D1178−D1186

doi: 10.1093/nar/gkr944
[50]

Lamesch P, Berardini TZ, Li DH, 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
[51]

Letunic L, Bork P. 2018. 20 years of the SMART protein domain annotation resource. Nucleic Acids Research 46:D493−D496

doi: 10.1093/nar/gkx922
[52]

Kumar S, Stecher G, Tamura K. 2016. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution 33:1870−74

doi: 10.1093/molbev/msw054
[53]

Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32:1792−97

doi: 10.1093/nar/gkh340
[54]

Cheng CJ, 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(8):1194−202

doi: 10.1016/j.molp.2020.06.009
[55]

Bailey TL, Boden M, Buske FA, Frith M, Grant CE, et al. 2009. MEME Suite: tools for motif discovery and searching. Nucleic Acids Research 37:W202−W208

doi: 10.1093/nar/gkp335
[56]

Li Y, Chen Y, Zhou L, You S, Deng H, et al. 2020. MicroTom metabolic network: Rewiring tomato metabolic regulatory network throughout the growth cycle. Molecular Plant 13:1203−18

doi: 10.1016/j.molp.2020.06.005
[57]

Metsalu T, Vilo J. 2015. ClustVis: a web tool for visualizing clustering of multivariate data using principal component analysis and heatmap. Nucleic Acids Research 43:W566−W570

doi: 10.1093/nar/gkv468
[58]

Livak KJ, Schmittgen TD. 2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT Method. Methods 25:402−8

doi: 10.1006/meth.2001.1262