[1]

Shen S, Li N, Wang Y, Zhou R, Sun P, et al. 2022. High-quality ice plant reference genome analysis provides insights into genome evolution and allows exploration of genes involved in the transition from C3 to CAM pathways. Plant Biotechnology Journal 20:2107−22

doi: 10.1111/pbi.13892
[2]

Drira R, Matsumoto T, Agawa M, Sakamoto K. 2016. Ice plant (Mesembryanthemum crystallinum) extract promotes lipolysis in mouse 3T3-L1 adipocytes through extracellular signal-regulated kinase activation. Journal of Medicinal Food 19:274−80

doi: 10.1089/jmf.2015.3470
[3]

Borland AM, Hartwell J, Weston DJ, Schlauch KA, Tschaplinski TJ, et al. 2014. Engineering crassulacean acid metabolism to improve water-use efficiency. Trends in Plant Science 19:327−38

doi: 10.1016/j.tplants.2014.01.006
[4]

Feng Y, Liu C, Gong B, Ai X, Bi H. 2024. Abscisic acid participates in melatonin-induced chilling tolerance of cucumber via regulating photosynthesis and the antioxidant system. Vegetable Research 4:e025

doi: 10.48130/vegres-0024-0024
[5]

Pan M, Xia C, Gu S, He H, Wang G, et al. 2024. Loss-function-of a UMP kinase leads to impaired chloroplast development and photosynthesis efficiency in cucumber. Vegetable Research 4:e034

doi: 10.48130/vegres-0024-0035
[6]

Yuan G, Hassan MM, Liu D, Lim SD, Yim WC, et al. 2020. Biosystems design to accelerate C3-to-CAM progression. Biodesign Research 2020:3686791

doi: 10.34133/2020/3686791
[7]

Sage RF, Sage TL, Kocacinar F. 2012. Photorespiration and the evolution of C4 photosynthesis. Annual Review of Plant Biology 63:19−47

doi: 10.1146/annurev-arplant-042811-105511
[8]

Silvera K, Neubig KM, Whitten WM, Williams NH, Winter K, et al. 2010. Evolution along the crassulacean acid metabolism continuum. Functional Plant Biology 37:995−1010

doi: 10.1071/fp10084
[9]

Niechayev NA, Pereira PN, Cushman JC. 2019. Understanding trait diversity associated with crassulacean acid metabolism (CAM). Current Opinion in Plant Biology 49:74−85

doi: 10.1016/j.pbi.2019.06.004
[10]

Winter K. 2019. Ecophysiology of constitutive and facultative CAM photosynthesis. Journal of Experimental Botany 70:6495−508

doi: 10.1093/jxb/erz002
[11]

Cushman JC. 2005. Crassulacean acid metabolism: recent advances and future opportunities. Functional Plant Biology 32:375−80

doi: 10.1071/FP05111
[12]

Yamori W, Hikosaka K, Way DA. 2014. Temperature response of photosynthesis in C3, C4, and CAM plants: temperature acclimation and temperature adaptation. Photosynthesis Research 119:101−17

doi: 10.1007/s11120-013-9874-6
[13]

Liu D, Palla KJ, Hu R, Moseley RC, Mendoza C, et al. 2018. Perspectives on the basic and applied aspects of crassulacean acid metabolism (CAM) research. Plant Science 274:394−401

doi: 10.1016/j.plantsci.2018.06.012
[14]

Yang X, Liu D, Tschaplinski TJ, Tuskan GA. 2019. Comparative genomics can provide new insights into the evolutionary mechanisms and gene function in CAM plants. Journal of Experimental Botany 70:6539−47

doi: 10.1093/jxb/erz408
[15]

Wang X, Jin D, Wang Z, Guo H, Zhang L, et al. 2015. Telomere-centric genome repatterning determines recurring chromosome number reductions during the evolution of eukaryotes. New Phytologist 205:378−89

doi: 10.1111/nph.12985
[16]

Meng F, Chu T, Feng P, Li N, Song C, et al. 2023. Genome assembly of Polygala tenuifolia provides insights into its karyotype evolution and triterpenoid saponin biosynthesis. Horticulture Research 10:uhad139

doi: 10.1093/hr/uhad139
[17]

Liu Z, Shen S, Wang Y, Sun S, Yu T, et al. 2024. The genome of Stephania japonica provides insights into the biosynthesis of cepharanthine. Cell Reports 43:113832

doi: 10.1016/j.celrep.2024.113832
[18]

Hill J, Rastas P, Hornett EA, Neethiraj R, Clark N, et al. 2019. Unprecedented reorganization of holocentric chromosomes provides insights into the enigma of lepidopteran chromosome evolution. Science Advances 5:eaau3648

doi: 10.1126/sciadv.aau3648
[19]

Wang X, Wang Z. 2020. Evolutionary genomics model of chromosome number reduction and B chromosome production. Scientia Sinica Vitae 50:524−37

doi: 10.1360/SSV-2020-0042
[20]

Liu J, Huang C, Xing D, Cui S, Huang Y, et al. 2024. The genomic database of fruits: a comprehensive fruit information database for comparative and functional genomic studies. Agriculture Communications 2:100041

doi: 10.1016/j.agrcom.2024.100041
[21]

Liu Z, Zhang C, He J, Li C, Fu Y, et al. 2024. plantGIR: a genomic database of plants. Horticulture Research 11:uhae342

doi: 10.1093/hr/uhae342
[22]

Feng S, Liu Z, Chen H, Li N, Yu T, et al. 2024. PHGD: an integrative and user-friendly database for plant hormone-related genes. iMeta 3:e164

doi: 10.1002/imt2.164
[23]

Nakamura T, Yamada KD, Tomii K, Katoh K. 2018. Parallelization of MAFFT for large-scale multiple sequence alignments. Bioinformatics 34:2490−92

doi: 10.1093/bioinformatics/bty121
[24]

Price MN, Dehal PS, Arkin AP. 2009. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Molecular Biology and Evolution 26:1641−50

doi: 10.1093/molbev/msp077
[25]

Guo D, Liu Q, Song Y, Cheng Y, Zhang A, et al. 2025. Genome-wide identification, evolution and expression analysis of the PP2C gene family in ice plant. Vegetable Research 5:e019

doi: 10.48130/vegres-0025-0015
[26]

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
[27]

Wang X, Wei Y, Liu Z, Yu T, Fu Y, et al. 2025. TEGR: a comprehensive Ericaceae genome resource database. Journal of Integrative Agriculture 24:1140−51

doi: 10.1016/j.jia.2023.11.026
[28]

Zhu F, Wen W, Cheng Y, Fernie AR. 2022. The metabolic changes that effect fruit quality during tomato fruit ripening. Molecular Horticulture 2:2

doi: 10.1186/s43897-022-00024-1
[29]

Chastain CJ, Xu W, Parsley K, Sarath G, Hibberd JM, et al. 2008. The pyruvate, orthophosphate dikinase regulatory proteins of Arabidopsis possess a novel, unprecedented Ser/Thr protein kinase primary structure. Plant Journal 53:854−63

doi: 10.1111/j.1365-313X.2007.03366.x
[30]

Izui K, Matsumura H, Furumoto T, Kai Y. 2004. Phosphoenolpyruvate carboxylase: a new era of structural biology. Annual Review of Plant Biology 55:69−84

doi: 10.1146/annurev.arplant.55.031903.141619
[31]

Ferrari RC, Bittencourt PP, Rodrigues MA, Moreno-Villena JJ, Alves FRR, et al. 2020. C4 and crassulacean acid metabolism within a single leaf: deciphering key components behind a rare photosynthetic adaptation. New Phytologist 225:1699−714

doi: 10.1111/nph.16265
[32]

O'Leary B, Park J, Plaxton WC. 2011. The remarkable diversity of plant PEPC (phosphoenolpyruvate carboxylase): recent insights into the physiological functions and post-translational controls of non-photosynthetic PEPCs. Biochemical Journal 436:15−34

doi: 10.1042/BJ20110078
[33]

Nimmo HG. 2000. The regulation of phosphoenolpyruvate carboxylase in CAM plants. Trends in Plant Science 5:75−80

doi: 10.1016/S1360-1385(99)01543-5
[34]

Sánchez R, Cejudo FJ. 2003. Identification and expression analysis of a gene encoding a bacterial-type phosphoenolpyruvate carboxylase from Arabidopsis and rice. Plant Physiology 132:949−57

doi: 10.1104/pp.102.019653
[35]

Moroney JV, Ma Y, Frey WD, Fusilier KA, Pham TT, et al. 2011. The carbonic anhydrase isoforms of Chlamydomonas reinhardtii: intracellular location, expression, and physiological roles. Photosynthesis Research 109:133−49

doi: 10.1007/s11120-011-9635-3
[36]

Lindskog S. 1997. Structure and mechanism of carbonic anhydrase. Pharmacology & Therapeutics 74:1−20

doi: 10.1016/S0163-7258(96)00198-2
[37]

Kandoi D, Ruhil K, Govindjee G, Tripathy BC. 2022. Overexpression of cytoplasmic C4 Flaveria bidentis carbonic anhydrase in C3 Arabidopsis thaliana increases amino acids, photosynthetic potential, and biomass. Plant Biotechnology Journal 20:1518−32

doi: 10.1111/pbi.13830
[38]

Hines KM, Chaudhari V, Edgeworth KN, Owens TG, Hanson MR. 2021. Absence of carbonic anhydrase in chloroplasts affects C3 plant development but not photosynthesis. Proceedings of the National Academy of Sciences of the United States of America 118:e2107425118

doi: 10.1073/pnas.2107425118
[39]

Moroney JV, Bartlett SG, Samuelsson G. 2001. Carbonic anhydrases in plants and algae. Plant, Cell & Environment 24:141−53

doi: 10.1111/j.1365-3040.2001.00669.x
[40]

DiMario RJ, Clayton H, Mukherjee A, Ludwig M, Moroney JV. 2017. Plant carbonic anhydrases: structures, locations, evolution, and physiological roles. Molecular Plant 10:30−46

doi: 10.1016/j.molp.2016.09.001
[41]

Sun Q, Yamada T, Han Y, Takano T. 2021. Influence of salt stress on C4 photosynthesis in Miscanthus sinensis Anderss. Plant Biology 23:44−56

doi: 10.1111/plb.13192
[42]

Beeler S, Liu HC, Stadler M, Schreier T, Eicke S, et al. 2014. Plastidial NAD-dependent malate dehydrogenase is critical for embryo development and heterotrophic metabolism in Arabidopsis. Plant Physiology 164:1175−90

doi: 10.1104/pp.113.233866
[43]

Chen X, Zhang J, Zhang C, Wang S, Yang M. 2021. Genome-wide investigation of malate dehydrogenase gene family in poplar (Populus trichocarpa) and their expression analysis under salt stress. Acta Physiologiae Plantarum 43:28

doi: 10.1007/s11738-020-03186-x
[44]

Zhang Y, Wang Y, Sun X, Yuan J, Zhao Z, et al. 2022. Genome-wide identification of MDH family genes and their association with salt tolerance in rice. Plants 11:1498

doi: 10.3390/plants11111498
[45]

Lakner MM, Chastain CJ. 2011. In silico analysis and molecular dissection of the PPDK: PDRP interaction. The FASEB Journal 25:765.12

doi: 10.1096/fasebj.25.1_supplement.765.12
[46]

Matsuoka M. 1995. The gene for pyruvate, orthophosphate dikinase in C4 plants: structure, regulation and evolution. Plant and Cell Physiology 36:937−43

doi: 10.1093/oxfordjournals.pcp.a078864
[47]

Kondo A, Nose A, Ueno O. 2001. Coordinated accumulation of the chloroplastic and cytosolic pyruvate, Pi dikinases with enhanced expression of CAM in Kalanchoë blossfeldiana. Physiologia Plantarum 111:116−22

doi: 10.1034/j.1399-3054.2001.1110115.x
[48]

Rojas BE, Hartman MD, Figueroa CM, Iglesias AA. 2021. Proteolytic cleavage of Arabidopsis thaliana phosphoenolpyruvate carboxykinase-1 modifies its allosteric regulation. Journal of Experimental Botany 72:2514−24

doi: 10.1093/jxb/eraa583
[49]

Villarreal JM, Bueno C, Arenas F, Jabalquinto AM, González-Nilo FD, et al. 2006. Nucleotide specificity of Saccharomyces cerevisiae phosphoenolpyruvate carboxykinase Kinetics, fluorescence spectroscopy, and molecular simulation studies. The International Journal of Biochemistry & Cell Biology 38:576−88

doi: 10.1016/j.biocel.2005.10.018
[50]

Long JJ, Wang JL, Berry JO. 1994. Cloning and analysis of the C4 photosynthetic NAD-dependent malic enzyme of amaranth mitochondria. Journal of Biological Chemistry 269:2827−33

doi: 10.1016/S0021-9258(17)42017-5
[51]

Zhao M, Yao P, Mao Y, Wu J, Wang W, et al. 2022. Malic enzyme 2 maintains protein stability of mutant p53 through 2-hydroxyglutarate. Nature Metabolism 4:225−38

doi: 10.1038/s42255-022-00532-w
[52]

Shi W, Yue L, Guo J, Wang J, Yuan X, et al. 2020. Identification and evolution of C4 photosynthetic pathway genes in plants. BMC Plant Biology 20:132

doi: 10.1186/s12870-020-02339-x
[53]

Alvarez CE, Saigo M, Margarit E, Andreo CS, Drincovich MF. 2013. Kinetics and functional diversity among the five members of the NADP-malic enzyme family from Zea mays, a C4 species. Photosynthesis Research 115:65−80

doi: 10.1007/s11120-013-9839-9
[54]

Arrigo N, Barker MS. 2012. Rarely successful polyploids and their legacy in plant genomes. Current Opinion in Plant Biology 15:140−46

doi: 10.1016/j.pbi.2012.03.010
[55]

Jackson S, Chen ZJ. 2010. Genomic and expression plasticity of polyploidy. Current Opinion in Plant Biology 13:153−59

doi: 10.1016/j.pbi.2009.11.004
[56]

Wang J, Yuan M, Feng Y, Zhang Y, Bao S, et al. 2022. A common whole-genome paleotetraploidization in Cucurbitales. Plant Physiology 190:2430−48

doi: 10.1093/plphys/kiac410
[57]

Murat F, Xu JH, Tannier E, Abrouk M, Guilhot N, et al. 2010. Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution. Genome Research 20:1545−57

doi: 10.1101/gr.109744.110
[58]

Kong X, Zhang Y, Wang Z, Bao S, Feng Y, et al. 2023. Two-step model of paleohexaploidy, ancestral genome reshuffling and plasticity of heat shock response in Asteraceae. Horticulture Research 10:uhad073

doi: 10.1093/hr/uhad073
[59]

Moroney JV, Ynalvez RA. 2007. Proposed carbon dioxide concentrating mechanism in Chlamydomonas reinhardtii. Eukaryotic Cell 6:1251−59

doi: 10.1128/EC.00064-07
[60]

Yer EN, Baloglu MC, Ayan S. 2018. Identification and expression profiling of all Hsp family member genes under salinity stress in different poplar clones. Gene 678:324−36

doi: 10.1016/j.gene.2018.08.049
[61]

Hu H, Boisson-Dernier A, Israelsson-Nordström M, Böhmer M, Xue S, et al. 2010. Carbonic anhydrases are upstream regulators of CO2-controlled stomatal movements in guard cells. Nature Cell Biology 12:87−93

doi: 10.1038/ncb2009
[62]

Yang X, Hu R, Yin H, Jenkins J, Shu S, et al. 2017. The Kalanchoë genome provides insights into convergent evolution and building blocks of crassulacean acid metabolism. Nature Communications 8:1899

doi: 10.1038/s41467-017-01491-7
[63]

Ming R, VanBuren R, Wai CM, Tang H, Schatz MC, et al. 2015. The pineapple genome and the evolution of CAM photosynthesis. Nature Genetics 47:1435−42

doi: 10.1038/ng.3435