{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,28]],"date-time":"2026-07-28T12:28:27Z","timestamp":1785241707661,"version":"3.55.0"},"reference-count":67,"publisher":"MDPI AG","issue":"1","license":[{"start":{"date-parts":[[2023,12,30]],"date-time":"2023-12-30T00:00:00Z","timestamp":1703894400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Zhejiang Science and Technology Major Program on Agricultural New Variety Breeding","award":["2021C02070-10"],"award-info":[{"award-number":["2021C02070-10"]}]},{"name":"Zhejiang Science and Technology Major Program on Agricultural New Variety Breeding","award":["32171828"],"award-info":[{"award-number":["32171828"]}]},{"name":"National Natural Science Foundation of China","award":["2021C02070-10"],"award-info":[{"award-number":["2021C02070-10"]}]},{"name":"National Natural Science Foundation of China","award":["32171828"],"award-info":[{"award-number":["32171828"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Calmodulin (CaM) and calmodulin-like (CML) proteins are major Ca2+ sensors involved in the regulation of plant development and stress responses by converting Ca2+ signals into appropriate cellular responses. However, characterization and expression analyses of CaM\/CML genes in the precious species, Phoebe\u00a0bournei, remain limited. In this study, five PbCaM and sixty PbCML genes were identified that only had EF-hand motifs with no other functional domains. The phylogenetic tree was clustered into 11 subgroups, including a unique clade of PbCaMs. The PbCaMs were intron-rich with four EF-hand motifs, whereas PbCMLs had two to four EF-hands and were mostly intronless. PbCaMs\/CMLs were unevenly distributed across the 12 chromosomes of P.\u00a0bournei and underwent purifying selection. Fragment duplication was the main driving force for the evolution of the PbCaM\/CML gene family. Cis-acting element analysis indicated that PbCaMs\/CMLs might be related to hormones, growth and development, and stress response. Expression analysis showed that PbCaMs were generally highly expressed in five different tissues and under drought stress, whereas PbCMLs showed specific expression patterns. The expression levels of 11 candidate PbCaMs\/CMLs were responsive to ABA and MeJA, suggesting that these genes might act through multiple signaling pathways. The overexpression of PbCaM3\/CML13 genes significantly increased the tolerance of yeast cells to drought stress. The identification and characterization of the CaM\/CML gene family in P.\u00a0bournei laid the foundation for future functional studies of these genes.<\/jats:p>","DOI":"10.3390\/ijms25010545","type":"journal-article","created":{"date-parts":[[2023,12,31]],"date-time":"2023-12-31T06:37:12Z","timestamp":1704004632000},"page":"545","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":17,"title":["Genome-Wide Identification and Expression Analysis of Calmodulin and Calmodulin-like Genes, Revealing CaM3 and CML13 Participating in Drought Stress in Phoebe bournei"],"prefix":"10.3390","volume":"25","author":[{"given":"Ningning","family":"Fu","sequence":"first","affiliation":[{"name":"State Key Laboratory of Subtropical Silviculture, School of Forestry & Biotechnology, Zhejiang A&F University, Lin\u2019an, Hangzhou 311300, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Li","family":"Wang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Subtropical Silviculture, School of Forestry & Biotechnology, Zhejiang A&F University, Lin\u2019an, Hangzhou 311300, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8110-9977","authenticated-orcid":false,"given":"Xiao","family":"Han","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Subtropical Silviculture, School of Forestry & Biotechnology, Zhejiang A&F University, Lin\u2019an, Hangzhou 311300, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qi","family":"Yang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Subtropical Silviculture, School of Forestry & Biotechnology, Zhejiang A&F University, Lin\u2019an, Hangzhou 311300, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuting","family":"Zhang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Subtropical Silviculture, School of Forestry & Biotechnology, Zhejiang A&F University, Lin\u2019an, Hangzhou 311300, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zaikang","family":"Tong","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Subtropical Silviculture, School of Forestry & Biotechnology, Zhejiang A&F University, Lin\u2019an, Hangzhou 311300, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4967-894X","authenticated-orcid":false,"given":"Junhong","family":"Zhang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Subtropical Silviculture, School of Forestry & Biotechnology, Zhejiang A&F University, Lin\u2019an, Hangzhou 311300, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2023,12,30]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1016","DOI":"10.1111\/ppl.13338","article-title":"Insights into the plant responses to drought and decoding the potential of root associated microbiome for inducing drought tolerance","volume":"172","author":"Mathur","year":"2021","journal-title":"Physiol. Plant."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"2357","DOI":"10.1105\/tpc.108.062992","article-title":"Phospholipase D\u03b11 and phosphatidic acid regulate NADPH oxidase activity and production of reactive oxygen species in ABA-mediated stomatal closure in Arabidopsis","volume":"21","author":"Zhang","year":"2009","journal-title":"Plant Cell"},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Li, Q.-F., Wang, J.-D., Xiong, M., Wei, K., Zhou, P., Huang, L.-C., Zhang, C.-Q., Fan, X.-L., and Liu, Q.-Q. (2018). iTRAQ-based analysis of proteins co-regulated by brassinosteroids and gibberellins in rice embryos during seed germination. Int. J. Mol. Sci., 19.","DOI":"10.3390\/ijms19113460"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1016\/j.cell.2016.08.029","article-title":"Abiotic stress signaling and responses in plants","volume":"167","author":"Zhu","year":"2016","journal-title":"Cell"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1126\/science.aaz7614","article-title":"The physiology of plant responses to drought","volume":"368","author":"Gupta","year":"2020","journal-title":"Science"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"969","DOI":"10.1007\/s11033-011-0823-1","article-title":"Signal transduction during cold, salt, and drought stresses in plants","volume":"39","author":"Huang","year":"2012","journal-title":"Mol. Biol. Rep."},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"La Verde, V., Dominici, P., and Astegno, A. (2018). Towards understanding plant calcium signaling through calmodulin-like proteins: A biochemical and structural perspective. Int. J. Mol. Sci., 19.","DOI":"10.3390\/ijms19051331"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"2054","DOI":"10.1016\/j.biochi.2011.05.019","article-title":"Calcium decoding mechanisms in plants","volume":"93","author":"Hashimoto","year":"2011","journal-title":"Biochimie"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"R667","DOI":"10.1016\/j.cub.2017.05.020","article-title":"The evolution of calcium-based signalling in plants","volume":"27","author":"Edel","year":"2017","journal-title":"Curr. Biol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"652","DOI":"10.1016\/j.sajb.2022.01.008","article-title":"Comprehensive genomic insight deciphers significance of EF-hand gene family in foxtail millet [Setaria italica (L.) P. Beauv.]","volume":"148","author":"Nehra","year":"2022","journal-title":"S. Afr. J. Bot."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"780","DOI":"10.1016\/j.molcel.2017.05.028","article-title":"Intracellular Ca2+ sensing: Its role in calcium homeostasis and signaling","volume":"66","author":"Bagur","year":"2017","journal-title":"Mol. Cell"},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Nie, S., Zhang, M., and Zhang, L. (2017). Genome-wide identification and expression analysis of calmodulin-like (CML) genes in Chinese cabbage (Brassica rapa L. ssp. pekinensis). BMC Genom., 18.","DOI":"10.1186\/s12864-017-4240-2"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"383","DOI":"10.1016\/j.tplants.2005.07.001","article-title":"Handling calcium signaling: Arabidopsis CaMs and CMLs","volume":"10","author":"McCormack","year":"2005","journal-title":"Trends Plant Sci."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"450","DOI":"10.1080\/17429145.2022.2047235","article-title":"Identification and expression analysis revealed drought stress-responsive calmodulin and calmodulin-like genes in maize","volume":"17","author":"Wang","year":"2022","journal-title":"J. Plant Interact."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1016\/j.plaphy.2016.02.020","article-title":"Genome-wide identification, characterization and expression analysis of calmodulin-like (CML) proteins in tomato (Solanum lycopersicum)","volume":"102","author":"Munir","year":"2016","journal-title":"Plant Physiol. Biochem."},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Li, Q., Gao, L., Yu, F., L\u00fc, S., and Yang, P. (2023). Evolution and diversification of CaM\/CML gene family in green plants. Plant Physiol. Biochem., 202.","DOI":"10.1016\/j.plaphy.2023.107922"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"153251","DOI":"10.1016\/j.jplph.2020.153251","article-title":"Genome-wide identification and expression analysis of CaM\/CML genes in Brassica napus under abiotic stress","volume":"255","author":"He","year":"2020","journal-title":"J. Plant Physiol."},{"key":"ref_18","first-page":"15","article-title":"Genome-wide analysis of CaM\/CML gene family in two orchidaceae species","volume":"31","author":"Yang","year":"2018","journal-title":"For. Res."},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Xue, N., Sun, M., Gai, Z., Bai, M., Sun, J., Sai, S., and Zhang, L. (2023). Genome-wide identification and expression analysis of calmodulin (CaM) and calmodulin-like (CML) genes in the brown algae Saccharina japonica. Plants, 12.","DOI":"10.3390\/plants12101934"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1007\/s11103-014-0220-y","article-title":"Arabidopsis thaliana calmodulin-like protein CML24 regulates pollen tube growth by modulating the actin cytoskeleton and controlling the cytosolic Ca2+ concentration","volume":"86","author":"Yang","year":"2014","journal-title":"Plant Mol. Biol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"153373","DOI":"10.1016\/j.jplph.2021.153373","article-title":"Tomato calmodulin-like protein SlCML37 is a calcium (Ca2+) sensor that interacts with proteasome maturation factor SlUMP1 and plays a role in tomato fruit chilling stress tolerance","volume":"258\u2013259","author":"Tang","year":"2021","journal-title":"J. Plant Physiol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1016\/j.envexpbot.2018.09.022","article-title":"Calmodulin-like gene MtCML40 is involved in salt tolerance by regulating MtHKTs transporters in Medicago truncatula","volume":"157","author":"Zhang","year":"2019","journal-title":"Environ. Exp. Bot."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1007\/s11032-017-0668-y","article-title":"OsDSR-1, a calmodulin-like gene, improves drought tolerance through scavenging of reactive oxygen species in rice (Oryza sativa L.)","volume":"37","author":"Yin","year":"2017","journal-title":"Mol. Breed."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"549","DOI":"10.1038\/s41477-022-01139-5","article-title":"Divergence in the ABA gene regulatory network underlies differential growth control","volume":"8","author":"Sun","year":"2022","journal-title":"Nat. Plants"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"575","DOI":"10.1111\/j.1365-313X.2008.03622.x","article-title":"Mutations in AtCML9, a calmodulin-like protein from Arabidopsis thaliana, alter plant responses to abiotic stress and abscisic acid","volume":"56","author":"Magnan","year":"2008","journal-title":"Plant J."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"100410","DOI":"10.1016\/j.xplc.2022.100410","article-title":"The chromosome-scale genome of Phoebe bournei reveals contrasting fates of terpene synthase (TPS)-a and TPS-b subfamilies","volume":"3","author":"Han","year":"2022","journal-title":"Plant Commun."},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Wang, L., Wang, Q., Fu, N., Song, M., Han, X., Yang, Q., Zhang, Y., Tong, Z., and Zhang, J. (2023). Cyanidin-3-O-glucoside contributes to leaf color change by regulating two bHLH transcription factors in Phoebe bournei. Int. J. Mol. Sci., 24.","DOI":"10.3390\/ijms24043829"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"1241","DOI":"10.1007\/s11738-014-1502-3","article-title":"Physiological and biochemical responses of Phoebe bournei seedlings to water stress and recovery","volume":"36","author":"Ge","year":"2014","journal-title":"Acta Physiol. Plant."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1007\/s11676-023-01661-y","article-title":"Genome wide investigation of Hsf gene family in Phoebe bournei: Identification, evolution, and expression after abiotic stresses","volume":"35","author":"Liao","year":"2023","journal-title":"J. For. Res."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"964888","DOI":"10.3389\/fpls.2022.964888","article-title":"Calmodulin and calmodulin-like gene family in barley: Identification, characterization and expression analyses","volume":"13","author":"Cai","year":"2022","journal-title":"Front. Plant Sci."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"877","DOI":"10.3389\/fpls.2017.00877","article-title":"Analysis of EF-hand proteins in soybean genome suggests their potential roles in environmental and nutritional stress signaling","volume":"8","author":"Zeng","year":"2017","journal-title":"Front. Plant Sci."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"275","DOI":"10.1111\/j.1469-8137.2008.02682.x","article-title":"Shaping the calcium signature","volume":"181","author":"McAinsh","year":"2009","journal-title":"New Phytol."},{"key":"ref_33","first-page":"145","article-title":"The role of calmodulin and related proteins in plant cell function: An ever-thickening plot","volume":"2","author":"Bergey","year":"2014","journal-title":"Springer Sci. Rev."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"97","DOI":"10.3109\/07388551.2012.672398","article-title":"Ca2+ signals: The versatile decoders of environmental cues","volume":"33","author":"Sarwat","year":"2013","journal-title":"Crit. Rev. Biotechnol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"2048","DOI":"10.1016\/j.biochi.2011.07.012","article-title":"Calmodulin and calmodulin-like proteins in plant calcium signaling","volume":"93","author":"Perochon","year":"2011","journal-title":"Biochimie"},{"key":"ref_36","doi-asserted-by":"crossref","unstructured":"Boonburapong, B., and Buaboocha, T. (2007). Genome-wide identification and analyses of the rice calmodulin and related potential calcium sensor proteins. BMC Plant Biol., 7.","DOI":"10.1186\/1471-2229-7-4"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"9652","DOI":"10.1038\/s41598-020-66670-x","article-title":"Expression patterns of NbrgsCaM family genes in Nicotiana benthamiana and their potential roles in development and stress responses","volume":"10","author":"Liu","year":"2020","journal-title":"Sci. Rep."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"2013646","DOI":"10.1080\/15592324.2021.2013646","article-title":"Genome-wide identification and expression analysis of calmodulin and calmodulin-like genes in wheat (Triticum aestivum L.)","volume":"17","author":"Liu","year":"2022","journal-title":"Plant Signal. Behav."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1016\/j.plaphy.2018.06.003","article-title":"Identification, characterization, and expression analysis of calmodulin and calmodulin-like genes in grapevine (Vitis vinifera) reveal likely roles in stress responses","volume":"129","author":"Vandelle","year":"2018","journal-title":"Plant Physiol. Biochem."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"600","DOI":"10.1016\/j.plaphy.2019.04.014","article-title":"Genome-wide identification and expression analysis of calmodulin and calmodulin-like genes in apple (Malus \u00d7 domestica)","volume":"139","author":"Li","year":"2019","journal-title":"Plant Physiol. Biochem."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"418","DOI":"10.1007\/s11105-021-01330-6","article-title":"Genome-wide identification and expression analysis of CaM\/CML gene family in sacred lotus (Nelumbo nucifera)","volume":"40","author":"Gao","year":"2022","journal-title":"Plant Mol. Biol. Rep."},{"key":"ref_42","doi-asserted-by":"crossref","unstructured":"Mohanta, T.K., Kumar, P., and Bae, H. (2017). Genomics and evolutionary aspect of calcium signaling event in calmodulin and calmodulin-like proteins in plants. BMC Plant Biol., 17.","DOI":"10.1186\/s12870-017-0989-3"},{"key":"ref_43","doi-asserted-by":"crossref","unstructured":"Arab, M., Najafi Zarrini, H., Nematzadeh, G., Heidari, P., Hashemipetroudi, S.H., and Kuhlmann, M. (2023). Comprehensive analysis of calcium sensor families, CBL and CIPK, in Aeluropus littoralis and their expression profile in response to salinity. Genes, 14.","DOI":"10.20944\/preprints202302.0407.v1"},{"key":"ref_44","doi-asserted-by":"crossref","unstructured":"Yaghobi, M., and Heidari, P. (2023). Genome-wide analysis of aquaporin gene family in Triticum turgidum and its expression profile in response to salt stress. Genes, 14.","DOI":"10.3390\/genes14010202"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"1693","DOI":"10.3390\/cimb45020109","article-title":"Genome-wide identification and expression analysis of calmodulin-like gene family in Paspalums vaginatium revealed their role in response to salt and cold stress","volume":"45","author":"Yang","year":"2023","journal-title":"Curr. Issues Mol. Biol."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s11103-021-01177-1","article-title":"Calmodulin 7: Recent insights into emerging roles in plant development and stress","volume":"107","author":"Basu","year":"2021","journal-title":"Plant Mol. Biol."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"375","DOI":"10.1007\/s11103-018-0703-3","article-title":"The calmodulin-like protein, CML39, is involved in regulating seed development, germination, and fruit development in Arabidopsis","volume":"96","author":"Midhat","year":"2018","journal-title":"Plant Mol. Biol."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"7474","DOI":"10.1038\/s41598-020-64178-y","article-title":"Identification, characterization and expression analysis of calmodulin and calmodulin-like proteins in Solanum pennellii","volume":"10","author":"Shi","year":"2020","journal-title":"Sci. Rep."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1007\/s12374-014-0349-x","article-title":"OsCML4 improves drought tolerance through scavenging of reactive oxygen species in rice","volume":"58","author":"Yin","year":"2015","journal-title":"J. Plant Biol."},{"key":"ref_50","doi-asserted-by":"crossref","unstructured":"Aslam, M.M., Waseem, M., Jakada, B.H., Okal, E.J., Lei, Z., Saqib, H.S.A., Yuan, W., Xu, W., and Zhang, Q. (2022). Mechanisms of abscisic acid-mediated drought stress responses in plants. Int. J. Mol. Sci., 23.","DOI":"10.3390\/ijms23031084"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1071\/FP18106","article-title":"The roles of methyl jasmonate to stress in plants","volume":"46","author":"Yu","year":"2019","journal-title":"Funct. Plant Biol."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1016\/j.plaphy.2021.05.018","article-title":"Overexpression of the white clover TrSAMDC1 gene enhanced salt and drought resistance in Arabidopsis thaliana","volume":"165","author":"Jia","year":"2021","journal-title":"Plant Physiol. Biochem."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"474","DOI":"10.1002\/dvg.22877","article-title":"The Arabidopsis information resource: Making and mining the \u201cgold standard\u201d annotated reference plant genome","volume":"53","author":"Berardini","year":"2015","journal-title":"Genesis"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"D412","DOI":"10.1093\/nar\/gkaa913","article-title":"Pfam: The protein families database in 2021","volume":"49","author":"Mistry","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"W200","DOI":"10.1093\/nar\/gky448","article-title":"HMMER web server: 2018 update","volume":"46","author":"Potter","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"D493","DOI":"10.1093\/nar\/gkx922","article-title":"20 years of the SMART protein domain annotation resource","volume":"46","author":"Letunic","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"D265","DOI":"10.1093\/nar\/gkz991","article-title":"CDD\/SPARCLE: The conserved domain database in 2020","volume":"48","author":"Lu","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"3784","DOI":"10.1093\/nar\/gkg563","article-title":"ExPASy: The proteomics server for in-depth protein knowledge and analysis","volume":"31","author":"Gasteiger","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"W585","DOI":"10.1093\/nar\/gkm259","article-title":"WoLF PSORT: Protein localization predictor","volume":"35","author":"Horton","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"ref_60","first-page":"2.3.1","article-title":"Multiple sequence alignment using ClustalW and ClustalX","volume":"2","author":"Thompson","year":"2003","journal-title":"Curr. Protoc. Bioinform."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"1547","DOI":"10.1093\/molbev\/msy096","article-title":"MEGA X: Molecular evolutionary genetics analysis across computing platforms","volume":"35","author":"Kumar","year":"2018","journal-title":"Mol. Biol. Evol."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"1696","DOI":"10.1093\/bioinformatics\/btr189","article-title":"MEME-ChIP: Motif analysis of large DNA datasets","volume":"27","author":"Machanick","year":"2011","journal-title":"Bioinformatics"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"1733","DOI":"10.1016\/j.molp.2023.09.010","article-title":"TBtools-II: A \u201cone for all, all for one\u201d bioinformatics platform for biological big-data mining","volume":"16","author":"Chen","year":"2023","journal-title":"Mol. Plant"},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"325","DOI":"10.1093\/nar\/30.1.325","article-title":"PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences","volume":"30","author":"Lescot","year":"2002","journal-title":"Nucleic Acids Res."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"389","DOI":"10.1016\/j.ijbiomac.2022.11.076","article-title":"Genome-wide identification and expression analysis of the bHLH gene family in passion fruit (Passiflora edulis) and its response to abiotic stress","volume":"225","author":"Liang","year":"2023","journal-title":"Int. J. Biol. Macromol."},{"key":"ref_66","doi-asserted-by":"crossref","unstructured":"Song, M., Wang, L., Zhang, Y., Wang, Q., Han, X., Yang, Q., Zhang, J., and Tong, Z. (2023). Temporospatial pattern of flavonoid metabolites and potential regulatory pathway of PbMYB211-coordinated kaempferol-3-O-rhamnoside biosynthesis in Phoebe bournei. Plant Physiol. Biochem., 202.","DOI":"10.1016\/j.plaphy.2023.107913"},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"e85","DOI":"10.1002\/imt2.85","article-title":"OmicStudio: A composable bioinformatics cloud platform with real-time feedback that can generate high-quality graphs for publication","volume":"2","author":"Lyu","year":"2023","journal-title":"iMeta"}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/25\/1\/545\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T21:45:00Z","timestamp":1760132700000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/25\/1\/545"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,12,30]]},"references-count":67,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2024,1]]}},"alternative-id":["ijms25010545"],"URL":"https:\/\/doi.org\/10.3390\/ijms25010545","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,12,30]]}}}