[1]

Schlüter PM, Arenas MAS, Harris SA. 2007. Genetic variation in Vanilla planifolia (Orchidaceae). Economic Botany 61:328−36

doi: 10.1663/0013-0001(2007)61[328:GVIVPO]2.0.CO;2
[2]

Hu Y, Resende MF, Jr, Bombarely A, Brym M, Bassil E, et al. 2019. Genomics-based diversity analysis of vanilla species using a Vanilla planifolia draft genome and genotyping-by-sequencing. Scientific Reports 9:3416

doi: 10.1038/s41598-019-40144-1
[3]

Jean Gabriel F, Laurent J. 1999. Vanilla planifolia: History, botany and culture in reunion island. Agronomie 19:689−703

doi: 10.1051/agro:19990804
[4]

Lubinsky P, Bory S, Hernández Hernández J, Kim SC, Gómez-Pompa A. 2008. Origins and dispersal of cultivated vanilla (Vanilla planifolia Jacks. [Orchidaceae])1. Economic Botany 62:127−38

doi: 10.1007/s12231-008-9014-y
[5]

Bythrow JD. 2005. Vanilla as a medicinal plant. Seminars in Integrative Medicine 3:129−31

doi: 10.1016/j.sigm.2006.03.001
[6]

Childers NF, Cibes HR, Hernandez-Medina E. 1959. Vanilla-the orchid of commerce. In The Orchids. A Scientific Survey, ed. Withner CL. New York: The Ronald Press Company. pp. 477–508
[7]

Masiero S, Colombo L, Grini PE, Schnittger A, Kater MM. 2011. The emerging importance of type I MADS-box transcription factors for plant reproduction. The Plant Cell 23:865−72

doi: 10.1105/tpc.110.081737
[8]

Riechmann JL, Meyerowitz EM. 1997. MADS domain proteins in plant development. Biological Chemistry 378:1079−101
[9]

Kaufmann K, Melzer R, Theißen G. 2005. MIKC-type MADS-domain proteins: structural modularity, protein interactions and network evolution in land plants. Gene 347:183−98

doi: 10.1016/j.gene.2004.12.014
[10]

Theißen G, Kim JT, Saedler H. 1996. Classification and phylogeny of the MADS-box multigene family suggest defined roles of MADS-box gene subfamilies in the morphological evolution of eukaryotes. Journal of Molecular Evolution 43:484−516

doi: 10.1007/BF02337521
[11]

Alvarez-Buylla ER, Liljegren SJ, Pelaz S, Gold SE, Burgeff C, et al. 2000. MADS-box gene evolution beyond flowers: expression in pollen, endosperm, guard cells, roots and trichomes. The Plant Journal 24:457−66

doi: 10.1111/j.1365-313X.2000.00891.x
[12]

De Bodt S, Raes J, Van de Peer Y, Theißen G. 2003. And then there were many: MADS goes genomic. Trends in Plant Science 8:475−83

doi: 10.1016/j.tplants.2003.09.006
[13]

Sun W, Wan H, Huang W, Yousaf Z, Huang H, et al. 2023. Characterization of B-and C-class MADS-box genes in medicinal plant Epimedium sagittatum. Medicinal Plant Biology 2:1

doi: 10.48130/mpb-2023-0001
[14]

Coen ES, Meyerowitz EM. 1991. The war of the whorls: genetic interactions controlling flower development. Nature 353:31−37

doi: 10.1038/353031a0
[15]

Pelaz S, Ditta GS, Baumann E, Wisman E, Yanofsky MF. 2000. B and C floral organ identity functions require SEPALLATA MADS-box genes. Nature 405:200−3

doi: 10.1038/35012103
[16]

Ditta G, Pinyopich A, Robles P, Pelaz S, Yanofsky MF. 2004. The SEP4 gene of Arabidopsis thaliana functions in floral organ and meristem identity. Current Biology 14:1935−40

doi: 10.1016/j.cub.2004.10.028
[17]

Theißen G. 2001. Development of floral organ identity: stories from the mads house. Current Opinion in Plant Biology 4:75−85

doi: 10.1016/S1369-5266(00)00139-4
[18]

Theißen G, Saedler H. 2001. Floral quartets. Nature 409:469−71

doi: 10.1038/35054172
[19]

Alhindi T, Al-Abdallat AM. 2021. Genome-wide identification and analysis of the MADS-box gene family in American beautyberry (Callicarpa americana). Plants 10:1805

doi: 10.3390/plants1009180
[20]

Chen M, Nie G, Yang L, Zhang Y, Cai Y. 2021. Homeotic transformation from stamen to petal in lilium is associated with MADS-box genes and hormone signal transduction. Plant Growth Regulation 95:49−64

doi: 10.1007/s10725-021-00724-6
[21]

Krizek BA, Fletcher JC. 2005. Molecular mechanisms of flower development: an armchair guide. Nature Reviews Genetics 6:688−98

doi: 10.1038/nrg1675
[22]

Teo ZWN, Zhou W, Shen L. 2019. Dissecting the function of MADS-box transcription factors in orchid reproductive development. Frontiers in Plant Science 10:1474

doi: 10.3389/fpls.2019.01474
[23]

Li Y, Zhang B, Yu H. 2022. Molecular genetic insights into orchid reproductive development. Journal of Experimental Botany 73:1841−52

doi: 10.1093/jxb/erac016
[24]

Kim S, Koh J, Yoo MJ, Kong H, Hu Y, et al. 2005. Expression of floral MADS-box genes in basal angiosperms: implications for the evolution of floral regulators. The Plant Journal 43:724−44

doi: 10.1111/j.1365-313X.2005.02487.x
[25]

Ambrose BA, Lerner DR, Ciceri P, Padilla CM, Yanofsky MF, et al. 2000. Molecular and genetic analyses of the Silky1 gene reveal conservation in floral organ specification between eudicots and monocots. Molecular Cell 5:569−79

doi: 10.1016/S1097-2765(00)80450-5
[26]

Jin J, Tian F, Yang DC, Meng YQ, Kong L, et al. 2017. PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants. Nucleic Acids Research 45:D1040−D1045

doi: 10.1093/nar/gkw982
[27]

Chen S, Zhou Y, Chen Y, Gu J. 2018. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34:i884−i890

doi: 10.1093/bioinformatics/bty560
[28]

Pertea M, Kim D, Pertea GM, Leek JT, Salzberg SL. 2016. Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nature Protocols 11:1650−67

doi: 10.1038/nprot.2016.095
[29]

Li B, Dewey CN. 2011. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12:323

doi: 10.1186/1471-2105-12-323
[30]

Ghahramani Z. 2001. An introduction to hidden Markov models and Bayesian networks. International Journal of Pattern Recognition and Artificial Intelligence 15:9−42

doi: 10.1142/S0218001401000836
[31]

Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, et al. 2009. BLAST+: architecture and applications. BMC Bioinformatics 10:421

doi: 10.1186/1471-2105-10-421
[32]

El-Gebali S, Mistry J, Bateman A, Eddy SR, Luciani A, et al. 2019. The pfam protein families database in 2019. Nucleic Acids Research 47:D427−D432

doi: 10.1093/nar/gky995
[33]

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

doi: 10.1093/nar/gkx922
[34]

Gasteiger E, Gattiker A, Hoogland C, Ivanyi I, Appel RD, et al. 2003. ExPASy: the proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Research 31:3784−88

doi: 10.1093/nar/gkg563
[35]

Hu B, Jin J, Guo AY, Zhang H, Luo J, et al. 2015. GSDS 2.0: an upgraded gene feature visualization server. Bioinformatics 31:1296−97

doi: 10.1093/bioinformatics/btu817
[36]

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
[37]

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

doi: 10.1093/nar/gkh340
[38]

Tamura K, Stecher G, Kumar S. 2021. MEGA11: molecular evolutionary genetics analysis version 11. Molecular Biology and Evolution 38:3022−27

doi: 10.1093/molbev/msab120
[39]

Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. 2015. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Molecular Biology and Evolution 32:268−74

doi: 10.1093/molbev/msu300
[40]

Lee TH, Tang H, Wang X, Paterson AH. 2013. PGDD: a database of gene and genome duplication in plants. Nucleic Acids Research 41:D1152−D1158

doi: 10.1093/nar/gks1104
[41]

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
[42]

Zuker M. 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Research 31:3406−15

doi: 10.1093/nar/gkg595
[43]

Zhang Z. 2022. KaKs_Calculator 3.0: calculating selective pressure on coding and non-coding sequences. Genomics, Proteomics & Bioinformatics 20:536−40

doi: 10.1016/j.gpb.2021.12.002
[44]

Langfelder P, Horvath S. 2008. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics 9:559

doi: 10.1186/1471-2105-9-559
[45]

Huang DW, Sherman BT, Lempicki RA. 2009. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature Protocols 4:44−57

doi: 10.1038/nprot.2008.211
[46]

Arditti J. 1980. Aspects of the physiology of orchids. Advances in Botanical Research. 7:421−655

doi: 10.1016/S0065-2296(08)60091-9
[47]

Jersáková J, Johnson SD, Kindlmann P. 2006. Mechanisms and evolution of deceptive pollination in orchids. Biological Reviews of the Cambridge Philosophical Society 81:219−35

doi: 10.1017/S1464793105006986
[48]

Aceto S, Gaudio L. 2011. The MADS and the beauty: genes involved in the development of orchid flowers. Current Genomics 12:342−56

doi: 10.2174/138920211796429754
[49]

Tsai WC, Chen HH. 2006. The orchid MADS-box genes controlling floral morphogenesis. The Scientific World Journal 6:1933−44

doi: 10.1100/tsw.2006.321
[50]

Brazel AJ, Fattorini R, McCarthy J, Franzen R, Rümpler F, et al. 2023. AGAMOUS mediates timing of guard cell formation during gynoecium development. PLoS Genetics 19:e1011000

doi: 10.1371/journal.pgen.1011000
[51]

Saedler H, Becker A, Winter KU, Kirchner C, Theissen G. 2001. MADS-box genes are involved in floral development and evolution. Acta Biochimica Polonica 48:351−58

doi: 10.18388/abp.2001_3920
[52]

Shen G, Yang CH, Shen CY, Huang KS. 2019. Origination and selection of ABCDE and AGL6 subfamily MADS-box genes in gymnosperms and angiosperms. Biological Research 52:25

doi: 10.1186/s40659-019-0233-8