Agarwal G, Clevenger J, Pandey MK, Wang H, Shasidhar Y, Chu Y, Fountain JC, Choudhary D, Culbreath AK, Liu X, Huang G (2018) High-density genetic map using whole-genome resequencing for fine mapping and candidate gene discovery for disease resistance in peanut. Plant Biotechnol J 16(11):1954–1967

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ai Y, Li Z, Sun WH, Chen J, Zhang D, Ma L, Zhang QH, Chen MK, Zheng QD, Liu JF, Jiang YT (2021) The Cymbidium genome reveals the evolution of unique morphological traits. Hortic Res 8(1):255

Baek S, Choi K, Kim GB, Yu HJ, Cho A, Jang H, Kim C, Kim HJ, Chang KS, Kim JH, Mun JH (2018) Draft genome sequence of wild Prunus yedoensis reveals massive inter-specific hybridization between sympatric flowering cherries. Genome Biol 19:1–17

Article  Google Scholar 

Bao F, Du D, An Y, Yang W, Wang J, Cheng T, Zhang Q (2017) Overexpression of Prunus mume dehydrin genes in tobacco enhances tolerance to cold and drought. Front Plant Sci 8:151

Article  PubMed  PubMed Central  Google Scholar 

Bolser DM, Kerhornou A, Walts B, Kersey P (2015) Triticeae resources in ensembl plants. Plant Cell Physiol 56(1):e3–e3

Article  PubMed  Google Scholar 

Cai J, Liu X, Vanneste K, Proost S, Tsai WC, Liu KW, Chen LJ, He Y, Xu Q, Bian C, Zheng Z (2015) The genome sequence of the orchid Phalaenopsis equestris. Nat Genet 47(1):65–72

Article  CAS  PubMed  Google Scholar 

Chan WS, Abdullah JO, Namasivayam P (2011) Isolation, cloning and characterization of fragrance-related transcripts from Vanda Mimi Palmer. Sci Hortic 127(3):388–397

Article  CAS  Google Scholar 

Chao YT, Chen WC, Chen CY, Ho HY, Yeh CH, Kuo YT, Su CL, Yen SH, Hsueh HY, Yeh JH, Hsu HL (2018) Chromosome-level assembly, genetic and physical mapping of Phalaenopsis aphrodite genome provides new insights into species adaptation and resources for orchid breeding. Plant Biotechnol J 16(12):2027–2041

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chao YU, Wan HH, Bourke PM, Cheng BX, Le LUO, Pan HT, Zhang QX (2021) High density genetic map and quantitative trait loci (QTLs) associated with petal number and flower diameter identified in tetraploid rose. J Integr Agric 20(5):1287–1301

Article  Google Scholar 

Chen F, Song Y, Li X, Chen J, Mo L, Zhang X, Lin Z, Zhang L (2019) Genome sequences of horticultural plants: past, present, and future. Hortic Res 6:112

Chen F, Su L, Hu S, Xue JY, Liu H, Liu G, Jiang Y, Du J, Qiao Y, Fan Y, Liu H (2021) A chromosome-level genome assembly of rugged rose (Rosa rugosa) provides insights into its evolution, ecology, and floral characteristics. Hortic Res 8:141

Chen H, Zeng X, Yang J, Cai X, Shi Y, Zheng R, Wang Z, Liu J, Yi X, Xiao S, Fu Q (2021) Whole-genome resequencing of Osmanthus fragrans provides insights into flower color evolution. Hortic Res 8(1):98

Cheng S, van den Bergh E, Zeng P, Zhong X, Xu J, Liu X, Hofberger J, de Bruijn S, Bhide AS, Kuelahoglu C, Bian C (2013) The Tarenaya hassleriana genome provides insight into reproductive trait and genome evolution of crucifers. Plant Cell 25(8):2813–2830

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cheng B, Wan H, Han Y, Yu C, Luo L, Pan H, Zhang Q (2021) Identification and QTL analysis of flavonoids and carotenoids in tetraploid roses based on an ultra-high-density genetic map. Front Plant Sci 12:682305

Article  PubMed  PubMed Central  Google Scholar 

Chuang YC, Hung YC, Tsai WC, Chen WH, Chen HH (2018) PbbHLH4 regulates floral monoterpene biosynthesis in Phalaenopsis orchids. J Exp Bot 69(18):4363–4377

Article  CAS  PubMed  PubMed Central  Google Scholar 

Darwish O, Slovin JP, Kang C, Hollender CA, Geretz A, Houston S, Liu Z, Alkharouf NW (2013) SGR: an online genomic resource for the woodland strawberry. BMC Plant Biol 13:1–8

Article  Google Scholar 

Deshmukh R, Sonah H, Patil G, Chen W, Prince S, Mutava R, Vuong T, Valliyodan B, Nguyen HT (2014) Integrating omic approaches for abiotic stress tolerance in soybean. Front Plant Sci 5:244

Article  PubMed  PubMed Central  Google Scholar 

Deshmukh RK, Sonah H, Bélanger RR (2016) Plant Aquaporins: genome-wide identification, transcriptomics, proteomics, and advanced analytical tools. Front Plant Sci 7:1896

Article  PubMed  PubMed Central  Google Scholar 

Dhandapani S, Jin J, Sridhar V, Chua NH, Jang IC (2019) CYP79D73 participates in biosynthesis of floral scent compound 2-phenylethanol in Plumeria rubra. Plant Physiol 180(1):171–184

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ding SX, Li JC, Hu K, Huang ZJ, Lu RS (2022) Morphological characteristics and comparative chloroplast genome analyses between red and white flower phenotypes of Pyracantha fortuneana (Maxim.) Li (Rosaceae), with implications for taxonomy and phylogeny. Genes 13(12):2404

Article  CAS  PubMed  PubMed Central  Google Scholar 

Du H, Wu J, Ji KX, Zeng QY, Bhuiya MW, Su S, Shu QY, Ren HX, Liu ZA, Wang LS (2015) Methylation mediated by an anthocyanin, O-methyltransferase, is involved in purple flower coloration in Paeonia. J Exp Bot 66(21):6563–6577

Article  CAS  PubMed  PubMed Central  Google Scholar 

Duvick J, Fu A, Muppirala U, Sabharwal M, Wilkerson MD, Lawrence CJ, Lushbough C, Brendel V (2007) PlantGDB: a resource for comparative plant genomics. Nucleic Acids Research 36(suppl_1):D959–D965

Article  PubMed  PubMed Central  Google Scholar 

Fornara F, de Montaigu A, Coupland G (2010) SnapShot: control of flowering in Arabidopsis. Cell 141(3):550–550

Article  PubMed  Google Scholar 

Friedhoff R, Wolff K, Pucker B (2024) Genome sequence of the ornamental plant Aquilegia vulgaris reveals the flavonoid biosynthesis gene repertoire. bioRxiv 2024.12.16.628782. https://doi.org/10.1101/2024.12.16.628782

Fu Y, Jiang S, Zou M, Xiao J, Yang L, Luo C, Rao P, Wang W, Ou Z, Liu F, Xia Z (2022) High-quality reference genome sequences of two Cannaceae species provide insights into the evolution of Cannaceae. Front Plant Sci 13:955904

Article  PubMed  PubMed Central  Google Scholar 

Gattolin S, Cirilli M, Chessa S, Stella A, Bassi D, Rossini L (2020) Mutations in orthologous PETALOSA TOE-type genes cause a dominant double-flower phenotype in phylogenetically distant eudicots. J Exp Bot 71(9):2585–2595

Article  CAS  PubMed  PubMed Central  Google Scholar 

Go S, Koo H, Jung M, Hong S, Yi G, Kim YM (2024) Pan-chloroplast genomes for accession-specific marker development in Hibiscus syriacus. Scientific Data 11(1):246

Article  CAS  PubMed  PubMed Central  Google Scholar 

Goodstein DM, Shu S, Howson R, Neupane R, Hayes RD, Fazo J, Mitros T, Dirks W, Hellsten U, Putnam N, Rokhsar DS (2012) Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res 40(D1):D1178–D1186

Article  CAS  PubMed  Google Scholar 

Gu Z, Men S, Zhu J, Hao Q, Tong N, Liu ZA, Zhang H, Shu Q, Wang L (2019) Chalcone synthase is ubiquitinated and degraded via interactions with a RING-H2 protein in petals of Paeonia ‘He Xie.’ J Exp Bot 70(18):4749–4762

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gupta P, Naithani S, Tello-Ruiz MK, Chougule K, D’Eustachio P, Fabregat A, Jiao Y, Keays M, Lee YK, Kumari S, Mulvaney J (2016) Gramene database: navigating plant comparative genomics resources. Current Plant Biology 7:10–15

Article  PubMed  Google Scholar 

Gurung B, Li J, Fang D, Lin Q, Guo X, Chen G (2025) Chromosome-level genome assembly of the threatened ornamental plant Hibiscus yunnanensis. Sci Data 12:503. https://doi.org/10.1038/s41597-025-04842-y

Article  CAS  PubMed  PubMed Central  Google Scholar 

He X, Wang C, Wang H, Li L, Wang C (2020) The function of MAPK cascades in response to various stresses in horticultural plants. Front Plant Sci 11:952

Article  PubMed  PubMed Central  Google Scholar 

Hibrand Saint-Oyant L, Ruttink T, Hamama L, Kirov I, Lakhwani D, Zhou NN, Bourke PM, Daccord N, Leus L, Schulz D, Van de Geest H (2018) A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits. Nature Plants 4(7):473–484

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hieno A, Naznin HA, Hyakumachi M, Sakurai T, Tokizawa M, Koyama H, Sato N, Nishiyama T, Hasebe M, Zimmer AD, Lang D (2014) ppdb: plant promoter database version 3.0. Nucleic acids research 42(D1):D1188–D1192

Article