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The  Phalaenopsis  orchid is an important potted flower of high economic value around the world. We report the 3.1 Gb draft genome assembly of an important winter flowering  Phalaenopsis  ‘KHM190’ cultivar. We generated 89.5 Gb RNA-seq and 113 million sRNA-seq reads to use these data to identify 41,153 protein-coding genes and 188 miRNA families. We also generated a draft genome for  Phalaenopsis pulcherrima  ‘B8802,’ a summer flowering species, via resequencing. Comparison of genome data between the two  Phalaenopsis  cultivars allowed the identification of 691,532 single-nucleotide polymorphisms. In this study, we reveal that the key role of  PhAGL6b  in the regulation of labellum organ development involves alternative splicing in the big lip mutant. Petal or sepal overexpressing  PhAGL6b  leads to the conversion into a lip-like structure. We also discovered that the gibberellin pathway that regulates the expression of flowering time genes during the reproductive phase change is induced by cool temperature. Our work thus depicted a valuable resource for the flowering control, flower architecture development, and breeding of the  Phalaenopsis  orchids.

The genome and transcriptome ofPhalaenopsisyield insights into floral organ development and flowering regulation