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Phalaenopsis  has a zygomorphic floral structure, including three outer tepals, two lateral inner tepals and a highly modified inner median tepal called labellum or lip; however, the regulation of its organ development remains unelucidated. We generated RNA-seq reads with the Illumina platform for floral organs of the  Phalaenopsis  wild-type and peloric mutant with a lip-like petal. A total of 43,552 contigs were obtained after  de novo  assembly. We used differentially expressed gene profiling to compare the transcriptional changes in floral organs for both the wild-type and peloric mutant. Pair-wise comparison of sepals, petals and labellum between peloric mutant and its wild-type revealed 1,838, 758 and 1,147 contigs, respectively, with significant differential expression.  PhAGL6a  (CUFF.17763),  PhAGL6b  (CUFF.17763.1),  PhMADS1  (CUFF.36625.1),  PhMADS4  (CUFF.25909) and  PhMADS5  (CUFF.39479.1) were significantly upregulated in the lip-like petal of the peloric mutant. We used real-time PCR analysis of lip-like petals, lip-like sepals and the big lip of peloric mutants to confirm the five genes’ expression patterns.  PhAGL6a ,  PhAGL6b  and  PhMADS4  were strongly expressed in the labellum and significantly upregulated in lip-like petals and lip-like sepals of peloric-mutant flowers. In addition,  PhAGL6b  was significantly downregulated in the labellum of the big lip mutant, with no change in expression of  PhAGL6a . We provide a comprehensive transcript profile and functional analysis of  Phalaenopsis  floral organs.  PhAGL6a PhAGL6b , and  PhMADS4  might play crucial roles in the development of the labellum in  Phalaenopsis . Our study provides new insights into how the orchid labellum differs and why the petal or sepal converts to a labellum in  Phalaenopsis  floral mutants.

A De Novo Floral Transcriptome Reveals Clues into Phalaenopsis Orchid Flower Development