The genome and transcriptome of the Phalaenopsis yield insights into floral organ development and flowering regulation

Abstract

Phalaenopsis orchid is an important potted flower with 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 the key role of PhAGL6b in the regulation of flower organ development involves alternative splicing. We also show gibberellin pathways that regulate the expression of genes control flowering time during the stage in reproductive phase change induced by cool temperature. Our work should contribute a valuable resource for the flowering control, flower architecture development, and breeding of the Phalaenopsis orchids.

Plastid phylogenomics resolves ambiguous relationships within the orchid family and provides a solid timeframe for biogeography and macroevolution

“…Numerous efforts have been made to understand the natural history, evolution and phylogenetic relationships within the family 2,7,9–13 . To date, there are seven nuclear genome sequences available, i.e., Apostasia shenzhenica 14 , Dendrobium catenatum 15 , D. officinale 16 , Gastrodia elata 17 , Phalaenopsis equestris 18 , a Phalaenopsis hybrid cultivar 19 , P. aphrodite 20 , Vanilla planifolia 21 , 221 complete plastid genomes and 2,678 sequence read archives for Orchidaceae in NCBI (accessed 22 August 2020).…”