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

Jian-Zhi Huang; Chih-Peng Lin; Ting-Chi Cheng; Ya-Wen Huang; Yi-Jung Tsai; Shu-Yun Cheng; Yi-Wen Chen; Chueh-Pai Lee; Wan-Chia Chung; Bill Chia-Han Chang; Shih-Wen Chin; Chen-Yu Lee; Fure-Chyi Chen

doi:10.7717/peerj.2017

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

PeerJ. 2016 May 12:4:e2017. doi: 10.7717/peerj.2017. eCollection 2016.

Authors

Affiliations

¹ Department of Plant Industry, National Pingtung University of Science and Technology, Pingtung, Taiwan.
² Yourgene Bioscience, Shu-Lin District, New Taipei City, Taiwan.
³ Department of Biotechnology, School of Health Technology, Ming Chuan University, Gui Shan District, Taoyuan, Taiwan.
⁴ Faculty of Veterinary Science, The University of Melbourne, Parkville, Victoria, Australia.

^# Contributed equally.

Abstract

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.

Keywords: Draft genome; Flower organ development; Flowering time; PhAGL6b; Phalaenopsis.

Grants and funding

This work was supported by grants from the Agriculture and Food Agency, Council of Agriculture, Taiwan (grant numbers 102AS-9.1.1-FD-Z2(1), 103AS-9.1.1-FD-Z2(1), and 104AS-9.1.1-FD-Z2(1)). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.