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.

Early alterations of circulating immune cell counts in severe trauma patients are related to later occurrence of nosocomial infection, sepsis and mortality

“…In addition, multivariate analysis showed that ALC (D3) and ALC (D3/D1) were independent risk factors for nosocomial infection, sepsis and mortality, and ALC (D7) was also an independent risk factor for mortality. These results are similar to previous findings in critically ill patients such as trauma and sepsis, the extent and delayed recovery of lymphopenia have been widely reported to be related to nosocomial infection, sepsis and death [28,30,[32][33][34][35]. Taking together, the importance of immediate recovery of ALC for prognosis is obvious.…”

Recent Advances in Phalaenopsis Orchid Improvement using Omics Approaches

“…Transcriptome sequencing using Illumina platform from floral organ tissues (sepal, petal, labellum and gynostemium) of the Phalaenopsis wild-type and peloric mutant has revealed the critical regulators of the MADS-box TFs in Phalaenopsis labellum formation, and also identified five MADS genes, PhAGL6a (CUFF.17763), PhAGL6b (CUFF.17763.1), PhMADS1 (CUFF.36625.1), PhMADS4 (CUFF.25909) and PhMADS5 (CUFF.39479.1) genes with differential expression in floral-organ development in Phalaenopsis. An increased PhMADS4, PhAGL6a and PhAGL6b transcript levels observed in lip-like petals and liplike sepals of peloric mutant flowers whereas PhMADS1 transcript was expressed strongly in the gynostemium of both wild types and peloric mutants and the PhMADS5 transcript level showed a positive regulator of petal and sepal development (Huang et al 2015) and identified the four isoforms of PhAGL6b on the C-terminus region with the MADS-box genes as potential regulatory components of labellum organ development which involved alternative splicing in the big lip mutant (Huang et al 2016). They showed the expression of flowering time genes control by the gibberellin synthesis pathway.…”

“…The genome sequence of Phalaenopsis equestris (Cai et al 2015) suggest that, gene duplication might have contributed to the CAM photosynthesis process in P. equestris and found MADS-box C/D-class, B-class AP3 and AGL6-class genes, play role in morphology of orchid flowers. A draft genome for Phalaenopsis pulcherrima 'B8802' and Phalaenopsis 'KHM190' cultivars have been generated by Huang et al (2016). The differences between two orchids allowed the identification of 691,532 single-nucleotide polymorphisms.…”

“…A sum of 23 novel miRNAs expressed in the flower, their targets was predicted by miRBase in P. aphrodite (Chao et al 2014). Huang et al (2016) reported draft sequence and assembly of the genome of Phalaenopsis 'KHM190' cultivar generated 89.5 Gb RNA-seq and 113 million sRNA-seq reads for identifying 188 miRNA families.…”

How different is similar – exploring development of Ceropegia sandersonii pitfall flowers to elucidate convergent evolution of floral synorganization

“…In Aristolochia, genes involved in oral development and organ identity are continuously better understood (25)(26)(27), and in orchids, deceptive species such as Phalaenopsis equestris and Erycina pusilla are well studied with regard to the genetic background of oral development (28)(29)(30)(31)(32)(33)(34). Here we present the rst data on MADS-box gene expression during development of radially symmetric pitfall owers of Ceropegia sandersonii, the parachute plant; it is the rst oral transcriptome analyses for Ceropegia in general.…”