Phytochrome gene expression and phylogenetic analysis in the short‐day plant Pharbitis nil (Convolvulaceae): Differential regulation by light and an endogenous clock

Abstract

To investigate the role of distinct phytochrome pools in photoperiodic timekeeping, we characterized four phytochrome genes in the short-day plant Pharbitis nil. Each PHY gene had different photosensory properties and sensitivity to night break that inhibits flowering. During extended dark periods, PHYE, PHYB, and PHYC mRNA accumulation exhibited a circadian rhythmicity indicative of control by an endogenous clock. Phylogenetic analysis recovered four clades of angiosperm phytochrome genes, phyA, phyB, phyC, and phyE. All except the phyE clade included sequences from both monocots and eudicots. In addition, phyA is sister to phyC and phyE sister to phyB, with gymnosperm sequences sister to either the phyA-phyC clade or to the phyB-phyE clade. These results suggest that a single duplication occurred in an ancestral seed plant before the divergence of extant gymnosperms from angiosperms and that two subsequent duplications occurred in an ancestral angiosperm before the divergence of monocots from eudicots. Thus in P. nil, a multigene family with different patterns of mRNA abundance in light and darkness contributes to the total phytochrome pool: one pool is light labile (phyA), whereas the other is light stable (phyB and phyE). In addition, PHYC mRNA represents a third phytochrome pool with intermediate photosensory properties.

Rhythms in Plants

“…However, other plants are also studied, such as rice Oryza sativa, mays Zea mays, morning glory Ipomoea nil (see page 208), and soybean Glycine max (Wong et al 2013). The results of these studies illuminate the similarities and differences between and among long-and short-day plants (Shrestha et al 2014;Zheng et al 2009;Hayama and Coupland 2004). Photoperiodic induction of flowering in annual and perennial plants is discussed by Khan et al (2014).…”

Photoperiodism: The Calendar of Plants

“…However, other plants are also studied, such as rice Oryza sativa, mays Zea mays, morning glory Ipomoea nil (see page 208), and soybean Glycine max (Wong et al 2013). The results of these studies illuminate the similarities and differences between and among long-and short-day plants (Shrestha et al 2014;Zheng et al 2009;Hayama and Coupland 2004). Photoperiodic induction of flowering in annual and perennial plants is discussed by Khan et al (2014).…”

“…Zheng et al (2009) investigated the role of distinct phytochromes in photoperiodic timekeeping in Ipomoea. The phytochrome pool consists of light labile phyA and light stable phyB and phyE.…”

De novo transcriptome assembly of Ipomoea nil using Illumina sequencing for gene discovery and SSR marker identification

“…In 2007, two orthologs of FLOWERING LOCUS T (FT), PnFT1 and PnFT2, were found in I. nil, and their expression correlating with PnCOs under darkness was analyzed as well (Hayama et al 2007). Furthermore, some other genes involved in photoperiodic flowering have been identified, such as PnGI (Higuchi et al 2011), PnPHY (Zheng et al 2009), PnMADS1 (Kikuchi et al 2008), and PnLFY, PnAG, PnCRC (Parfitt et al 2004). However, an understanding of how I. nil responds to daylength at molecular level is still limited, and the relevant floral transition pathways in I. nil have not been fully documented.…”