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

Functions of Phytochrome Interacting Factors (PIFs) in Adapting Plants to Biotic and Abiotic Stresses

Plants possess the remarkable ability to sense detrimental environmental stimuli and launch sophisticated signal cascades that culminate in tailored responses to facilitate their survival, and transcription factors (TFs) are closely involved in these processes. Phytochrome interacting factors (PIFs) are among these TFs and belong to the basic helix-loop-helix family. PIFs are initially identified and have now been well established as core regulators of phytochrome-associated pathways in response to the light signal in plants. However, a growing body of evidence has unraveled that PIFs also play a crucial role in adapting plants to various biological and environmental pressures. In this review, we summarize and highlight that PIFs function as a signal hub that integrates multiple environmental cues, including abiotic (i.e., drought, temperature, and salinity) and biotic stresses to optimize plant growth and development. PIFs not only function as transcription factors to reprogram the expression of related genes, but also interact with various factors to adapt plants to harsh environments. This review will contribute to understanding the multifaceted functions of PIFs in response to different stress conditions, which will shed light on efforts to further dissect the novel functions of PIFs, especially in adaption to detrimental environments for a better survival of plants.

Red And far-red regulation of filament movement correlates with the expression of phytochrome and FHY1 genes in Spirogyra varians (Zygnematales, Streptophyta)1

Spirogyra filaments show unique photomovement that differs in response to blue, red, and far-red light. Phototropins involved in the blue-light movement have been characterized together with downstream signaling components, but the photoreceptors and mechanical effectors of red- and far-red light movement are not yet characterized. The filaments of Spirogyra varians slowly bent and aggregated to form a tangled mass in red light. In far-red light, the filaments unbent, stretched rapidly, and separated from each other. Mannitol and/or sorbitol treatment significantly inhibited this far-red light movement suggesting that turgor pressure is the driving force of this movement. The bending and aggregating movements of filaments in red light were not affected by osmotic change. Three phytochrome homologues isolated from S. varians showed unique phylogenetic characteristics. Two canonical phytochromes, named SvPHY1 and SvPHY2, and a noncanonical phytochrome named SvPHYX2. SvPHY1 is the first PHY1 family phytochrome reported in zygnematalean algae. The gene involved in the transport of phytochromes into the nucleus was characterized, and its expression in response to red and far-red light was measured using quantitative PCR. Our results suggest that the phytochromes and the genes involved in the transport system into the nucleus are well conserved in S. varians.

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

Ipomoea nil is widely used as an ornamental plant due to its abundance of flower color, but the limited transcriptome and genomic data hinder research on it. Using illumina platform, transcriptome profiling of I. nil was performed through high-throughput sequencing, which was proven to be a rapid and cost-effective means to characterize gene content. Our goal is to use the resulting information to facilitate the relevant research on flowering and flower color formation in I. nil. In total, 268 million unique illumina RNA-Seq reads were produced and used in the transcriptome assembly. These reads were assembled into 220,117 contigs, of which 137,307 contigs were annotated using the GO and KEGG database. Based on the result of functional annotations, a total of 89,781 contigs were assigned 455,335 GO term annotations. Meanwhile, 17,418 contigs were identified with pathway annotation and they were functionally assigned to 144 KEGG pathways. Our transcriptome revealed at least 55 contigs as probably flowering-related genes in I. nil, and we also identified 25 contigs that encode key enzymes in the phenylpropanoid biosynthesis pathway. Based on the analysis relating to gene expression profiles, in the phenylpropanoid biosynthesis pathway of I. nil, the repression of lignin biosynthesis might lead to the redirection of the metabolic flux into anthocyanin biosynthesis. This may be the most likely reason that I. nil has high anthocyanins content, especially in its flowers. Additionally, 15,537 simple sequence repeats (SSRs) were detected using the MISA software, and these SSRs will undoubtedly benefit future breeding work. Moreover, the information uncovered in this study will also serve as a valuable resource for understanding the flowering and flower color formation mechanisms in I. nil.

Open and closed inflorescences: more than simple opposites

The absence of a terminal flower in inflorescences ('open inflorescences') is currently explained by the maintenance of putative stem-cells in the central zone (CZ) of the inflorescence meristem (IM) governed by the CLAVATA-WUSCHEL regulatory loop. Disruption of this regulatory pathway, as in Arabidopsis TERMINAL FLOWER LOCUS 1 mutants, leads to terminal flower production. However, recent studies in other taxa reveal novel mechanisms of inflorescence termination; for example, the SEPALLATA-like MADS-box floral identity gene GERBERA REGULATOR OF CAPITULUM DEVELOPMENT 2 in Gerbera excludes the retention of a CZ as an ontogenetic cause for the openness of these inflorescences. Moreover, comparative histological studies show that the retention of a CZ in the IM, mostly a feature of the 'typical open families', is absent in open inflorescences of other families. Concerning these groups, new evidence suggests that spatial constraints at the IM could play a role at the time when terminal flower production (or not) is determined. This indicates that the multiple loss and re-gain of the terminal flower in angiosperms is necessarily based on more than one ontogenetic pathway.