Paralogous SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) genes differentially regulate leaf initiation and reproductive phase change in petunia

Duplicated petunia clade-VISPLgenes differentially promote the timing of inflorescence and flower development, and leaf initiation rate. The timing of plant reproduction relative to favorable environmental conditions is a critical component of plant fitness, and is often associated with variation in plant architecture and habit. Recent studies have shown that overexpression of the microRNA miR156 in distantly related annual species results in plants with perennial characteristics, including late flowering, weak apical dominance, and abundant leaf production. These phenotypes are largely mediated through the negative regulation of a subset of genes belonging to the SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) family of transcription factors. In order to determine how and to what extent paralogous SPL genes have partitioned their roles in plant growth and development, we functionally characterized petunia clade-VI SPL genes under different environmental conditions. Our results demonstrate that PhSBP1and PhSBP2 differentially promote discrete stages of the reproductive transition, and that PhSBP1, and possibly PhCNR, accelerates leaf initiation rate. In contrast to the closest homologs in annual Arabidopsis thaliana and Mimulus guttatus, PhSBP1 and PhSBP2 transcription is not mediated by the gibberellic acid pathway, but is positively correlated with photoperiod and developmental age. The developmental functions of clade-VI SPL genes have, thus, evolved following both gene duplication and speciation within the core eudicots, likely through differential regulation and incomplete sub-functionalization

Functional Characterization of Duplicated <i>SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1</i>-Like Genes in Petunia

<div><p>Flowering time is strictly controlled by a combination of internal and external signals that match seed set with favorable environmental conditions. In the model plant species <i>Arabidopsis thaliana</i> (Brassicaceae), many of the genes underlying development and evolution of flowering have been discovered. However, much remains unknown about how conserved the flowering gene networks are in plants with different growth habits, gene duplication histories, and distributions. Here we functionally characterize three homologs of the flowering gene <i>SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1</i> (<i>SOC1</i>) in the short-lived perennial <i>Petunia hybrida</i> (petunia, Solanaceae). Similar to <i>A. thaliana soc1</i> mutants, co-silencing of duplicated petunia <i>SOC1</i>-like genes results in late flowering. This phenotype is most severe when all three <i>SOC1</i>-like genes are silenced. Furthermore, expression levels of the <i>SOC1</i>-like genes <i>UNSHAVEN</i> (<i>UNS</i>) and <i>FLORAL BINDING PROTEIN 21</i> (<i>FBP21</i>), but not <i>FBP28</i>, are positively correlated with developmental age. In contrast to <i>A. thaliana</i>, petunia <i>SOC1</i>-like gene expression did not increase with longer photoperiods, and <i>FBP28</i> transcripts were actually more abundant under short days. Despite evidence of functional redundancy, differential spatio-temporal expression data suggest that <i>SOC1</i>-like genes might fine-tune petunia flowering in response to photoperiod and developmental stage. This likely resulted from modification of <i>SOC1</i>-like gene regulatory elements following recent duplication, and is a possible mechanism to ensure flowering under both inductive and non-inductive photoperiods.</p></div

VIGS efficiency in petunia.

<p>(A) Typical agarose gel showing ethidium bromide stained amplicons using the TRV2-specific primers. Each lane represents a different individual in the VIGS experiment. −ve, negative control lacking cDNA. Of the 20 plants screened per treatment results for only 8 (<i>FBP28</i>-TRV2) or 10 (<i>CHS</i>-TRV2 and <i>FBP21</i>-TRV2) are shown as examples of efficiency. (B) Boxplots showing relative qPCR cT values for <i>UNS, FBP21</i>, and <i>FBP28</i> amplification. Each gene was amplified in ten plants infected with <i>CHS</i>-TRV2 (gray), <i>FBP21</i>-TRV2 (V1) (red), or <i>FBP28</i>-TRV2 (V2) (blue). Asterisks indicate at least a 2-fold average difference in gene expression between <i>FBP21</i>- or <i>FBP28</i>-TRV2 and control plants. Circles denote outliers.</p

Relative expression of petunia <i>UNS</i> (gray), <i>FBP21</i> (red), and <i>FBP28</i> (blue).

<p>(A–C) Transcript levels of <i>SOC1</i>-like genes vary in the youngest (upper) leaves throughout 16 h long days relative to the zeitgeber (dawn), but these trends are not significant. (D–F) <i>SOC1</i>-like gene transcripts are most abundant in SAMs relative to leaves and nodes. However, the peak of expression in each tissue type varies between genes. Bars are averages for two to three biological replicates with standard deviations. Significant differences at the 0.05 level are denoted by letters: a, leaves; b, SAMs; and c, nodes.</p

Maximum likelihood phylogeny of <i>SOC1</i>-like genes in petunia (bold) and other angiosperms.

<p>The tree is rooted on TM3 MADS-box genes in the <i>AGL14/19</i> clade sister to <i>SOC1/AGL42/AGL71/AGL72</i> genes <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0096108#pone.0096108-Becker1" target="_blank">[30]</a>. Numbers indicate maximum likelihood bootstrap values, with 100% being represented by an asterisk. Sol Genomics Network (SGN) and Genbank accession numbers are shown after each gene name.</p

VIGS phenotypes.

<p>(A) Flowering <i>CHS</i>-TRV2 positive plants showing lack of anthocyanin pigment in normally purple petals. (B) Late flowering <i>FBP21</i>-TRV2 plant. (C) Later flowering <i>FBP28</i>-TRV2 plant. (D) Boxplots showing number of days to flowering for plants positive for <i>CHS</i>-TRV2 (gray), <i>FBP21</i>-TRV2 (red), <i>FBP28</i>-TRV2 (blue), or <i>FBP21</i>/<i>FBP28</i>-TRV2 (green) constructs. Vertical lines separate batches of plants that were grown at different times of the year. Circles denote outlier values. Three asterisks indicate p values <0.001 relative to control plants. A single asterisk indicates p values <0.05 relative to control plants.</p

Quantifying seascape structure: extending terrestrial spatial pattern metrics to the marine realm

Spatial pattern metrics have routinely been applied to characterize and quantify structural features of terrestrial landscapes and have demonstrated great utility in landscape ecology and conservation planning. The important role of spatial structure in ecology and management is now commonly recognized, and recent advances in marine remote sensing technology have facilitated the application of spatial pattern metrics to the marine environment. However, it is not yet clear whether concepts, metrics, and statistical techniques developed for terrestrial ecosystems are relevant for marine species and seascapes. To address this gap in our knowledge, we reviewed, synthesized, and evaluated the utility and application of spatial pattern metrics in the marine science literature over the past 30 yr (1980 to 2010). In total, 23 studies characterized seascape structure, of which 17 quantified spatial patterns using a 2-dimensional patch-mosaic model and 5 used a continuously varying 3-dimensional surface model. Most seascape studies followed terrestrial-based studies in their search for ecological patterns and applied or modified existing metrics. Only 1 truly unique metric was found (hydrodynamic aperture applied to Pacific atolls). While there are still relatively few studies using spatial pattern metrics in the marine environment, they have suffered from similar misuse as reported for terrestrial studies, such as the lack of a priori considerations or the problem of collinearity between metrics. Spatial pattern metrics offer great potential for ecological research and environmental management in marine systems, and future studies should focus on (1) the dynamic boundary between the land and sea; (2) quantifying 3-dimensional spatial patterns; and (3) assessing and monitoring seascape change

Pilot RNA‐seq data from 24 species of vascular plants at Harvard Forest

Premise: Large-scale projects such as the National Ecological Observatory Network (NEON) collect ecological data on entire biomes to track climate change. NEON provides an opportunity to launch community transcriptomic projects that ask integrative questions in ecology and evolution. We conducted a pilot study to investigate the challenges of collecting RNA-seq data from diverse plant communities. Methods: We generated >650 Gbp of RNA-seq for 24 vascular plant species representing 12 genera and nine families at the Harvard Forest NEON site. Each species was sampled twice in 2016 (July and August). We assessed transcriptome quality and content with TransRate, BUSCO, and Gene Ontology annotations. Results: Only modest differences in assembly quality were observed across multiple k-mers. On average, transcriptomes contained hits to >70% of loci in the BUSCO database. We found no significant difference in the number of assembled and annotated transcripts between diploid and polyploid transcriptomes. Discussion: We provide new RNA-seq data sets for 24 species of vascular plants in Harvard Forest. Challenges associated with this type of study included recovery of high-quality RNA from diverse species and access to NEON sites for genomic sampling. Overcoming these challenges offers opportunities for large-scale studies at the intersection of ecology and genomics.National Science FoundationOpen access journalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]