Using gene networks in EvoDevo analyses

Leaf-size control beyond transcription factors: Compensatory mechanisms

Plant leaves display abundant morphological richness yet grow to characteristic sizes and shapes. Beginning with a small number of undifferentiated founder cells, leaves evolve via a complex interplay of regulatory factors that ultimately influence cell proliferation and subsequent post-mitotic cell enlargement. During their development, a sequence of key events that shape leaves is both robustly executed spatiotemporally following a genomic molecular network and flexibly tuned by a variety of environmental stimuli. Decades of work on Arabidopsis thaliana have revisited the compensatory phenomena that might reflect a general and primary size-regulatory mechanism in leaves. This review focuses on key molecular and cellular events behind the organ-wide scale regulation of compensatory mechanisms. Lastly, emerging novel mechanisms of metabolic and hormonal regulation are discussed, based on recent advances in the field that have provided insights into, among other phenomena, leaf-size regulation.

Leaf form diversification in an ornamental heirloom tomato results from alterations in two different HOMEOBOX genes

Domesticated plants display diverse phenotypic traits. However, the influence of breeding effort on this phenotypic diversity remains unknown. Here, we demonstrate that a single nucleotide deletion in the homeobox motif of BIPINNATA, a BEL-LIKE HOMEODOMAIN gene, led to a highly complex leaf phenotype in an heirloom tomato (Solanum lycopersicum), Silvery Fir Tree (SiFT), which is used as a landscaping and ornamental plant. A comparative gene network analysis revealed that repression of SOLANIFOLIA, the ortholog of WUSCHEL RELATED HOMEOBOX 1, caused the narrow leaflet phenotype seen in SiFT. Comparative genomics indicated that the bip mutation in SiFT likely arose de novo and is unique to SiFT and not introgressed from other tomato genomes. These results provide new insights into the natural variation in phenotypic traits introduced into crops during improvement processes after domestication and establish homeobox genes as evolutionary hotspots.

Q&A: How do gene regulatory networks control environmental responses in plants?

A gene regulatory network (GRN) describes the hierarchical relationship between transcription factors, associated proteins, and their target genes. Studying GRNs allows us to understand how a plant's genotype and environment are integrated to regulate downstream physiological responses. Current efforts in plants have focused on defining the GRNs that regulate functions such as development and stress response and have been performed primarily in genetically tractable model plant species such as Arabidopsis thaliana. Future studies will likely focus on how GRNs function in non-model plants and change over evolutionary time to allow for adaptation to extreme environments. This broader understanding will inform efforts to engineer GRNs to create tailored crop traits.

Comparative transcriptomics with self-organizing map reveals cryptic photosynthetic differences between two accessions of North American Lake cress

Because natural variation in wild species is likely the result of local adaptation, it provides a valuable resource for understanding plant-environmental interactions. Rorippa aquatica (Brassicaceae) is a semi-aquatic North American plant with morphological differences between several accessions, but little information available on any physiological differences. Here, we surveyed the transcriptomes of two R. aquatica accessions and identified cryptic physiological differences between them. We first reconstructed a Rorippa phylogeny to confirm relationships between the accessions. We performed large-scale RNA-seq and de novo assembly; the resulting 87,754 unigenes were then annotated via comparisons to different databases. Between-accession physiological variation was identified with transcriptomes from both accessions. Transcriptome data were analyzed with principal component analysis and self-organizing map. Results of analyses suggested that photosynthetic capability differs between the accessions. Indeed, physiological experiments revealed between-accession variation in electron transport rate and the redox state of the plastoquinone pool. These results indicated that one accession may have adapted to differences in temperature or length of the growing season.

High Impact Gene Discovery: Simple Strand-Specific mRNA Library Construction and Differential Regulatory Analysis Based on Gene Co-Expression Network

Plant transcription factors have potential to behave as hubs in gene regulatory networks through altering the expression of many downstream genes, and identification of such hub transcription factors strongly enhances our understating of biological processes. Transcriptome analysis has become a staple of gene expression analyses. In addition to current advances in Next Generation Sequencing (NGS) technology, various methods for mRNA library construction and downstream data analyses have been enthusiastically developed. Here, we describe Breath Adapter Directional sequencing (BrAD-seq), a simple strand-specific mRNA library preparation for the Illumina platform, allowing easy scaling of transcriptome experiments with low reagent and labor costs. This protocol includes our recent modifications and the detailed practical procedure for BrAD-seq. Because extracting biological meanings from large-scale transcriptome data presents a significant challenge, we also describe a new analytical method that goes beyond differential expression. Differential regulatory analysis (DRA) is based on a gene co-expression network to address which regulatory factor or factors have the ability to predict the abundance of differentially expressed genes between two groups or conditions. This protocol provides a ready-to-use informatics pipeline from raw sequence data to DRA for plant transcriptome datasets.