Research

Classes of plant miRNAs and siRNAs can be very evolutionary dynamic. While there are several ancient miRNA families conserved across all land plants, a very rapidly evolving set of miRNA/siRNAs have been found to be species-specific. I am interested in understanding the evolutionary process and developmental relevance of recently evolved miRNAs.

Aquilegia miRNA/siRNA evolution: I am currently studying miRNA/siRNA evolution in 10 recently diverged Aquilegia species. Specifically, I am looking at how siRNA hotspots, new species-specific miRNAs, and ancient miRNAs evolve in a recently radiated species flock. Collaborators: Scott Hodges (UC Santa Barbara), Mike Axtell (Penn State), Elena Kramer (Harvard)

Evolution of immune response regulation by smallRNAs: Levi Yant (a postdoc in the Kramer Lab) and I are study the evolution of miRNA/siRNA regulation of immune response Resistance genes (R-genes) in the same Aquilegia species.

Evolution of immune response regulation by smallRNAs: I am working to curate and assemble a phylogeny for the miRNA biogenesis enzymes from taxa across the green plants. These phylogenies will be used to interpret the conspicuous absence of 24 nucleotide long smallRNAs in the gymnosperms. Collaborators: Sarah Mathews (Arnold Arboretum, Harvard), Josh Cofsky (Undergraduate, Yale)

Structural determinants of miRNA processing: Two excellent undegrads, Aubrey Faust (Harvard) and Josh Cofsky (Yale), are working to develop a pipeline to incorporate smallRNA sequencing data and miRNA precursor secondary structure to understand the structural determinants of miRNA excision from a double stranded foldback.

The distinguishing characteristic of Aquilegia (columbine) is the presence of petal spurs (see picture to the right). Aquilegia petal spurs are long tubular pockets that are matched to the size and shape of pollinator tongues or beaks, and range from 1 cm to 16 cm in length. Petal spurs are key innovations and have facilitated the rapid adaptive radiation of Aquilegia by allowing the plants to exploit specialized pollinator niches. Some of the specific projects include:

Spur initiation: How does an initially flat laminar organ develop an elaborated tubular spur? Collaborators: L. Mahadevan (Harvard), Levi Dudte (Harvard), Elena Kramer (Harvard)

The role of Aquilegia TCP4 in petal spur development: Levi Yant is heading up this project. I am helping to characterize the phenotypes by linking cellular changes (number, size, orientation) with organ level shape changes. Collaborators: Levi Yant (Harvard), Elena Kramer (Harvard)

Genes controlling spur initiation. RNA-seq comparing microdissected spur primorida and non-spurred petal tissue is being used to identify developmental modules controlling spur initiation. Collaborators: Levi Yant (Harvard), Elena Kramer (Harvard)

Linking genotype and environment to phenotype is a fundamental goal of quantitative genetics. This projects seeks to make significant progress in linking these by providing an efficient and automatic method of phenotyping using time-lapse imaging and automated image analysis. Furthermore, using the genomic tools developed in Mimulus in conjunction with our automated phenotyping system, I will explicitly link phenotype and genotype for hundreds of developmental variable Mimulus inbred lines. Importantly, much in the same way raw material is extracted for selective breeding, genetic variation was extracted from a single polymorphic population for synthesis of these Mimulus lines.

This project has three main objectives: (1) Develop an automated high-throughput phenotyping system for tracking growth trajectories (size and shape as a function of time) of plant traits, (2) use this phenotyping system, in conjunction with next generation high-throughput genotyping, to link genotypic and phenotypic variation in Mimulus lines that exhibit variation for a wide variety of growth related traits, and (3) link variations in macroscopic organ shape with variations in their cell number, size, and shape and ultimately, through select NIL crosses, dissect organ size/shape compensation at the cellular level, which could be a phenotypic manifestation of epistasis.

A genome wide association study (GWAS) will be used to connect genotype to phenotype. Illumina Hi-seq will be used to sequence the genomes of several hundred inbred individuals.

Columbine flower with pronounced petal spurs

Monkeyflower

Columbine petal spur evolution and development

Monkeyflower development and shape diversity

Plant microRNA evolution