The Floral Genome Project initiated comparative genomic analyses of diverse flowering plant lineages with sampling focused on basal angiosperms including magnoliids (e.g. tulip tree and avocado), water lilies and Amborella trichopoda. Comparative analyses of gene sequences and expression patterns has allowed us to infer ancestral characteristics for these important clades and test hypotheses concerning the roles that gene and genome duplications and shifts in gene function have played in generating the amazing diversity of flowering plants we see today. The Ancestral Angiosperm Genome Project applied next generation sequencing technologies to expand our transcriptome sampling for representative basal angiosperm taxa with special focus on Amborella. Phylogenomic analyses have identified Amborella as the sister lineage to all other extant flowering plants. In addition to deep transcriptome sequencing, a draft physical map and genome sequence for Amborella have been constructed and these are being used to elucidate the evolution of genome structure across angiosperm history. The Amborella Genome Project has successfully completed a draft genome assembly and annotation of the genome has been done in my lab. Amborella gene and genome sequences are available through the project website and NCBI.
The monocots are a diverse group including some 65,000 species and two of the most species rich plant families (Orchidaceae and Poaceae). Nearly all of what we know about monocot genomes is limited to economically important cereals within the grass family. While the vast amount genomic data for cereal species is quite valuable, recent work has shown that many genomic features of the grass family including GC content, codon usage, gene copy numbers and the identity and distribution of repetitive elements are distinct. Comparative analyses of grass and non-grass chloroplast genomes implicate rapid change in genome structure, substitution rates and codon usage biases occurred within the Poales but sometime before the radiation of major grass lineages at least 55 million years ago. The extensive amount of genomics research within the grass family, including whole genome sequencing of the rice and sorghum genomes and sequencing of genic regions in the maize genome, is providing deep insights into genome evolution within the family. An understanding of the processes that generated unique genome characteristics in the grasses, however, will require genome level research on non-grass monocots. Moreover, an understanding of ecological and genetic events associate with rapid radiations in monocot history will require resolution of uncertainty in the relationships among major monocot lineages. Much of our research is aimed at understanding these processes through phylogenetic analyses of organismal relationships and comparative analyses of cDNA and genomic sequences obtained from the grasses and non-grass monocot species including palms, banana, onion, asparagus, agave, yucca, irises, orchids and Acorus, the basal-most monocot lineage in the angiosperm phylogeny.
Theoretical models provide predictions for the genetic events giving rise to the origin of separate sexes and sex chromosome in diverse animal, plant and fungal lineages. Flowering plants are especially well suited for testing these prediction because there have been dozens of independent origins of dioecy in angiosperms. Despite the fact that some 6% of all angiosperms are dioecious, the genes responsible for gender determination have not yet been identified in any plant species. My lab is developing garden asparagus (A. officinalis) as a model system to test hypothesized mechanisms for evolution of sex chromosomes. We have localized the non-recombining proto-Y and proto-X loci to a small (< 2 Mb) region on a chromosomal arm and we are sequencing clones from male and female BAC libraries that map to this region. In collaboration with others in China and Italy, we have initiated a genome sequencing project for garden asparagus and we are using BAC and genome sequences to characterize and compare the male and female gender determination regions. Alex Harkess's disertation research is focused on unraveling the molecular basis of the evolution of dioecy and incipient sex chromosomes within the genus Asparagus.
I have a long-standing interest in plant-pollinator systems, and in collaboration with Olle Pelmyr, Chris Smith, Kari Segraves and Dave Althof, I have been investigating various aspects of the pollination mutualism between yuccas and yucca moths. My lab continues to explore diversification and the evolution of plant - insect interactions using the yucca - yucca moth system as a model. The thrust of this research is aimed at understanding the proximal mechanisms for pollinator host specificity and the evolution of reproductive isolation between yucca species. Variation in floral fragrance and flowering time both within and among species is influencing patterns of inter- and intraspecific gene flow. Former student, Jeremy Rentsch, investigated genetic structure within and among yucca species of the southerstern U.S.. Jeremy's research revealed that Y. gloriosa is a hybrid species (Rentsch & Leebens-Mack 2012) derived from the C3 speciesY. filamentosa and a CAM species, Y aloifolia.
Building on Jeremy's work, Karolina Heyduk is developing Y. gloriosa as a model system for understanding the evolution of CAM photosynthesis within the Agavaceae. Photosynthesis is a fundamental biological process supporting the vast majority of life on Earth. For plants living under water-limited conditions, however, photosynthetic productivity can be greatly reduced by hotter and drier climatic conditions. To counteract these conditions, some plants utilize forms of photosynthesis that increase the efficiency with which they use water. One such innovation seen in plants growing in deserts or other water-limited habitats is Crassulacean Acid Metabolism or CAM. CAM has evolved independently across diverse plant lineages and it is typically associated with stem (e.g. cacti) or leaf (e.g. agaves, some orchids) succulence. Working with collaborators at UC Riverside and the University of Buffalo we are integrating ecophysiological, genomics and evolutioary approaches to address fundamental questions about how plants use CAM, how genes involved in performing CAM are regulated in response to varying environmental conditions, and how the evolution of CAM facilitates diversification in water-limited habitats. To achieve these aims, we are investigating independent evolutionary tansitions between typical C3 photosynthesis and CAM in the orchid and agave plant families, both of which have species known for their ability to thrive in water-limited environments. This research will provide a foundation for understanding the genetic basis of CAM pathways and contribute to ongoing efforts introduce CAM to economically important plants for improved water use efficiency when growing under drought conditions.
Our lab develops pipelines for evolutonary analysis genome structure, gene birth and death and gene expression. Together with collaborators at Penn State, the University of Texas and iPlant, we are developing bioinformatic tools and databases to facilitate phylogenomic analyses. Chloroplast genome (ChloroplastDB) and gene family (PlantTribes) databases have been developed in collaborations with the dePamphilis lab, and working with the Warnaw lab and iPlant we are using the PlantTribes gene family classification system to perform phylogenomic analyses on protein coding genes extracted from plant genome and transcriptome sequences being generated through the Ancestral Angiosperm Gemone Project, the Monoct Tree of Life Project and the One Thousand Plant Transcriptomes sequencing project (1KP).