Current Research
 Aquilegia as a new model species
Researchers: Bharti Sharma, Elena Kramer, Levi Yant, Emily Gleason, Joshua Puzey (past researcher), Anji Ballerini (past researcher), Faye Rosin (past researcher)
We are part of a large collaborative group that is working to develop a wide range of genomic and genetic tools in the lower eudicot genus Aquilegia. This group is led by Scott Hodges of the Univ. of CA, Santa Barbara and also includes Magnus Norborg of the Gregor Mendel Institute and Justin Borevitz of the Australian National University.
Why Aquilegia?
Five major features of Aquilegia make it an extraordinary opportunity for development as a model system for the study of adaptations to the environment: 1) species vary widely with respect to both the biotic and abiotic environments, 2) species are largely interfertile allowing the genetic dissection of traits, 3) speciation has occurred extremely rapidly resulting in low sequence variation among species, 4) species are diploid (n = 7) with a small genome (1C = 320-400 Mbp), and 5) genomic resources have already been developed including a genetic map, QTL identification for a number of traits, the isolation and characterization of floral developmental genes, two fingerprinted BAC libraries and an EST database.
The genus Aquilegia (Ranunculaceae) has been the subject of ecological, evolutionary and genetic studies for over 50 years (Hodges and Fulton, 2004). The genus consists of approximately 70 perennial taxa distributed in temperate North America, Europe and Asia and is noted for the nectar spurs that occur on each of the five petals of its flowers. These spurs are tubular outgrowths of the petals with a nectary at their base. Animals probe these tubes to obtain nectar and in doing so pollinate the plants. Although all species exhibit this general floral bauplan, the genus is remarkable for wide variation in floral morphology and color associated with different pollinators (Figure above). Floral features among species can range, for example, in nectar spur length (from < 1cm to > 12 cm), petal blade length (from 0 cm to > 3 cm), flower orientation (from pendant to upright), and flower color, (including blue, purple, red, yellow, green, and white species). Columbines also occur in diverse habitats, including shaded forests, alpine zones, desert springs, and serpentine outcrops (Munz, 1946). Some species have dramatic latitudinal and altitudinal ranges such as A. formosa (southern California to Alaska; sea level to 10,000 ft) and A. canadensis (Texas and Georgia to Canada). Thus, striking ranges of habitat occur both within and between species.
Thanks to a NSF-funded project, we developed a deep EST database for A. formosa and A. pubescens, created mapped BAC libraries for both taxa (Fang et al., 2010), developed efficient RNAi based functional tools (Gould and Kramer 2007) and tissue-culture based regeneration, annotated conserved miRNA families (Puzey and Kramer 2009) and initiated the characterization of flowering time control in Aquilegia. Currently, this foundation is being dramatically expanded thanks to genome sequencing efforts directed by the Joint Genome Institute of the DOE. The complete genome sequence of A. coerulea ‘Origami’ is now publicly available with further Illumina sequencing of significant numbers of additional species and outgroup genera underway (see below). Once complete, we believe this will represent an exceptional tool for researchers interested in evolutionary and ecological questions.
In the Kramer lab, the current focus is on development of stable transformation techniques, assembly of de novo genome sequences from additional species, analysis of R gene evolution, broad annotation and evolution of miRNAs and siRNA production across the genus, and annotation of major transcription factor families.
Fang, G.C., Blackmon, B.P., Henry, D.C., Staton, M.E., Saski, C.A., Hodges, S.A., Tomkins, J.
        P. and Luo, H. (2010) Genomic tools development for Aquilegia: Construction of a BAC-
        based physical map. BMC Genomics, 11:621.
Gould, B. and E.M. Kramer. (2007) Virus-induced gene silencing as a tool for functional    
         analyses in the emerging model plant Aquilegia (columbine, Ranunculaceae). Plant
Hodges, S.A., and Fulton, M. (2004). Verne Grant and evolutionary studies of Aquilegia. New Phytol 161, 113-120.
Munz, P.A. (1946). Aquilegia: The cultivated and wild columbines. Gentes Herbarium 7, 1-150.
Puzey, J. R. and Kramer, E.M. (2009) Identification of conserved Aquilegia coerulea microRNAs
        and their targets. Gene, 448:46-56.
See also:
Hodges, S.A. and Kramer, E.M. 2007, Curr Biol 17, R992-994 Hodges and Kramer CurrBiol 2007.pdf
Kramer, E.M. and Hodges, S.A. (2009). Aquilegia as a model system for the evolution and
        ecology of petals. Proceedings of the Royal Society of London, Series B, 365:477-490.
Kramer, E.M. (2009). Aquilegia – A new model for plant development, ecology and evolution.
        Annual Reviews of Plant Biology, 60:261-277.
PDS silenced
ANS silenced
Taxa with sequenced genomes as part of the Aquilegia Genome Consortium’s efforts.