Assistant Professor of Plant Biology
Ph.D. (1995) University of Texas

Phone: 706-583-5573
Email: jleebensmack@plantbio.uga.edu

Research in the Leebens-Mack Lab

Phylogenomics employs genome scale sequence data to resolve organismal relationships and investigate gene family evolution within the context of organismal relationships. Our lab uses phylogenomic approaches to explore the ecological, genetic and developmental processes that contribute to phenotypic diversification and speciation. We focus most of our attention on the evolution of reproductive characters in flowering plants. Much of our research involves phylogenetically based analyses, and we are working with collaborators to develop new empirical and analytical tools to extend the use of phylogenetic methods in comparative genomics. These tools form the foundation for comparative studies aimed at testing the degree to which characterizations of gene function and regulatory networks in model systems are applicable to other plant species.

Lab Members

Awards

Research Interests

Origin and Early Diversification of Flowering Plants

The Floral Genome Project is a multi-institutional investigation of genes and regulatory networks involved in the origin and early diversification of flowering plants. We have generated cDNA libraries and EST sets for a diverse set of angiosperm and gymnosperm species. Taxon sampling for the project has focused on key positions in the seed plant phylogeny for which there has been a paucity of genomic data. Comparative analyses of gene sequences and expression patterns are allowing 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. Interestingly, we are seeing common duplication patterns in many of our gene family studies (e.g. Zahn et al 2005a, 2005b, 2006, Cui et al 2006) which are leading us to hypothesize that genome-wide duplication events have been associated with the early diversification of flowering plants. This hypothesis will be tested in the Ancestral Angiosperm Genome Project through expanded cDNA sequencing in representative magnoliids, water lilies and Amborella trichopoda . Amborella is the sister lineage to all other flowering plants, and a physical map being developed in collaboration with theArizona Genomics Institute will allow us to make inferences about gene content and gene order in the most recent common ancestor of all extant angiosperms.

Monocot Systematics and Evolution

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.

Evolution of Dioecy and Sex Determination in Asparagus

Asparagus (A. officinalis) is a high value vegetable species with great nutritive value. While breeding programs have yielded improvements in production, spear quality, and disease resistance, asparagus breeders have been limited by a paucity of genomic resources to aid positional cloning of genes influencing these and other traits of interest. Beyond its value as a crop species, asparagus has much potential as a model for investigating genome structure and chromosomal evolution across flowering plants. The phylogenetic position of asparagus relative to the grass family (including rice, maize, wheat and other cereals) would facilitate efforts to reconstruct events that hinder comparisons of physical maps for model grass and eudicot (Arabidopsis , legumes, tomato, potato, sunflowers, etc.) species. To our knowledge, the only monocot species having comprehensive physical maps are in the Poaceae. Comparison of physical maps for the cereal species reveals a high level of synteny, and provides novel insights into the evolution of genome structure within the Poaceae. The lineage leading to asparagus and onion (Asparagales) diverged from the commelinid branch (including the Poaceae) some 120 million years ago and a physical map for asparagus will allow us and others to make inferences about genome structure in the most recent Asparagales-commelinid ancestor.

In addition, asparagus serves as a model for the evolution of sex chromosomes. The origin of separate sexes and the genetic basis of sex determination are of general biological interest. Much research has been devoted to the evolution of sex chromosomes in animal systems, but the large number of independent shifts between dioecy and hermaphroditism at various times since the origin of flowering plants, makes angiosperms the best system for testing general models for the evolution of dioecy and sex chromosomes. Dioecious Silene, Carica (papaya) and Asparagus species represent three stages in the evolution of XX/XY sex determination systems, and improved understanding of the proto-X and proto-Y regions in the Asparagus genome will provide insights into the earliest events in sex chromosome evolution.

Plant-Pollinator Coevolution

I have a long-standing interest in plant-pollinator systems, and over the last ten years in collaboration with Olle Pellmyr, Kari Segraves and Dave Althod, I have been investigating various aspects of the pollination mutualism between yuccas and yucca moths. I continue 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. In order to elucidate the molecular basis of phenological evolution in Yucca, we have constructed a cDNA library from and early stage flower buds and reproductive meristems harvested before flower stalks emerged from whorls of developing leaf blades. Nearly 2000 ESTs have been sequenced and analyzed using the comparative genomics pipeline developed for the Floral Genome Project. Together with ESTs being generated for Agave by collaborators in Mexico, these genomic resources will provide new nuclear markers that will be used to resolve relationships across the Agavaceae and investigate the molecular basis of floral diversification, shifts in flowering time and speciation in the family.

Bioinformatics

Together with collaborators at Penn State and the University of Georgia, we are developing bioinformatic tools and databases to facilitate phylogenomic analyses. Chloroplast genome and gene family databases have been developed in collaborations with Claude dePamphilis, Kerr Wall and colleagues at Penn State University. At UGA, we are working with Marie-Michèle Cordonnier-Pratt and Lee Pratt to add functionality to their suite of MAGIC sequence processing and gene discovery tools.

Selected Publications

Soltis, D. E., J.H. Leebens-Mack and P.S. Soltis (eds.). 2006. Developmental Genetics of the Flower. Advances in Botanical Research series. Elsevier Limited, London.

Cai Z, C. Penaflor, J.V. Kuehl, J. H. Leebens-Mack, J.E. Carlson, C.W. dePamphilis, J.L. Boore, and R.K. Jansen. 2006. Complete plastid genome sequences of Drimys, Liriodendron, and Piper: implications for the phylogenetic relationships of magnoliids. BMC Evolutionary Biology 6:77.

Tuskan, G.A., S. DiFazio, S. Jansson, J. Bohlmann, I. Grigoriev, U. Hellsten, N. Putnam, S. Ralph, S. Rombauts, A. Salamov, J. Schein, L. Sterck, et al. 2006. The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray). Science 313(5793):1596-604.

Gilbert M.T., J. Binladen, W. Miller, C. Wiuf, E. Willerslev, H. Poinar, J.E. Carlson, J.H. Leebens-Mack, and S.C. Schuster. 2006. Recharacterization of ancient DNA miscoding lesions: insights in the era of sequencing-by-synthesis. Nucleic Acids Research.

Leebens-Mack, J.H., T. Vision, E. Brenner, J.E. Bowers, S. Cannon, M.J. Clement, C.W. Cunningham, C. dePamphilis, R. Desalle, J.J. Doyle, J.A. Eisen, X. Gu, J. Harshman, R.K. Jansen, E.A. Kellogg, E.V. Koonin, B.D. Mishler, H. Philippe, J.C. Pires, Y-L. Qiu, S.Y. Rhee, K. Sjolander, D.E. Soltis, P.S. Soltis, D.W. Stevenson, K. Wall, T. Warnow, C. Zmasek. 2006. Taking the First Steps towards a Standard for Reporting on Phylogenies: Minimum Information about a Phylogenetic Analysis (MIAPA). OMICS 10(2):231-237.

Althoff, D.M., K.A. Segraves. J.H. Leebens-Mack, and O. Pellmyr. 2006. Patterns of Speciation in the Yucca Moths: Parallel Species Radiations within the Tegeticula yuccasella Species Complex. Systematic Biology 55(3):398-410.

Cui, L., Wall K., B.G. Lindsay, J.H. Leebens-Mack, J.J. Doyle, D.E. Soltis, P.S. Soltis, J. Carlson, H. Ma, and C.W. dePamphilis, 2006. Widespread genome duplications in flowering plants. Genome Research 16(6):738-49

Cui, L., J.H. Leebens-Mack, L-S. Wang, J. Tang, L. Rymarquis, L., D. B. Stern, and C.W. dePamphilis, 2006. Adaptive evolution of chloroplast genome structure inferred using a parametric bootstrap approach. BMC Evolutionary Biology 6:13.

Duarte, J. M., L. Cui, P.K. Wall, Q. Zhang, X. Zhang, J.H. Leebens-Mack, H. Ma, N. Altman, and C.W. dePamphilis. 2006. Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis. Molecular Biology and Evolution 23(2):469-78

McNeal, J.R., J.H. Leebens-Mack, K. Arumuganathan, J.V. Kuehl, J.L. Boore, and C. W. dePamphilis. 2006. Using partial genomic fosmid libraries for sequencing complete organellar genomes. Biotechniques 41(1):69-73

Cui, L., N. Veeraraghavan, P.K. Wall, R.K. Jansen, J.H. Leebens-Mack, I. Makalowska, and C. W. dePamphilis. 2006. ChloroplastDB: the chloroplast genome database. Nucleic Acids Research 34:D692-696.

Pellmyr, O., K.A. Segraves, D.M. Althoff, M. Balcàzar-Lara, and J.H. Leebens-Mack. 2006. Phylogeny and life history evolution of Prodoxus yucca moths (Lepidoptera: Prodoxidae). Systematic Entomology 31:1-20.

Zahn, L.M., J.H. Leebens-Mack, J.M. Arrington, Y. Hu, L. Landherr, C.W. dePamphilis,, A. Becker, G, Theissen, and H. Ma. 2006. Conservation and divergence in the AGAMOUS Subfamily of MADS-Box Genes: Evidence of Independent Sub- and Neofunctionalization Events. Evolution and Development 8:30-45.