From Plant Press, Vol. 12, No. 2 from April 2009.
The eighth annual Smithsonian Botanical Symposium was held 27-28 March 2009. The symposium, “Genes, Genomics, and Genome Evolution in Plants,” explored the results of current studies on plant genes and genomes, especially as they apply to fundamental questions in evolutionary biology, crop improvement and ecosystem sustenance in rapidly changing environments. Below are the speakers’ abstracts from the papers that were presented.
Smithsonian Institution, U.S.A.
“Phylogenomics and the End of Incongruence?”
The future of molecular systematics seems to lie in amassing ever larger datasets with more genes and more taxa in pursuit of more robust trees. Such a “total evidence” approach shows promise for resolving deeper nodes, placing difficult taxa (e.g., parasitic plants), and resolving challenging rapid radiations (i.e., Malpighiales or Saxifragales). Furthermore, genome-scale data do provide a powerful tool towards realizing these goals by providing the vast quantity of characters needed and enabling gene choices better tailored to the problems addressed. However, both complexity and the risk of systematic errors grow rapidly with such large datasets. For instance, individual gene trees can conflict which presents an opportunity to explore its causes (i.e., horizontal gene transfer), although some consider such incongruence to be a nuisance that is preferably avoided through better experimental design (i.e., better gene selection or methods of analysis). There are certain challenges and opportunities emerging with regard to the types of evolutionary questions that can be addressed with genomic data and its use in phylogenetic inference.
University of Kansas, U.S.A.
“Importance of Multigene Transcription Factor Families for Flower Development and Its Diversification”
Inflorescences and flowers vary greatly in both architecture and identity, suggesting repeated evolutionary modifications to a shared ancestral ground plan. In model organisms, such as Arabidopsis thaliana and Antirrhinum majus, the genetic basis of floral development is fairly well understood. However, less is known about similar pathways in morphologically divergent species. Theoretical and empirical studies suggest that gene duplications may be important for the evolution of plant form, since relaxed selection following gene doubling may allow functional divergence of one or both genes, commonly distinguished as non-, sub- or neo-functionalization. Here, I present two studies examining the evolution of genes from multigene families, and their possible roles in diversification of floral form. The first examines the role of duplicated AP1/FUL MADS-box genes in the evolution of Poaceae flowers (spikelets) and the second determines the role of TCP- and MYB-family transcription factors in evolution of petal symmetry and stamen number in Veronicaceae.
University of Texas, U.S.A.
“Comparative Plastid Genomics Resolves Phylogenetic Relationships among Major Angiosperm Lineages and Reveals Genome-scale Evolutionary Patterns”
Currently there are 149 plastid genome sequences available on GenBank with 93 of these from angiosperms. The genomic data has provided a wealth of new data for resolving phylogenetic relationships among the major clades of angiosperms and for improving our understanding of genome evolution. Phylogenetic analyses of a data set that includes 81 genes from all available angiosperm genomes provide excellent resolution and support for resolving relationships among the major clades. This includes: confirmation that Amborella is the earliest diverging lineage of angiosperms; resolution of the placement of Chloranthales sister to magnoliids; placement of Chloranthales/magnoliids clade sister to a strongly supported eudicot/monocot clade; placement of Ceratophyllum sister to eudicots; and placement of Caryophyllales sister to asterids. Genomic-wide comparisons across angiosperms identified a strong positive correlation between rates of nucleotide substitutions and genomic rearrangements. Comparisons of genome organization of Geraniaceae identified extensive rearrangements, including large expansions/contractions of the inverted repeat and numerous gene order changes. These rearrangements are associated with dispersed repeats, suggesting that they may play an important role in genomic rearrangements. Comparisons of rates of sequence evolution among protein-coding genes in Geraniaceae and Poaceae identify extensive rate heterogeneity among lineages and genes but the overall pattern in these two families is distinct. In Geraniaceae, rapid rate accelerations occur both on the branch leading to the family as well as the internal branches, whereas in Poaceae rate acceleration is restricted to the branch leading to the family. In both groups accelerated substitution rates are associated with only certain functional groups of genes.
American Museum of Natural History, U.S.A.
“Are Whole Genomes the Way to Go?”
Genome level information and high throughput methods have opened a new phase of modern systematics. Some unanswered questions and difficulties have surfaced as a result of incorporating data from high throughput methods that require immediate attention. One question that always arises is “how much?” Another question that is very persistent with genome level information concerns the problem of incongruence and how to treat incongruent information in systematics. Using several examples from the tree of life the question of “how much” and the problem of incongruence will be examined from a genomic perspective. The utility of a fully fleshed out tree of life for determining function in an evolutionary context will also be discussed.
Oak Ridge National Laboratory, U.S.A.
“The Entangled History of Populus and Humans – Genomics, Accelerated Domestication and Napoleon”
From origin myths onto the Roman Empire, Davy Crockett, the minuteman missiles and through to modern biofuels development Populus has shared a common history with humans. As one of the fastest growing woody perennial plants, one which can be easily clonally propagated through the use of unrooted lateral branches, Populus has been used to provide shade, demarcate roadway, control soil erosion, and provide fiber for pulp, paper, veneer, and bioenergy feedstocks. The domestication process however has been erratic and slow due to the large size and delayed reproductive habit of this woody perennial tree. Modern genomics tools and approaches are being brought to bear on the efforts to accelerate the domestication process in Populus. The genome of Populus trichocarpa was sequenced, assembled, and annotated in 2006 through an international effort that included over 250 scientists from over 20 countries. The assembled genome contains 45,500 predicted gene models and revealed a recent whole-genome duplication that suggested the molecular clock in Populus is ticking at one sixth the rate seen in herbaceous annual plants such as Arabidopsis. Utilizing this information has made it possible to refine genetic maps, improve candidate gene isolation through QTL analyses and association genetics, and test hypotheses on accelerated domestication. Candidate genes related to drought tolerance, crown architecture, cell wall chemistry and disease resistance are currently being evaluated in greenhouse and field trials.
Cornell University, U.S.A.
“Gene Flow and Genetic Isolation during Crop Evolution”
Knowledge about the structure and evolutionary history of naturally occurring variation in crops and their wild relatives provides a road map for understanding domestication and new opportunities for utilizing novel alleles in crop improvement. Domesticated Asian rice (Oryza sativa L.) is comprised of five, well-differentiated subpopulations that evolved from a common, out-crossing wild ancestor, O. rufipogon. We seek to understand the evolutionary forces that acted on this tropical ancestor to generate the subpopulation structure of modern O. sativa. Using recently isolated domestication genes, we trace the evolutionary history of alleles that both define and transcend the deep population subdivisions of domesticated rice. Documented patterns of allele-sharing and dispersal suggest a complex pattern of gene flow and genetic exchange coupled with an increase in genetic isolation reinforced by inbreeding. Understanding the biological, social and cultural dynamics of these opposing processes challenges existing models of crop domestication and provides a framework for conserving, characterizing and utilizing wild and exotic germplasm in crop improvement.
University of Georgia, U.S.A.
“Leveraging Evolutionary Genomics for Crop Improvement in Sub-Saharan Africa”
The genomes of most plants are large, and quite complex. The average flowering plant genome, for instance, is twice the size of the human genome. Much of the DNA within these plant chromosomes is comprised of transposable elements that have expanded and rearranged their host genomes at an exceptional rate. Afloat in these seas of repetitive DNA are the gene islands that actually determine plant development, physiology and adaptability. A few angiosperm (flowering plant) genomes have been sequenced, and several more are in the works. With this sequence information, the genes that specify the common properties of angiosperms (like photosynthesis, root development and seed production) are being identified. Most exciting, the genes responsible for the differences in plant biology that make each species unique are also under investigation, both at the level of their functions and in their modes of evolution. We are now attempting to use this information, extracted largely by comparative genomics, to accelerate the improvement of crops like tef millet that are vital to millions of Africans, but have been largely ignored by most scientists in advanced research environments. Because so few plant species have been investigated at the molecular and genomic level, surprises abound, but comparative genomics provides a framework whereby such novel observations are being integrated and utilized for the study and improvement of any targeted crop.
Sponsors of the 8th Smithsonian Botanical Symposium
- Cuatrecasas Family Foundation
- NationalMuseum of Natural History
- Department of Botany
- Office of the Associate Director for Research and Collections
- National Science Foundation
- United StatesBotanic Garden
The success of the Symposium was due to the significant time and efforts of the following people
- Jeff Bennetzen
- Laurence Dorr
- Ellen Farr
- Vicki Funk
- W. John Kress
- Gary Krupnick
- Sue Lutz
- Warren L. Wagner
- Jun Wen
- Kenneth Wurdack
- Elizabeth Zimmer
- Mary Ann Apicelli
- Patricia Davis
- Elaine Haug
And many others who had helped in a myriad number of ways.
Supplementary Symposium Links on the Web
The Web site to the 8th Annual Smithsonian Botanical Symposium <https://botany.si.edu/sbs/> has many links and documents related to the conference. Included on the Web site is the full program, abstracts of the talks, links related to the speaker’s presentations, and selected images from the various events. A digital video recording of the presentations will be posted soon. Additional items related to the Symposium can be added to the list of links and documents by sending an e-mail to firstname.lastname@example.org.
The Symposium archive pages <https://botany.si.edu/events/sbsarchives/> also includes programs, abstracts and images from the past six symposia: “Linnaean Taxonomy in the 21st Century” (2001); “The Convention on Biological Diversity” (2002); “Botanical Frontiers in Southeast Asia” (2003); “Botanical Progress, Horticultural Innovations, and Cultural Changes” (2004); “The Future of Floras: New Frameworks, New Technologies, New Uses” (2005); “Island Archipelagos: Cauldrons of Evolution” (2006); and, “Partners in Evolution: Interactions, Adaptations, and Speciation” (2008).