BioGenomics2017 - Global Biodiversity Genomics Conference
February 21-23, 2017
Smithsonian National Museum of Natural History | Washington, D.C.

Program - Single Session


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10
Plant Genomics

Room: Salon 4, Marriott Hotel

10:50 - 12:40

Moderator: Pam Soltis, University of Florida



10.1  11:00  Completing the Plant and Fungal Trees of Life. Forest F*, Royal Botanic Gardens, Kew; Barker A, Royal Botanic Gardens, Kew; Dodsworth S, Royal Botanic Gardens, Kew; Eiserhardt WLT, Royal Botanic Gardens, Kew; Gaya E, Royal Botanic Gardens, Kew; Kim J, Royal Botanic Gardens, Kew; Maurin O, Royal Botanic Gardens, Kew; Parker J, Royal Botanic Gardens, Kew; Pokorny L, Royal Botanic Gardens, Kew; Baker WJ, Royal Botanic Gardens, Kew

Evolutionary trees are powerful tools for prediction, species discovery, monitoring and conservation. To better understand how the world's plants and fungi are related to each other and how they have evolved, we have initiated a project at the Royal Botanic Gardens, Kew to complete the Plant and Fungal Trees of Life. Through comparative analysis of DNA sequence data, the backbones of these Trees of Life are already relatively well understood, and many components have been studied in great detail. However, DNA data are still lacking for many genera and the vast majority of species of plants and fungi, preventing their accurate placement within this evolutionary framework. To complete the Plant and Fungal Trees of Life (PAFTOL) for all genera, we will utilise our collections and work with our collaborative networks to produce genome-scale DNA data for a representative of each genus of plant and fungus using high-throughput sequencing technologies. This comprehensive investigation of evolutionary relationships will provide a unifying framework for comparative plant and fungal research. The project is an essential step towards the compilation of genomic data for all known species.


10.2  11:20  Phylogenomics and biogeography of grapes and the close relatives in Vitaceae. Wen Jun*, Smithsonian Institution

Grapes are the economically most important woody fruit crop. Phylogenomic tools have been recently employed to reconstruct the evolutionary history of the grape family Vitaceae and the economically important grape genus Vitis. Phylogenetic relationships in Vitaceae as well as in Vitis have been historically very difficult to resolve. Congruent deep relationships of the grape family were obtained based on 417 nuclear genes from transcriptomics, and 16 mitochondrial genes and complete chloroplast genomes. The phylogeny and biogeography of the grape genus were explored with the complete chloroplast genome sequences and extensive nuclear data from whole-genome resequencing. The results support the New World origin of Vitis, and the sister-clade relationship of European and eastern Asian Vitis species.


10.3  11:40  Examining relationships within Pityopsis using chloroplast genomes. Hatmaker EA*, University of Tennessee/Oak Ridge National Laboratory; Wadl PA, USDA-Agricultural Research Service ; Rinehart TA, USDA-Agricultural Research Service; Carroll JB, USDA-Agricultural Research Service; Lane TS, University of Tennessee; Trigiano RN, University of Tennessee; Schilling EE, University of Tennessee; Staton ME, University of Tennessee

Pityopsis includes several regionally and one federally endangered species of herbaceous perennials. Four species are highly localized, including the federally endangered P. ruthii. Three species are found throughout the eastern United States, with the range of one extending into Mexico. The genus includes several ploidy levels and adaptive traits such as drought tolerance and fire-dependent flowering. Morphological studies have separated the genus into two distinct clades, but due to the lack of molecular studies, intergeneric relationships have not been fully resolved. Chloroplast genomes have been successful at providing higher resolution for intergeneric relationships; therefore, we sequenced and assembled the chloroplast genomes of all twelve species and/or varieties of Pityopsis. A reference chloroplast genome (152,447 bp) including 128 genes was assembled de novo from P. falcata. Reads from the other individuals were then aligned to the reference and individual chloroplast genomes were assembled. Utilizing all informative sites from the chloroplast genomes, a multiple sequence alignment of the twelve chloroplast genomes was used to construct phylogenies of the genus using the maximum likelihood and maximum parsimony methods. Additionally, we constructed phylogenies from the nuclear ETS region after mapping to Chrysopsis mariana, a close relative of Pityopsis. We found support for two clades in the chloroplast phylogenies. Previously proposed clades and taxonomic sections within the genus were largely unsupported by our nuclear and chloroplast trees. Differences between nuclear and chloroplast trees allowed formulation of hypotheses regarding polyploidization of two P. graminifolia varieties. With conservation of the endangered species P. ruthii, multiple ploidy levels of species in the genus, and the current trend toward xeric landscaping with native species, Pityopsis has garnered attention as a complicated and interesting genus for research opportunities.


10.4  12:00  Investigating diploid and polyploid genomes to discover genes associated with polyploid advantage. Mathews S*, Australian National Herbarium; Godfree R, Australian National Herbarium

Whole genome duplication (WGD) has been a pervasive force in the evolution of vascular plants as a driver of reproductive isolation, phenotypic diversity, and speciation. Geographically and ecologically structured variation in ploidy level is common, and a long-standing hypothesis is that polyploids have higher fitness in climatically variable or extreme habitats due to ecological flexibility that arises from WGD. Empirical evidence for polyploid advantage has been lacking, however, and the causal links between ploidy and the environmental factors that govern plant fitness remain a subject of debate. We have obtained empirical evidence of polyploid advantage in kangaroo grass (Themeda triandra Forssk.) tetraploids under elevated abiotic stress and have shown that it results from two distinct processes, homeostatic maintenance of reproductive output and fixed differences in seed size and morphology. In an outdoor climate manipulation experiment, we found a significant effect of cytotype or cytotype-by-climate in the data for seven out of nine fitness traits. Remarkably, total output of viable seed in tetraploids under heat and drought treatments was over four times higher than in diploids. Tetraploids also produced heavier seeds with longer awns (used in locomotion). Fixed advantage under stress was evident in data for seed morphology, while a homeostatic advantage (no advantage in the absence of or under most extreme stress) was evident in data for traits associated with resource allocation. These advantages were retained across regionally isolated diploid-tetraploid population pairs. Our study suggests that multiple processes underlie polyploid advantage, including biochemical flexibility promoted by gene duplication and subfunctionalisation, and changes in the size, number, and geometry of cells. We currently are conducting genome scans to discover regions of the T. triandra genome that are differentiated between diploids and polyploids and might harbor genes associated with polyploid advantage.


10.5  12:20  The origin and evolution of sex chromosomes in Asparagus. LEEBENS-MACK J*, University of Georgia; Danforth D, Plant Science Center; VAN DER HULST R, 3Limgroup B.V. Horst, The Netherlands; BOWERS J, University of Georgia; AYYAMPALAYAM S, University of Georgia

Sex chromosomes have evolved from autosomes hundreds of times across the tree of life yet the molecular and evolutionary processes underlying these transitions remain obscure. Garden asparagus (Asparagus officinalis), a dioecious species with a recently evolved homomorphic sex chromosome pair, is ideal for studying the earliest events in sex chromosome evolution. Comparative analysis of male and female asparagus genomes has implicated a 1 Mb male-specific region on the asparagus Y chromosome. We have identified two independent male-to-hermaphrodite mutants that implicate a single gene in this male-specific region as responsible for dominantly interrupting pistil development. Anther development is not affected in these mutants but male to female conversions are seen in two other mutants with deletions spanning the 1 Mb non-recombining sex determination region. This region contains 10 gene models in addition to the female suppressor including defective in tapetal development and function 1 (TDF1). In support of the a model proposed by Charlesworth & Charlesworth (The American Naturalist 1978) for the origin of sex chromosomes, these finding imply that the origin of a non-recombining sex determining region on the Asparagus proto-Y chromosome involved the linkage of a male promoting gene with a dominant female suppressor.


12:40 - 14:00 Lunch


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