Phylogenomics of Australian (non-Orchidaceae) Asparagales
Bee F. Gunn1, Daniel J. Murphy1, Neville G. Walsh1, John G. Conran2, J. Chris Pires3, Terry D.
Macfarlane4 & Joanne L. Birch5
1Royal Botanic Gardens Victoria, Australia; 2University of Adelaide, Australia; 3University of Missouri, Columbia, USA; 4Dept. of Parks and Wildlife, Western Australia; 5University of Melbourne, Australia. bee.gunn@rbg.vic.gov.au
Asparagales comprise a third of monocots (14 families, 1,122 genera, ca. 36,205 species) and have the highest diversification rate among monocots. Despite the high diversity of “non-orchid”
Asparagales in Australia (9 fam.; 48 gen.; ca. 327 spp.), phylogenetic studies to-date have included
only limited sampling of native Australian taxa. The order has the greatest range of genome sizes, 0.3 – 82.2 pg, among angiosperms and has undergone massive genome and chromosome evolution.
As a result of the lack of dense sampling of Australian taxa for phylogenetics little is known about the monophyly of genera and species diversification. Our study sought to: i) infer phylogenetic relationships, ii) estimate divergence times of major clades, and iii) investigate plastid genome evolution for Australian lineages. All native Australian genera are included in this study and are represented by 200 individuals. Genome skimming techniques and HTS were used to generate sequence data. Whole chloroplast genomes were de-novo assembled, mapped to reference, and aligned in Geneious. The maximum likelihood phylogeny supports monophyly of Asparagales subfamilies. Here we present improved understanding of relationships within Lomandroideae, Asphodelaceae, and of Boryaceae and Orchidaceae relationships. Survey of genome sizes showed heterogeneity among Australian lineages reflecting polyploidy in some taxa.
Key words: divergence times, genome size, Lomandroideae, plastid, polyploidy.
Changing tribal and generic concepts in Cyperaceae, new insights from phylogenomics Isabel Larridon1, Ilias Semmouri2, Étienne Léveillé-Bourret3, Grace Brewer1, Niroshini
Epitawalage1, Felix Forest1, Paul Goetghebeur4, Jan Kim1, Olivier Maurin1, Lisa Pokorny1, Julian R. Starr3 & William J. Baker1
1Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK; 2Ghent University, Faculty of Bioscience Engineering, Laboratory of Environmental Toxicology and Aquatic Ecology, 9000 Gent, Belgium; 3University of Ottawa, Department of Biology, Ottawa, ON, K1N 6N5 Canada;
4Ghent University Research Group Spermatophytes & Botanical Garden, K.L. Ledeganckstraat 35, 9000 Gent, Belgium. i.larridon@kew.org
Despite recent advances in molecular phylogenetics, deep evolutionary relationships in Cyperaceae are not resolved. Reduction of floral morphology and complex inflorescences pose difficulties to unravel relationships based on morphology. One of the most phylogenetically informative structures in Cyperaceae is embryos. The utility of embryo characters and types in Cyperaceae systematics has been reviewed in a molecular phylogenetic context using a DNA supermatrix incorporating sequences from five plastid (matK, ndhF, rbcL, rps16, trnL-F) and two nuclear ribosomal (ETS, ITS) regions. The phylogenetic hypothesis presented includes the most extensive sampling of Cyperaceae to date. Fourteen qualitative morphological embryo characters were coded, ancestral state reconstructions were performed, and the embryo of each sampled genus was classified in a typological system based on key morphological features. Embryo morphology provides a valuable source of independent data for Cyperaceae systematics that can be used to place species with unknown affinities, when molecular data is not available, or when results of analyses are inconclusive or conflicting. This work is now being compared with the first generic-level phylogenomic tree generated using the angiosperm-wide bait kit developed for Kew’s PAFTOL programme. Together, these efforts will allow generating a new molecular-based classification for the family.
Key words: Cyperaceae, embryo, evolution, PAFTOL, phylogenomics.
Funded by: Plant and Fungal Trees of Life (https://www.kew.org/science/who-we-are-and-what-wedo/strategic-outputs-2020/plant-and-fungal-trees-life)
The Asphodelaceae tree of life: a phylogenomic evaluation of relationships among genera
Olwen M. Grace1, Grace Brewer1, Robyn Cowan1, Steven Dodsworth2, Niroshini Epitawalage1, Felix Forest1, Jan Kim1, Olivier Maurin1 & William J. Baker1
1Comparative Plant & Fungal Biology, Royal Botanic Gardens, Kew, Surrey TW9 3AE, United Kingdom; 2School of Life Sciences, University of Bedfordshire, University Square, Luton LU1 3JU, United Kingdom. o.grace@kew.org
The family Asphodelaceae comprises 41 genera and approximately 1,000 species in three subfamilies: the predominantly African Asphodeloideae; Eurasian and Australian Hemerocallidoideae; and the Australian Xanthorrhoeoideae. The family has undergone multiple nomenclatural changes in recent years, with the conservation of the name Asphodelaceae over Xanthorrhoeaceae, circumscription of multiple segregate genera among the alooid taxa in subfamily Asphodeloideae, and the recognition of Chamaescilla in subfamily Hemerocallidoideae, a genus previously included in Asparagaceae subfamily Lomandroideae. To assess generic relationships as they are currently circumscribed in Asphodelaceae, we generated genomic data for all 41 genera using a HybSeq approach with a universal angiosperm probe set applied in the Plant & Fungal Tree of Life (PAFTOL) project, targeting 353 low copy nuclear genes. We extracted the coding sequences and introns from high-throughput sequencing reads using the HybPiper pipeline and generated a species tree with Astral on our set of unrooted gene trees. The resulting tree provides phylogenetic evidence to support many accepted generic relationships within the three subfamilies, and critically evaluate those relationships that have hitherto remained unclear.
Key words: Asphodelaceae, PAFTOL, phylogenomics, systematics, taxonomy.
Phylogenomic analyses of hundreds of nuclear loci and plastomes yield new insights on orchid diversification
Oscar Alejandro Pérez-Escobar1, Guillaume Chomicki2, Diego Bogarín3, Steven Dodsworth4, Sidonie Bellot1, Izai Kikuchi3, Rowan Schley1, Robyn Cowan1, Jan T. Kim1, Grace Brewer1, Niroshini Epitawalage1, Olivier Maurin1, Andre Schuiteman1, Alexandre Antonelli5, Wolf Eiserhardt6, Mark W. Chase1, Ilia J. Leitch1, Felix Forest1, Barbara Gravendeel3 & William J.
Baker1
1Royal Botanic Gardens Kew, TW9 3AE, Richmond, UK; 2Department of Plant Sciences, University of Oxford, UK; 3Naturalis Biodiversity Centre, Netherlands; 4University of Bedfordshire, UK; 5University of Gothenburg, Gothenburg Global Biodiversity Centre, and Gothenburg Botanic Garden, Sweden; 6University of Aarhus, Denmark. oapereze@yahoo.com
High-throughput sequencing methods have made it possible to access hundreds of loci for evolutionary studies in plants. Nevertheless, evolutionary relationships in the iconic and species-rich orchid family (c. 25,000 species) are still mostly inferred using sequence data from plastid loci and relatively limited taxon sampling. Thus, while such analyses have been used to provide the phylogenetic framework for understanding orchid macroevolutionary dynamics, they are based on limited data. Here, we have produced the most extensive phylogenomic framework for the orchid family to date. This was achieved by first sequencing 353 nuclear genes and partial plastid genomes (Angiosperms 353 universal probe set) in 410 orchid species. We then used this phylogenomic framework to constrain the species tree hypothesis inferred from a DNA sequence matrix made up of four plastid loci and one nuclear ribosomal marker sequenced for 2,500 orchid species and representing ~10% of orchid species diversity. Our combined multi-locus approach supports many of the previously recovered orchid relationships, but it also reveals distinct phylogenetic positions for several orchid genera compared to previous results. Our new
phylogenomic framework unveiled the relationships of previously unplaced orchid clades, including insights on the origin and evolution of the orchid family.
Key words: bioinformatics, diversification, historical biogeography, next-generation sequence data, Orchidaceae.
Completing the Plant Tree of Life
Wolf L. Eiserhardt1, Vanessa Barber1, Abigail Barker1, Laura R. Botigué2, Grace Brewer1, Robyn S. Cowan1, Steven Dodsworth3, Niroshini Epitawalage1, Matthew Johnson4, Jan Kim1, Ilia Leitch1, Olivier Maurin1, Lisa Pokorny1, Norman Wickett5, Felix Forest1 & William J. Baker1
1Royal Botanic Gardens, Kew; 2Centre for Research in Agricultural Genomics, Barcelona;
3University of Bedfordshire; 4Texas Tech University; 5Chicago Botanic Garden.
wolf.eiserhardt@bios.au.dk
The Plant and Fungal Trees of Life (PAFTOL) project at the Royal Botanic Gardens, Kew, uses high-throughput DNA sequencing technology to generate extensive new data for at least one species of every genus of plant and fungi. Here, we report on progress in the plant component of PAFTOL. We have established a targeted sequence capture (HybSeq) approach and designed a single probe (bait) kit that isolatesup to 353 nuclear genes across all angiosperm families. Data obtained with this kit effectively resolve both deep and species-level relationships and are currently being evaluated as a “next generation” barcode. The kit is publicly available and is being adopted by numerous researchers. It is effective with degraded herbarium DNA from specimens up to ca.
200 years old. A refined bioinformatic pipeline is also in preparation. We have already sequenced at least one representative of every angiosperm family and we now aim to generate data for 25% of the 14,000 angiosperm genera within the coming year. Focused studies on families such as orchids, palms, and sedges are also underway. PAFTOL aspires to be highly open and collaborative, and researchers who share an interest in our project are warmly invited to get in touch.
Key words: angiosperms, museomics, next generation sequencing, phylogenomics, Tree of Life.
Funded by: This research was supported by grants from the Calleva Foundation, the Garfield Weston Foundation and the Sackler Trust to the Plant and Fungal Trees of Life project at the Royal Botanic Gardens, Kew.