| Abstract Detail
Angiosperms353: A new essential tool for plant systematics Pokorny, Lisa [1], Johnson, Matthew [2], Dodsworth, Steven [3], Maurin, Olivier [4], Epitawalage, Niroshini [5], Bellot, Sidonie [6], Botigué, Laura R. [7], Brewer, Grace E. [8], Chase, Mark [9], Cowan, Robyn S. [8], Eiserhardt, Wolf L. [10], de la Estrella, Manuel [11], Hidalgo, Oriane [12], Kersey, Paul J. [13], Kim, Jan T. [14], Larridon, Isabel [15], McDonnell, Angela [16], Murphy, Bruce [17], Pellicer, Jaume [12], de Vos, Jurriaan [18], Wickett, Norman [19], Leitch, Ilia [20], Forest, Félix [21], Baker, William J. [21]. A phylogenomic approach to decode contentious relationships across flowering plants. Here we describe the first order- and family-complete (APG IV) phylogenomic analysis across all flowering plants (~1K accessions representing ~300K species). We demonstrate that the probe kit we developed—within the Plant and Fungal Trees of Life (PAFTOL) research programme—for target capture of 353 single-copy nuclear orthologs, works across flowering plant lineages. Additionally, we recover high-copy off-target regions (e.g., organellar DNA), as well as non-coding target-flanking nuclear regions (of use at shallow phylogenetic levels). Our phylogenomic pipeline explores the effects of sequence data provenance (NCBI SRAs vs. target capture), data matrix completeness (missing and fragmentary sequence data), alignment, trimming, and partitioning strategies, model selection (including heterotachy), as well as gene tree and species tree inference under the coalescent. Furthermore, we address sources of conflict (concordance), explore recalcitrant “knots” in the topology (e.g., Mesangiospermae, Pentapetalae) to discuss robustness of alternative contentious relationships, and we present a backbone hypothesis for the flowering plant tree of life.
Related Links: Plant and Fungal Trees of Life (PAFTOL)
1 - Centre For Plant Biotechnology And Genomics UPM-INIA, Computational/Systems Biology And Genomics Program, Autopista M-40, Km 38, Pozuelo De Alarcón, 28223, Spain 2 - Texas Tech University, Biological Sciences, 2901 Main Street, Ms3131, Lubbock, TX, 79409, United States 3 - University of Bedfordshire, School of Life Science, Luton, UK 4 - Royal Botanic Gardens, Kew, TW9 3AE, UK 5 - Royal Botanic Gardens, Kew, Jodrell Laboratory, TW9 3DS, UK 6 - Royal Botanic Garden, Kew, Comparative Plant and Fungal Biology, Jodrell Laboratory, TW9 3DS, UK 7 - Centre for Research in Agricultural Genomics (CRAG), Cerdanyola, Barcelona, 08193, Spain 8 - Royal Botanic Gardens, Kew, Jodrell Laboratory, Richmond, TW9 3DS, UK 9 - Royal Botanic Gardens, Kew, Jodrell Laboratory, Kew Road, Richmond, TW9 3DS, United Kingdom 10 - Aarhus University, Department of Bioscience, Aarhus, Denmark 11 - Universidad de Córdoba, Department of Botany, Córdoba, 14014, Spain 12 - Royal Botanic Gardens, Kew, Comparative Plant and Fungal Biology, Jodrell Laboratory, Richmond, TW9 3DS, UK 13 - Royal Botanic Gardens, Kew, Richmond, TW9 3AE, UK 14 - University of Hertfordshire, School of Computer Science, College Lane, Hatfield, AL10 9AB, UK 15 - Royal Botanic Gardens Kew, Royal Botanic Gardens Kew, Royal Botanic Gardens Kew, Richmond, TW9 3AE, United Kingdom 16 - Chicago Botanic Garden, Science Dept., 1000 Lake Cook Road, Glencoe, IL, 60022, United States 17 - Royal Botanic Gardens, Kew, Richmond, TW9 3AE, UK 18 - University of Basel, Department of Environmental Sciences, Schönbeinstrasse 6, Basel, 4056, Switzerland 19 - Chicago Botanic Garden, 1000 Lake Cook Rd., Glencoe, IL, 60022, United States 20 - Jordell Laboratory, Royal Botanic Gardens Kew, Richmond, SRY, TW9-3AB, United Kingdom 21 - Royal Botanic Gardens, Kew, Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
Keywords: phylogenomics phylogeny target capture HTS Angiosperms-353 bioinformatic workflow APG IV.
Presentation Type: Symposium Presentation Session: SY4, Angiosperms353: A new essential tool for plant systematics Location: Virtual/Virtual Date: Thursday, July 30th, 2020 Time: 11:00 AM Number: SY4003 Abstract ID:487 Candidate for Awards:Margaret Menzel Award |