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 Alarcn, 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


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