Global Brassicaceae phylogeny based on filtering of 1,000-gene dataset

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dc.contributor.authorHendriks, Kasper P.
dc.contributor.authorKiefer, Christiane
dc.contributor.authorAl-Shehbaz, Ihsan A.
dc.contributor.authorBailey, C. Donovan
dc.contributor.authorvan Huysduynen, Alex Hooft
dc.contributor.authorNikolov, Lachezar A.
dc.contributor.authorNauheimer, Lars
dc.contributor.authorZuntini, Alexandre R.
dc.contributor.authorGerman, Dmitry A.
dc.contributor.authorFranzke, Andreas
dc.contributor.authorKoch, Marcus A.
dc.contributor.authorLysak, Martin A.
dc.contributor.authorToro-Nunez, Oscar
dc.contributor.authorOzudogru, Baris
dc.contributor.authorInvernon, Vanessa R.
dc.contributor.authorWalden, Nora
dc.contributor.authorMaurin, Olivier
dc.contributor.authorHay, Nikolai M.
dc.contributor.authorShushkov, Philip
dc.contributor.authorMandakova, Terezie
dc.contributor.authorSchranz, M. Eric
dc.contributor.authorThulin, Mats
dc.contributor.authorWindham, Michael D.
dc.contributor.authorResetnik, Ivana
dc.contributor.authorSpaniel, Stanislav
dc.contributor.authorLy, Elfy
dc.contributor.authorPires, J. Chris
dc.contributor.authorHarkess, Alex
dc.contributor.authorNeuffer, Barbara
dc.contributor.authorVogt, Robert
dc.contributor.authorBrauchler, Christian
dc.contributor.authorRainer, Heimo
dc.contributor.authorJanssens, Steven B.
dc.contributor.authorSchmull, Michaela
dc.contributor.authorForrest, Alan
dc.contributor.authorGuggisberg, Alessia
dc.contributor.authorZmarzty, Sue
dc.contributor.authorLepschi, Brendan J.
dc.contributor.authorScarlett, Neville
dc.contributor.authorStauffer, Fred W.
dc.contributor.authorSchonberger, Ines
dc.contributor.authorHeenan, Peter
dc.contributor.authorBaker, William J.
dc.contributor.authorForest, Felix
dc.contributor.authorMummenhoff, Klaus
dc.contributor.authorLens, Frederic
dc.date.accessioned2024-01-04T10:38:15Z-
dc.date.available2024-01-04T10:38:15Z-
dc.date.issued2023
dc.identifier.issn0960-9822
dc.identifier.urihttp://osnascholar.ub.uni-osnabrueck.de/handle/unios/73320-
dc.description.abstractThe mustard family (Brassicaceae) is a scientifically and economically important family, containing the model plant Arabidopsis thaliana and numerous crop species that feed billions worldwide. Despite its relevance, most phylogenetic trees of the family are incompletely sampled and often contain poorly supported branches. Here, we present the most complete Brassicaceae genus-level family phylogenies to date (Bras-sicaceae Tree of Life or BrassiToL) based on nuclear (1,081 genes, 319 of the 349 genera; 57 of the 58 tribes) and plastome (60 genes, 265 genera; all tribes) data. We found cytonuclear discordance between the two, which is likely a result of rampant hybridization among closely and more distantly related lineages. To eval-uate the impact of such hybridization on the nuclear phylogeny reconstruction, we performed five different gene sampling routines, which increasingly removed putatively paralog genes. Our cleaned subset of 297 genes revealed high support for the tribes, whereas support for the main lineages (supertribes) was moder-ate. Calibration based on the 20 most clock-like nuclear genes suggests a late Eocene to late Oligocene origin of the family. Finally, our results strongly support a recently published new family classification, dividing the family into two subfamilies (one with five supertribes), together representing 58 tribes. This includes five recently described or re-established tribes, including Arabidopsideae, a monogeneric tribe accommodating Arabidopsis without any close relatives. With a worldwide community of thousands of researchers working on Brassicaceae and its diverse members, our new genus-level family phylogeny will be an indispensable tool for studies on biodiversity and plant biology.
dc.description.sponsorshipGerman Research Foundation (DFG) [MU1137/17-1, KO2302/23-2]; Czech Science Foundation [21-03909S, 21-06839S]; Calleva Foundation; CONICYT PAI Subvenciin, la Instalaciin, en La Academia Convocatoria [77190055]; Extreme Science and Engineering Discovery Environment (XSEDE) - National Science Foundation [ACI-1548562]; We thank Helen Barnes, Roxali Bijmoer, Manuel Benito Crespo, Ivalu Cacho, Cyrille Chatelain, Suzanne Cubey, Gabi Droege, Catherine Gallagher, Mary Korver, Alicia Marticorena, Pina Milne, Hamid Moazzeni, Peter Sack, Yasaman Salmaki, Marnel Scherrenberg, Jan Wieringa, Hasan Y & imath;ld & imath;r & imath;m, and Shahin Zarre for assistance in sampling herbarium material. Elza Duijm, Izai Sabino Ki- kuchi, and Marina Ventayol Garcia kindly provided fruitful discussions on optimization of laboratory techniques. David Alejandro Duchene Garzon provided valuable ideas on calculations of clocklikeness of gene trees. Museum national d'Histoire naturelle kindly provided V.R.I. access to the collections in the framework of the RECOLNAT national Research Infrastructure. This work was supported by the German Research Foundation (DFG; grant numbers MU1137/17-1 to K.M. and KO2302/23-2 to M.A.K.) , the Czech Science Foundation (grant numbers 21-03909S to M.A.L. and 21-06839S to T.M.) , grants from the Calleva Foundation to the Plant and Fungal Trees of Life project at the Royal Botanic Gardens, Kew, and CONICYT PAI Subvenciin, la Instalaciin, en La Academia Convocatoria 2019 (grant number n degrees 77190055 to O.T.-N.) . This work used the Extreme Science and Engineering Discovery Environment (XSEDE, project BIO210079) , which is supported by the National Science Foundation (grant number ACI-1548562) .
dc.language.isoen
dc.publisherCELL PRESS
dc.relation.ispartofCURRENT BIOLOGY
dc.subjectARABIDOPSIS
dc.subjectBiochemistry & Molecular Biology
dc.subjectBIOGEOGRAPHY
dc.subjectBiology
dc.subjectCell Biology
dc.subjectDIPLOIDIZATION
dc.subjectDIVERSIFICATION
dc.subjectEVOLUTION
dc.subjectLife Sciences & Biomedicine - Other Topics
dc.subjectMOLECULAR SYSTEMATICS
dc.subjectMULTIPLE SEQUENCE ALIGNMENT
dc.subjectPENALIZED LIKELIHOOD
dc.subjectPLANT
dc.subjectTRANSITION
dc.titleGlobal Brassicaceae phylogeny based on filtering of 1,000-gene dataset
dc.typejournal article
dc.identifier.doi10.1016/j.cub.2023.08.026
dc.identifier.isiISI:001098689800001
dc.description.volume33
dc.description.issue19
dc.description.startpage4052+
dc.contributor.orcidhttps://orcid.org/0000-0002-1693-6829
dc.contributor.orcidhttps://orcid.org/0000-0001-8258-0472
dc.contributor.orcidhttps://orcid.org/0000-0002-6176-1669
dc.contributor.orcidhttps://orcid.org/0000-0002-5001-0149
dc.contributor.researcheridA-4924-2011
dc.contributor.researcheridABD-9839-2021
dc.contributor.researcheridB-8482-2011
dc.identifier.eissn1879-0445
dc.publisher.place50 HAMPSHIRE ST, FLOOR 5, CAMBRIDGE, MA 02139 USA
dcterms.isPartOf.abbreviationCurr. Biol.
dcterms.oaStatushybrid
local.import.remainsaffiliations : University Osnabruck; Naturalis Biodiversity Center; Ruprecht Karls University Heidelberg; Missouri Botanical Gardens; New Mexico State University; University of Antwerp; University of California System; University of California Los Angeles; James Cook University; Royal Botanic Gardens, Kew; Altai State University; Ruprecht Karls University Heidelberg; Masaryk University Brno; Universidad de Concepcion; Hacettepe University; Museum National d'Histoire Naturelle (MNHN); Sorbonne Universite; Universite PSL; Ecole Pratique des Hautes Etudes (EPHE); Duke University; Indiana University System; Indiana University Bloomington; Wageningen University & Research; Uppsala University; University of Zagreb; Slovak Academy of Sciences; Delft University of Technology; Colorado State University; HudsonAlpha Institute for Biotechnology; KU Leuven; Harvard University; Swiss Federal Institutes of Technology Domain; ETH Zurich; La Trobe University; Landcare Research - New Zealand; Leiden University - Excl LUMC; Leiden University
local.import.remainsweb-of-science-index : Science Citation Index Expanded (SCI-EXPANDED)
crisitem.author.deptFB 05 - Biologie/Chemie-
crisitem.author.deptFB 05 - Biologie/Chemie-
crisitem.author.deptidfb05-
crisitem.author.deptidfb05-
crisitem.author.orcid0000-0002-8449-1593-
crisitem.author.parentorgUniversität Osnabrück-
crisitem.author.parentorgUniversität Osnabrück-
crisitem.author.netidNeBa468-
crisitem.author.netidMuKl919-
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