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Resolving recalcitrant clades in the pantropical ochnaceae: insights from comparative phylogenomics of plastome and nuclear genomic data derived from targeted sequencing

  • Plastid DNA sequence data have been traditionally widely used in plant phylogenetics because of the high copy number of plastids, their uniparental inheritance, and the blend of coding and non-coding regions with divergent substitution rates that allow the reconstruction of phylogenetic relationships at different taxonomic ranks. In the present study, we evaluate the utility of the plastome for the reconstruction of phylogenetic relationships in the pantropical plant family Ochnaceae (Malpighiales). We used the off-target sequence read fraction of a targeted sequencing study (targeting nuclear loci only) to recover more than 100 kb of the plastid genome from the majority of the more than 200 species of Ochnaceae and all but two genera using de novo and reference-based assembly strategies. Most of the recalcitrant nodes in the family’s backbone were resolved by our plastome-based phylogenetic inference, corroborating the most recent classification system of Ochnaceae and findings from a phylogenomic study based on nuclear loci. Nonetheless, the phylogenetic relationships within the major clades of tribe Ochnineae, which comprise about two thirds of the family’s species diversity, received mostly low support. Generally, the phylogenetic resolution was lowest at the infrageneric level. Overall there was little phylogenetic conflict compared to a recent analysis of nuclear loci. Effects of taxon sampling were invoked as the most likely reason for some of the few well-supported discords. Our study demonstrates the utility of the off-target fraction of a target enrichment study for assembling near-complete plastid genomes for a large proportion of samples.

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Metadaten
Author:Julio Valentin SchneiderORCiDGND, Juraj PauleORCiDGND, Tanja JungcurtGND, Domingos CardosoORCiD, André Márcio AmorimORCiD, Thomas BerberichORCiD, Georg ZizkaORCiDGND
URN:urn:nbn:de:hebis:30:3-572275
DOI:https://doi.org/10.3389/fpls.2021.638650
ISSN:1664-462X
Parent Title (German):Frontiers in plant science
Publisher:Frontiers Media
Place of publication:Lausanne
Document Type:Article
Language:English
Date of Publication (online):2021/02/04
Date of first Publication:2021/02/04
Publishing Institution:Universitätsbibliothek Johann Christian Senckenberg
Release Date:2021/02/18
Tag:Malpighiales; hybrid enrichment; off-target reads; phylogenetic conflict; phylogenomics; plastome; taxon sampling
Volume:12
Issue:article 63865
Page Number:16
First Page:1
Last Page:16
HeBIS-PPN:477522394
Institutes:Biowissenschaften / Biowissenschaften
Angeschlossene und kooperierende Institutionen / Senckenbergische Naturforschende Gesellschaft
Biowissenschaften / Institut für Ökologie, Evolution und Diversität
Fachübergreifende Einrichtungen / Biodiversität und Klima Forschungszentrum (BiK-F)
Dewey Decimal Classification:5 Naturwissenschaften und Mathematik / 57 Biowissenschaften; Biologie / 570 Biowissenschaften; Biologie
Sammlungen:Universitätspublikationen
Open-Access-Publikationsfonds:Biowissenschaften
Licence (German):License LogoCreative Commons - Namensnennung 4.0