Resolving Recalcitrant Clades in the Pantropical Ochnaceae: Insights From Comparative Phylogenomics of Plastome and Nuclear Genomic Data Derived From Targeted Sequencing

Abstract

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.

Keywords: Malpighiales; hybrid enrichment; off-target reads; phylogenetic conflict; phylogenomics; plastome; taxon sampling.

FIGURE 1

Recovery of plastomes from targeted enrichment. (A) Amount of the plastome recovered (i.e., number of nucleotides) across Ochnaceae in relation to the reference plastome (based on dataset 2). (B) Percentage of the reference plastome recovered in relation to the number of sequence reads that map to the reference (based on dataset 2).

FIGURE 2

Overview of the phylogenetic relationships of the major clades of Ochnaceae based on RAxML analysis of plastome dataset 2 and 213 accessions. Bootstrap support is given for all backbone nodes including all major clades (black circle = 100% BS). The classification follows Schneider et al. (2014). Ochninae is by far the most species-rich clade comprising about two thirds of the family’s species and six genera. Quiin., Quiinoideae; Medu., Medusagynoideae.

FIGURE 3

Co-phylogeny plot of plastome and nuclear phylogenies of Ochnaceae from targeted enrichment. The plastome tree is based on dataset 2, the nuclear phylogeny is taken from Schneider et al. (2020). Conflict between trees is indicated by branch swaps as illustrated by the interconnecting lines that link identical plant accessions. Lack of interconnecting lines indicates taxa not present in the complementary tree. Bootstrap support is grouped by range and shown as black or open circles at the internal nodes (diamond as a third symbol for BS <50% in Ouratea only). Colored circles at tips indicate major clades. A to D refer to clades of Ochna retrieved in Schneider et al. (2020). A dashed line links the topology of the relationships of the subfamilies of Ochnaceae with the topology of Ochnoideae.