Phylogenomics of the tropical plant family Ochnaceae using targeted enrichment of nuclear genes and 250+ taxa

Abstract

Targeted capture of nuclear genes increasingly contributes to unravelling phylogenetic relationships that hitherto remained unresolved because of limitations of traditional Sanger sequencing. In particular, the study of tropical plant families has been compromised because they often rely on highly degraded DNA obtained from herbarium specimens. One such example is the pantropical Ochnaceae, which comprises 33 genera and approximately 550 species, occurring mostly in savannas and moist tropical forests. Here, we developed a set of baits covering about 660,000 bp from 275 nuclear genes used for the targeted enrichment based on all but one genus and more than 250 species. Using this novel dataset, we resolved the phylogenetic backbone of Ochnaceae, including that of Ochninae, and we established new relationships. Most importantly, our findings highlight that the neotropical and palaeotropical taxa of Sauvagesia form independent clades, requiring the re-erection of formerly separate genera. Ouratea and Ochna (both Ochninae), by far the most species-rich genera and represented by 120 and 41 species, respectively, came out as monophyletic. In contrast, the third-most species-rich genus, Campylospermum, is polyphyletic in two distinct clades. Ouratea, the only neotropical genus of Ochninae, was sister to the five palaeotropical genera of this subtribe. The bait kit developed in this study proved to be particularly useful for unravelling relationships within Ochninae, which includes about two-thirds of the species diversity in the family. Keywords baits; hybrid enrichment; Malpighiales; multispecies coalescent approach; remapping strategies; species tree Supporting Information may be found online in the Supporting Information section at the end of the article.

Joining forces in Ochnaceae phylogenomics: a tale of two targeted sequencing probe kits

“…This result was expected due to the Ochnaceae‐specific kit being developed using a transcriptome of Ochna serrulata , which should essentially share more loci with closely related genera. Although the results suggest there is some taxonomic bias with the Ochnaceae‐specific kit toward Ochna and closely related genera, some more distantly related genera do have moderately high gene recovery, perhaps pertaining to sample quality rather than taxonomic affinity (Schneider et al, 2020). Efficiency of family‐specific probe kits can be enhanced by expanding the genomic resources used in the development of the kit.…”

“…Conflicting evolutionary histories within Ochnaceae in recent studies and persistence of some uncertain relationships even with large taxon sampling and huge amounts of DNA sequence data has stimulated our investigation into the use of different probe kits in resolving recalcitrant clades and how species tree reconstruction methods and the impact of missing data influence phylogenetic resolution. Adding more genes such as those obtained with the Angiosperms353 kit (i.e., added to the family‐specific data set of Schneider et al [2020]) is likely to improve phylogenetic resolution, although there is evidence that increasing data can also result in diminishing returns (Hosner et al, 2016). In Ochnaceae, the novel Angiosperms353 data set was primarily valuable in corroborating relationships obtained by other studies.…”

“…Raw sequence data for the Ochnaceae-specific probe kit are available from GenBank SRA under the Bioproject number PRJNA602196: http://www.ncbi.nlm.nih.gov/biopr oject/ 602196 (Schneider et al, 2020). Raw sequence data for the universal Angiosperms353 probe kit are available from European Nucleotide Archive under the umbrella project number PRJEB35285: https://www.ebi.ac.uk/ena/ brows er/view/PRJEB 35285.…”

“…In contrast, Bissiengou (2014) resolved Brackenridgea as sister to Ochna, with the Brackenridgea-Ochna clade sister to Campylospermum, Ouratea Aubl., and Rhabdophyllum. Schneider et al (2020) used a custom bait kit that was designed to resolve relationships in Ochnaceae based on a sole ingroup transcriptome from Ochneae. Although most of the phylogenetic backbone of the family was resolved in that study, the bias toward Ochneae in terms of the number of successfully captured genes might have been one reason for the few remaining unclear relationships that still require additional data.…”

“…Relationships within Ochnaceae have been the focus of recent Sanger sequencing (Bissiengou, 2014; Schneider et al, 2014) and phylogenomic studies (Schneider et al, 2020). Overall, these studies confirmed the monophyly of the wider family and presented a new infrafamilial classification.…”