Abstract
Universal angiosperm enrichment probe sets designed to enrich hundreds of putatively orthologous nuclear single-copy loci are increasingly being applied to infer phylogenetic relationships of different lineages of angiosperms at a range of evolutionary depths. Studies applying such probe sets have focused on testing the universality and performance of the target nuclear loci, but they have not taken advantage of off-target data from other genome compartments generated alongside the nuclear loci. Here we do so to infer phylogenetic relationships in the orchid genus Epidendrum and closely related genera of subtribe Laeliinae. Our aims are to: 1) test the technical viability of applying the plant anchored hybrid enrichment (AHE) method (Angiosperm v.1 probe kit) to our focal group, 2) mine plastid protein coding genes from off-target reads; and 3) evaluate the performance of the target nuclear and off-target plastid loci in resolving and supporting phylogenetic relationships along a range of taxonomical depths. Phylogenetic relationships were inferred from the nuclear data set through coalescent summary and site-based methods, whereas plastid loci were analyzed in a concatenated partitioned matrix under maximum likelihood. The usefulness of target and flanking non-target nuclear regions and plastid loci was assessed through the estimation of their phylogenetic informativeness. Our study successfully applied the plant AHE probe kit to Epidendrum, supporting the universality of this kit in angiosperms. Moreover, it demonstrated the feasibility of mining plastome loci from off-target reads generated with the Angiosperm v.1 probe kit to obtain additional, uniparentally inherited sequence data at no extra sequencing cost. Our analyses detected some strongly supported incongruences between nuclear and plastid data sets at shallow divergences, an indication of potential lineage sorting, hybridization, or introgression events in the group. Lastly, we found that the per site phylogenetic informativeness of the ycf1 plastid gene surpasses that of all other plastid genes and several nuclear loci, making it an excellent candidate for assessing phylogenetic relationships at medium to low taxonomic levels in orchids.
Highlights
Powerful hybrid enrichment strategies (HES), a toolset for selectively capturing genomic regions of interest prior to sequencing (Summerer, 2009; Mamanova et al, 2010; Lemmon and Lemmon, 2013), are increasingly being applied to plant phylogenomics, boosting generation of massive sequence data and, opening exciting new possibilities for plant evolutionary studies
We explore the utility of the plant AHE method to resolve phylogenetic relationships in the orchid genus Epidendrum
Phylogenetic trees were rooted with Pleurothallis cardiothallis of subtribe Pleurothallidinae, because this subtribe was recovered in previous phylogenetic analyzes of Orchidaceae as sister to subtribe Laeliinae (Table 1; Chase et al, 2015)
Summary
Powerful hybrid enrichment strategies (HES), a toolset for selectively capturing genomic regions of interest prior to sequencing (Summerer, 2009; Mamanova et al, 2010; Lemmon and Lemmon, 2013), are increasingly being applied to plant phylogenomics, boosting generation of massive sequence data and, opening exciting new possibilities for plant evolutionary studies. HES applied to angiosperm phylogenomics include an assortment of nuclear-exon and organelle (plastid) enrichment methods targeting a range of taxonomic levels and lineages Some differences among these techniques include 1) how capture probes are designed, e.g., whether they target dozens (de Sousa et al, 2014) to thousands (Mandel et al, 2014; Weitemier et al, 2014) of more or less conserved genomic regions; 2) if the focus is taxon-specific (e.g., Gossypium, Grover et al, 2015; Sabal, Heyduk et al, 2016; Helianthus, Stephens et al, 2015) or has a wider taxonomic scope (e.g., angiosperms, Johnson et al, 2019; Zingiberales, Sass et al, 2016; eudicots, Stull et al, 2013); 3) the targeted genome i.e., nuclear (de Sousa et al, 2014; Mandel et al, 2014; Grover et al, 2015) or plastid (Stull et al, 2013). Off-target plastid reads can potentially be recovered after nuclear enrichment, providing a valuable added source of orthologous, uniparentally inherited sequence data (Weitemier et al, 2014; Stephens et al, 2015; Nikolov et al, 2019) to complement nuclear data
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