Target sequence capture in orchids: Developing a kit to sequence hundreds of single‐copy loci

Abstract

Targeted enrichment methods allow for the extraction of hundreds of low-copy loci, which is useful for phylogenomic inference under the multispecies coalescent model (Lemmon et al., 2012;Heyduk et al., 2016). However, the bait sets required for target enrichment can be costly to produce and require genomic resources including reference genomes or transcriptome sequences (Hale et al., 2020). Universal bait sets, such as Angiosperms353 (Johnson et al., 2019), can ameliorate these challenges by enabling the generation of target gene sequences across a broad phylogenetic scale. Although this is an attractive option for some phylogenetic investigations, a "one-size-fits-all" approach may not be sufficient for disentangling phylogenetic relationships at lower taxonomic levels in many groups. Rapid species radiations, low sequence divergence, and gene and genome duplications (all rampant within the angiosperm clade) are likely to reduce the efficacy of using a universal bait set for species-level phylogeny reconstruction. Rather, it is likely that lineage-specific bait sets will be necessary to obtain sufficient variation to address questions at lower phylogenetic scales.In this study, we address this issue by generating a single-copy gene bait set for the hyperdiverse Orchidaceae, the second-largest

Orchid Phylotranscriptomics: The Prospects of Repurposing Multi-Tissue Transcriptomes for Phylogenetic Analysis and Beyond

“…in the ML and ASTRAL species tree ( Supplementary Figure 2 and Text for further information). This point of uncertainty is consistent with findings in other recent broad-scale nuclear orchid phylogenomic studies ( Eserman et al, 2021 ; Pérez-Escobar et al, 2021 ). This now well characterized disparity is postulated to reflect widespread incomplete lineage sorting of nuclear genes during the rapid radiations at the early stages of the evolution of the Vandeae, Epidendreae, and Cymbideae tribes ( Eserman et al, 2021 ).…”

“…The outcomes of our phylotranscriptomic analysis ( Figure 1 ) revealed robust and largely consistent findings with other phylogenomics datasets ( Givnish et al, 2015 ; Kim et al, 2020 ; Liu et al, 2020 ; Eserman et al, 2021 ; Pérez-Escobar et al, 2021 ; Serna-Sánchez et al, 2021 ). As expected, the backbone phylogeny of the Orchidaceae revealed five distinct clades: Apostasioideae (4 species) was placed sister to the other four subfamilies, followed by Vanilloideae (4 species), and by Cypripedioideae (7 species) which is placed sister to Orchidoideae (30 species) and Epidendroideae (24 species).…”

“…Putative single-copy genes are already being used to design target enrichment probe sets capable of spanning broad evolutionary scales. Two universal probe sets that provide orchid coverage are: Angiosperms353 ( Johnson et al, 2019 ) and Orchidaceae963 ( Eserman et al, 2021 ). For example, a recent phylogenomic analysis of 75 species representing 69 genera, 16 tribes, and 24 subtribes used the Angiosperms353 universal probe set to target 294 low-copy nuclear genes ( Pérez-Escobar et al, 2021 ).…”

“…Past and emerging transcriptome datasets can also be mined for the Angiosperms353 ( Johnson et al, 2019 ) and Orchidaceae963 single-copy genes ( Eserman et al, 2021 ) for downstream phylotranscriptomic analysis. This approach bypasses the need for the arduous ortholog inference that often scales poorly with large datasets spanning hundreds of species.…”

Reconstructing Dipsacales phylogeny using Angiosperms353: issues and insights

“…Transcriptomes have also become popular tools for building broad phylogenies (e.g., Wang et al, 2019 ; One Thousand Plant Transcriptomes Initiative, 2019 ); while combinable, orthology inference from transcriptomes is less straightforward than using highly conserved low‐ or single‐copy targets like the Angiosperms353 set. Finally, probe sets merging universal and lineage‐specific target loci increase combinability across data sets (Jantzen et al, 2020 ; Christe et al, 2021 ; Eserman et al, 2021 ; Ogutcen et al, 2021 ). In direct comparisons between these sets, lineage‐specific loci may not provide additional resolving power in the case of rapid radiations, as in Cyperaceae (Larridon et al, 2020 ), but can still be effective in clades of comparable size and age to Viburnum and Lonicera (e.g., Buddleja , Chau et al, 2018 ; Memecylon and Tibouchina , Jantzen et al, 2020 ).…”