A two‐tier bioinformatic pipeline to develop probes for target capture of nuclear loci with applications in Melastomataceae

Abstract

Premise Putatively single‐copy nuclear (SCN) loci, which are identified using genomic resources of closely related species, are ideal for phylogenomic inference. However, suitable genomic resources are not available for many clades, including Melastomataceae. We introduce a versatile approach to identify SCN loci for clades with few genomic resources and use it to develop probes for target enrichment in the distantly related Memecylon and Tibouchina (Melastomataceae). Methods We present a two‐tiered pipeline. First, we identified putatively SCN loci using MarkerMiner and transcriptomes from distantly related species in Melastomataceae. Published loci and genes of functional significance were then added (384 total loci). Second, using HybPiper, we retrieved 689 homologous template sequences for these loci using genome‐skimming data from within the focal clades. Results We sequenced 193 loci common to Memecylon and Tibouchina. Probes designed from 56 template sequences successfully targeted sequences in both clades. Probes designed from genome‐skimming data within a focal clade were more successful than probes designed from other sources. Discussion Our pipeline successfully identified and targeted SCN loci in Memecylon and Tibouchina, enabling phylogenomic studies in both clades and potentially across Melastomataceae. This pipeline could be easily applied to other clades with few genomic resources.

A target enrichment probe set for resolving the flagellate land plant tree of life

“…Our strategy was to develop a “universal” probe set that covers the majority of these groups, and the GoFlag 451 probe set and the analysis pipeline provide a core set of validated tools accessible to all scientists. However, some evolutionary questions in the flagellate land plants may require more loci or a more specific probe set (e.g., Jantzen et al, 2020). While the GoFlag 451 probe set facilitates target enrichment projects in any flagellate land plant group, a probe set designed for a particular lineage could easily have more specific probes that cover either more loci, loci of special interest (e.g., Medina et al, 2019; Montes et al, 2019), or loci with higher substitution rates (de La Harpe et al, 2019).…”

Enabling evolutionary studies at multiple scales in Apocynaceae through Hyb‐Seq

“…MarkerMiner yielded loci that were conserved enough to be targeted across the whole family, and very few of the loci turned out not to be single copy, as has been observed in other studies that compared MarkerMiner‐based designs to those generated by other pipelines (Kadlec et al, 2017; Vatanparast et al, 2018). Additionally, several studies that have compared the success of taxon‐specific and universal probe sets have found that taxon‐specific designs yield the largest number of most useful loci (Kadlec et al, 2017; Chau et al, 2018; Jantzen et al, 2020), although this has not been universally observed (Larridon et al, 2020). When feasible, a combination of lineage‐specific and universal probe sets, such as the Angiosperms353 probe set (Johnson et al, 2019), can yield the largest pool of nuclear loci appropriate for phylogenomic studies (Jantzen et al, 2020).…”

“…Additionally, several studies that have compared the success of taxon‐specific and universal probe sets have found that taxon‐specific designs yield the largest number of most useful loci (Kadlec et al, 2017; Chau et al, 2018; Jantzen et al, 2020), although this has not been universally observed (Larridon et al, 2020). When feasible, a combination of lineage‐specific and universal probe sets, such as the Angiosperms353 probe set (Johnson et al, 2019), can yield the largest pool of nuclear loci appropriate for phylogenomic studies (Jantzen et al, 2020).…”

“…The alignments are useful for targeted enrichment probe design and other downstream applications (Chamala et al, 2015). This approach has been successful in aiding development of targeted sequencing probes in multiple plant lineages (Villaverde et al, 2018; Morais et al, 2019; Jantzen et al, 2020).…”

Capturing single-copy nuclear genes, organellar genomes, and nuclear ribosomal DNA from deep genome skimming data for plant phylogenetics: A case study in Vitaceae

“…Generally, a stringent selection criterion will facilitate the downstream gene assembly and phylogenetic analyses using Geneious Prime (Kearse et al, 2012) and/or the script GoldFinder developed by Vargas et al (2019). Although universal single-copy nuclear gene sets have been developed, such as the Angiosperm-353 generic baits set (Johnson et al, 2019), several studies have compared the success of taxon-specific and universal SCNs and have found that taxon-specific single-copy nuclear loci dataset yield a higher number of phylogenetically informative loci (Kadlec et al, 2017;Chau et al, 2018;Jantzen et al, 2020;Straub et al, 2020). When feasible, we recommend a combination of lineage-specific and universal SCNs sets to yield the largest pool of nuclear loci appropriate for phylogenomic studies (also see Jantzen et al, 2020).…”