Targeting legume loci: A comparison of three methods for target enrichment bait design in Leguminosae phylogenomics

Abstract

Premise of the StudyThe development of pipelines for locus discovery has spurred the use of target enrichment for plant phylogenomics. However, few studies have compared pipelines from locus discovery and bait design, through validation, to tree inference. We compared three methods within Leguminosae (Fabaceae) and present a workflow for future efforts.MethodsUsing 30 transcriptomes, we compared Hyb‐Seq, MarkerMiner, and the Yang and Smith (Y&S) pipelines for locus discovery, validated 7501 baits targeting 507 loci across 25 genera via Illumina sequencing, and inferred gene and species trees via concatenation‐ and coalescent‐based methods.ResultsHyb‐Seq discovered loci with the longest mean length. MarkerMiner discovered the most conserved loci with the least flagged as paralogous. Y&S offered the most parsimony‐informative sites and putative orthologs. Target recovery averaged 93% across taxa. We optimized our targeted locus set based on a workflow designed to minimize paralog/ortholog conflation and thus present 423 loci for legume phylogenomics.ConclusionsMethods differed across criteria important for phylogenetic marker development. We recommend Hyb‐Seq as a method that may be useful for most phylogenomic projects. Our targeted locus set is a resource for future, community‐driven efforts to reconstruct the legume tree of life.

A customized nuclear target enrichment approach for developing a phylogenomic baseline for Dioscorea yams (Dioscoreaceae)

“…In our study, the average target length of the Dioscorea‐ specific kit was 1699 bp. This is comparable to 1362 bp for a Heuchera L. kit (Folk et al., ), 1667 bp for a Leguminosae kit (Vatanparast et al., ), and ~1645 bp for a Euphorbia L. kit (Villaverde et al., ). However, average target length was shorter (820 bp) for Buddleja L.‐specific locus sets compared to three different non‐taxon‐specific locus sets (1267 bp; Chau et al., ).…”

“…The MarkerMiner pipeline we used for LSCN gene selection has previously been shown to select more conserved loci compared to two other commonly used methods, at least for LSCN gene discovery in Leguminosae (Vatanparast et al., ). However, our data set contained sufficient parsimony informative sites (average 24%) to strongly resolve most species‐level relationships.…”

“…The MarkerMiner pipeline we implemented here recovered fewer loci that were flagged as potential paralogy instances by HybPiper, compared to two other methods used for LSCN gene identification in Leguminosae (Vatanparast et al., ). We detected potential paralogy, either through HybPiper warnings or by visual inspection of all generated gene alignments and trees, in 27 (10.4%) of the 260 genes for which baits were designed; orthologs were teased apart in most cases after inspection of gene trees.…”

Resolving the backbone of the Brassicaceae phylogeny for investigating trait diversity

“…Targeting single‐copy nuclear genes provides a promising way to generate abundant phylogenetically informative data while minimizing potential issues arising from complex gene lineage evolution (Lemmon & Lemmon, ). This approach has been used extensively to resolve difficult phylogenetic relationships in plants, including sunflowers (Mandel et al ., ), milkweeds (Weitemier et al ., ), sages (Fragoso‐Martínez et al ., ), legumes (Vatanparast et al ., ), Dutchman's pipes (Wanke et al ., ) and breadfruit (Johnson et al ., ), and is widely used in metazoan phylogenomics (e.g. Faircloth et al ., ; Prum et al ., ; Alfaro et al ., ; Espeland et al ., ).…”

Methods for exploring the plant tree of life

“…() and Vatanparast et al. () provide reviews of different methods for sequence capture, focusing on marker selection. Chau et al.…”