{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Vatanparast M"],"funding":["National Science Foundation"],"pagination":["e1036"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC5895186"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["6(3)"],"pubmed_abstract":["<h4>Premise of the study</h4>The 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.<h4>Methods</h4>Using 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.<h4>Results</h4>Hyb-Seq discovered loci with the longest mean length. MarkerMiner discovered the most conserved loci with the least fla"],"journal":["Applications in plant sciences"],"pubmed_title":["Targeting legume loci: A comparison of three methods for target enrichment bait design in Leguminosae phylogenomics."],"pmcid":["PMC5895186"],"funding_grant_id":["DEB‐1352217","DEB‐0948800"],"pubmed_authors":["Vatanparast M","Egan AN","Doyle JJ","Powell A"],"additional_accession":[]},"is_claimable":false,"name":"Targeting legume loci: A comparison of three methods for target enrichment bait design in Leguminosae phylogenomics.","description":"<h4>Premise of the study</h4>The 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.<h4>Methods</h4>Using 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.<h4>Results</h4>Hyb-Seq discovered loci with the longest mean length. MarkerMiner discovered the most conserved loci with the least fla","dates":{"release":"2018-01-01T00:00:00Z","publication":"2018 Mar","modification":"2026-05-04T05:19:45.236Z","creation":"2019-03-26T23:36:05Z"},"accession":"S-EPMC5895186","cross_references":{"pubmed":["29732266"],"doi":["10.1002/aps3.1036"]}}