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

ABSTRACT:

Premise of the study

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.

Methods

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.

Results

Hyb-Seq discovered loci with the longest mean length. MarkerMiner discovered the most conserved loci with the least fla

SUBMITTER: Vatanparast M 

PROVIDER: S-EPMC5895186 | biostudies-literature | 2018 Mar

REPOSITORIES: biostudies-literature