Data from: Targeted capture of complete coding regions across divergent species
Data files
Jan 31, 2018 version files 3.10 MB
-
Supplementary File 2 - Probe Design and Sequences.zip
2.46 MB
-
Supplementary File 3 - Assembly and Analysis Pipelines and Scripts.zip
23.87 KB
-
Supplementary File 4 - Anolis Reference.fas
257.79 KB
-
Supplementary File 5 - Snake Reference.fas
202.07 KB
-
Supplementary File 6 - Gekko Reference.fas
150.61 KB
Feb 20, 2017 version files 3.10 MB
-
Supplementary File 2 - Probe Design and Sequences.zip
2.46 MB
-
Supplementary File 3 - Assembly and Analysis Pipelines and Scripts.zip
27.89 KB
-
Supplementary File 4 - Anolis Reference.fas
257.79 KB
-
Supplementary File 5 - Snake Reference.fas
202.07 KB
-
Supplementary File 6 - Gekko Reference.fas
150.61 KB
Abstract
Despite continued advances in sequencing technologies, there is a need for methods that can efficiently sequence large numbers of genes from diverse species. One approach to accomplish this is targeted capture (hybrid enrichment). While these methods are well established for genome resequencing projects, cross-species capture strategies are still being developed and generally focus on the capture of conserved regions, rather than complete coding regions from specific genes of interest. The resulting data is thus useful for phylogenetic studies, but the wealth of comparative data that could be used for evolutionary and functional studies is lost. Here we design and implement a targeted capture method that enables recovery of complete coding regions across broad taxonomic scales. Capture probes were designed from multiple reference species and extensively tiled in order to facilitate cross-species capture. Using novel bioinformatics pipelines we were able to recover nearly all of the targeted genes with high completeness from species that were up to 200 myr divergent. Increased probe diversity and tiling for a subset of genes had a large positive effect on both recovery and completeness. The resulting data produced an accurate species tree, but importantly this same data can also be applied to studies of molecular evolution and function that will allow researchers to ask larger questions in broader phylogenetic contexts. Our method demonstrates the utility of cross-species approaches for the capture of full length coding sequences, and will substantially improve the ability for researchers to conduct large-scale comparative studies of molecular evolution and function.