Data from: Phylogenomics from whole genome sequences using aTRAM

• Main Authors: Allen, Julie M., Boyd, Bret, Nguyen, Nam-Phuong, Vachaspati, Pranjal, Warnow, Tandy, Huang, Daisie I., Grady, Patrick G. S., Bell, Kayce C., Cronk, Quentin C.B., Mugisha, Lawrence, Pittendrigh, Barry R., Soledad Leonardi, M., Reed, David L., Johnson, Kevin P.
• Format: Dataset
• Language: unknown
• Published: 2016
• Subjects: Bureelia antiqua; Osborniella crotophagae; Pedicinus badii; gene assembly; Haematopinus eurysternus; Degeeriella rufa; Pthirus gorillae; Neohaematopinus pacificus; Genome sequencing; Linognathus spicatus; Pthirus pubis; Pediculus humanus; Pediculus schaeffi; Proechinopthirus fluctus; aTRAM; Hoplopleura arboricola; Stimulopalpus japonicus; present day; Antarctopthirus microchir; Bothriometopus macrocnemus; Holocene; Antarc*
• Online Access: https://zenodo.org/record/4992900; https://doi.org/10.5061/dryad.26j38

Novel sequencing technologies are rapidly expanding the size of data sets that can be applied to phylogenetic studies. Currently the most commonly used phylogenomic approaches involve some form of genome reduction. While these approaches make assembling phylogenomic data sets more economical for organisms with large genomes, they reduce the genomic coverage and thereby the long-term utility of the data. Currently, for organisms with moderate to small genomes (<1000 Mbp) it is feasible to sequence the entire genome at modest coverage (10−30×). Computational challenges for handling these large data sets can be alleviated by assembling targeted reads, rather than assembling the entire genome, to produce a phylogenomic data matrix. Here we demonstrate the use of automated Target Restricted Assembly Method (aTRAM) to assemble 1107 single-copy ortholog genes from whole genome sequencing of sucking lice (Anoplura) and out-groups. We developed a pipeline to extract exon sequences from the aTRAM assemblies by annotating them with respect to the original target protein. We aligned these protein sequences with the inferred amino acids and then performed phylogenetic analyses on both the concatenated matrix of genes and on each gene separately in a coalescent analysis. Finally, we tested the limits of successful assembly in aTRAM by assembling 100 genes from close- to distantly related taxa at high to low levels of coverage. Concatenated alignment and treeAlignment and phylogenetic tree of the concatenated 1,101 exon DNA alignment from 15 louse taxa. Genes were assembled from raw genomic DNA with aTRAM and exons extracted and stitched together. Third codon position was removed due to base composition bias, and tree build in RAxML.Dataset_1.zipIndividual Gene Trees and AlignmentsAll 1,101 gene trees and alignments for the 15 taxon dataset. Each gene was aligned using PASTA and UPP for fragmentary sequences. Each gene tree was built using ASTRAL.Dataset_2.zipSupplementaryTableDNA extraction, and quality clean up for each ...