Data from: Phylogenomics from whole genome sequences using aTRAM

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.