Phylogenomics from Whole Genome Sequences Using aTRAM.

Area of Science:

• Genomics
• Bioinformatics
• Evolutionary Biology

Background:

• Novel sequencing technologies generate vast datasets for phylogenetics.
• Current phylogenomic methods often use genome reduction, limiting data utility.
• Whole genome sequencing is feasible for smaller genomes, but computational challenges exist.

Purpose of the Study:

• To demonstrate the utility of automated Target Restricted Assembly Method (aTRAM) for phylogenomics.
• To develop a pipeline for extracting and analyzing exon sequences from aTRAM assemblies.
• To assess the performance of aTRAM across varying coverages and taxonomic distances.

Main Methods:

• Used aTRAM to assemble 1107 single-copy ortholog genes from whole genome sequencing of sucking lice (Anoplura) and out-groups.
• Developed a pipeline to extract exon sequences, align them with inferred amino acids, and perform phylogenetic analyses.
• Tested aTRAM's assembly limits using 100 genes from diverse taxa at different coverages.

Main Results:

• Both concatenated and coalescent-based phylogenetic analyses yielded identical tree topologies, consistent with prior research.
• aTRAM successfully assembled 80-90% of contigs at coverages as low as 5-10x.
• The method proved effective in generating phylogenomic datasets from raw genome sequencing reads.

Conclusions:

• The demonstrated approach is effective for developing phylogenomic datasets from raw genome sequencing data.
• aTRAM facilitates the mining of whole genome sequencing data for phylogenomic and other applications.
• As sequencing costs decrease, aTRAM will become increasingly valuable for diverse organisms.