Automating the Search for Lateral Gene Transfer

Abstract

Most genes have attained their observed distribution among ge omes by transmission from parent to offspring through time. In prokaryotes (bacteria and archa ea), however, some genes are where they are as the result of transfer from an unrelated lineage. To el ucidate the biological origins and functional consequences of lateral gene transfer (LGT), we have constructed an automated computational pipeline to recognise protein families among prokaryotic g enomes, generate high-quality multiple sequence alignments of orthologs, infer statistically sound phylogenetic trees, and find topologically incongruent subtrees (prima facie instances of LGT). This pip eline requires that we automate workflows, design and optimize algorithms, mobilise high-performanc e computing resources, and efficiently manage federated data. I will summarise results from the automa ted comparison of 422971 proteins in 22437 families across 144 sequenced prokaryotic genomes, i nclud ng the nature and extent of LGT among these lineages, major donors and recipients, the bioc hemi al pathways and physiological functions most affected, and implications for the role of LGT in e volution of biochemical pathways.