ezTree: an automated pipeline for identifying phylogenetic marker genes and inferring evolutionary relationships among uncultivated prokaryotic draft genomes

摘要

BackgroundInferring phylogenetic trees for newly recovered genomes from metagenomic samples is very useful in determining the identities of uncultivated microorganisms. Even though 16S ribosomal RNA small subunit genes have been established as “gold standard” markers for inferring phylogenetic trees, they usually cannot be assembled very well in metagenomes due to shared regions among 16S genes. Using single-copy marker genes to build genome trees has become increasingly popular for uncultivated species. Predefined marker gene sets were discovered and have been applied in various genomic studies; however these gene sets might not be adequate for novel, uncultivated, draft, or incomplete genomes. The automatic identification of marker gene sets among a set of genomes with different assembly qualities has thus become a very important task for inferring reliable phylogenetic relationships for microbial populations.