Detection of Homologous Recombination Events in Bacterial Genomes

Abstract

We study the detection of mutations, sequencing errors, and homologous recombination events (HREs) in a set of closely related microbial genomes. We base the model on single nucleotide polymorphisms (SNPs) and break the genomes into blocks to handle the rearrangement problem. Then we apply a dynamic programming algorithm to model whether changes within each block are likely a result of mutations, sequencing errors, or HREs. Results from simulation experiments show that we can detect 31%–61% of HREs and the precision of our detection is about 48%–90% depending on the rates of mutation and missing data. The HREfinder software for predicting HREs in a set of whole genomes is available as open source (http://sourceforge.net/projects/hrefinder/).

Current Methods for Recombination Detection in Bacteria

“…ClonalFrameML [ 73 ], Gubbins [ 44 ], and RDP4/5 [ 66 , 67 ] manage to detect recent HR events in moderately divergent sequences, while fastGEAR [ 10 ] is suitable for digging ancestral and recent recombination events in sequences with high divergence. If highly accurate detection of true recombination events is needed, ptACR [ 40 ] and HREfinder [ 99 ] seem to be useful, while, at the same time, they lack sensitivity. Similar to HR, RecentHGT [ 96 ] shows a lower false-positive rate being appropriately utilized to uncover recent transfers in similar sequences, whereas HGT-Finder [ 91 ] and HGTector [ 93 ] are tuned to trace events in distant genomes.…”

“…Similar to compatibility approaches, substitution distribution methods have regained attention due to their high speed as compared with phylogenetic approaches. HREfinder is a dynamic algorithm that divides the genome into blocks where each polymorphism is estimated to result from mutation, homologous recombination, or sequencing error [ 99 ]. The stepped validation guarantees obtaining events with high probability as tested in a Xanthomonas oryzae evolution study [ 100 ].…”

“…The stepped validation guarantees obtaining events with high probability as tested in a Xanthomonas oryzae evolution study [ 100 ]. The sensitivity of HREfinder continuously grows with sequence diversity, while at the same time, a false-positive rate is coupled with it [ 99 ]. Hence, HREfinder just like ptACR, is suitable when dealing with moderately divergent sequences.…”

“…Hence, HREfinder just like ptACR, is suitable when dealing with moderately divergent sequences. Within the optimal diversion range, HREfinder detects mostly true events, however, it also tends to miss a lot of them because of detection thresholds [ 99 ].…”

Phylogenetic Networks: A Review of Methods to Display Evolutionary History

“…Homologous recombination [69,70] and viral reassortment [71] are two processes that involve homologous parts of a genome breaking apart and re-arranging themselves. This usually occurs within a species, or between closely related species.…”