TY - JOUR

T1 - Current Methods for Recombination Detection in Bacteria

AU - Shikov, Anton E.

AU - Malovichko, Yury V.

AU - Nizhnikov, Anton A.

AU - Antonets, Kirill S.

PY - 2022/6/1

Y1 - 2022/6/1

N2 - The role of genetic exchanges, i.e., homologous recombination (HR) and horizontal gene transfer (HGT), in bacteria cannot be overestimated for it is a pivotal mechanism leading to their evolution and adaptation, thus, tracking the signs of recombination and HGT events is importance both for fundamental and applied science. To date, dozens of bioinformatics tools for revealing recombination signals are available, however, their pros and cons as well as the spectra of solvable tasks have not yet been systematically reviewed. Moreover, there are two major groups of soft-ware. One aims to infer evidence of HR, while the other only deals with horizontal gene transfer (HGT). However, despite seemingly different goals, all the methods use similar algorithmic ap-proaches, and the processes are interconnected in terms of genomic evolution influencing each other. In this review, we propose a classification of novel instruments for both HR and HGT detection based on the genomic consequences of recombination. In this context, we summarize available methodologies paying particular attention to the type of traceable events for which a certain program has been designed.

AB - The role of genetic exchanges, i.e., homologous recombination (HR) and horizontal gene transfer (HGT), in bacteria cannot be overestimated for it is a pivotal mechanism leading to their evolution and adaptation, thus, tracking the signs of recombination and HGT events is importance both for fundamental and applied science. To date, dozens of bioinformatics tools for revealing recombination signals are available, however, their pros and cons as well as the spectra of solvable tasks have not yet been systematically reviewed. Moreover, there are two major groups of soft-ware. One aims to infer evidence of HR, while the other only deals with horizontal gene transfer (HGT). However, despite seemingly different goals, all the methods use similar algorithmic ap-proaches, and the processes are interconnected in terms of genomic evolution influencing each other. In this review, we propose a classification of novel instruments for both HR and HGT detection based on the genomic consequences of recombination. In this context, we summarize available methodologies paying particular attention to the type of traceable events for which a certain program has been designed.

KW - HGT

KW - HGT detection

KW - homologous recombination

KW - horizontal gene transfer

KW - HR

KW - phylogenetic methods

KW - recombination detection

KW - synteny

UR - http://www.scopus.com/inward/record.url?scp=85131186361&partnerID=8YFLogxK

U2 - 10.3390/ijms23116257

DO - 10.3390/ijms23116257

M3 - Review article

C2 - 35682936

AN - SCOPUS:85131186361

VL - 23

JO - International Journal of Molecular Sciences

JF - International Journal of Molecular Sciences

SN - 1422-0067

IS - 11

M1 - 6257

ER -