On the Distribution of Synteny Blocks Under a Neutral Model of Genome Dynamics

Sagi Snir, Yuri Wolf, Shelly Brezner, Eugene Koonin, Mike Steel

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review


Prokaryotes are a rich source of versatile molecular functional systems that typically consist of multiple, interacting proteins. The study of such systems leads to fundamental biological discoveries, for example, understanding of the origins of innate and adaptive immunity in animals and also provides for the development of various biotechnology applications. The discovery of functional systems by microbial genome mining is facilitated by the fact that functionally coupled genes in bacterial and archaeal genomes often cluster in operons that are conserved across long evolutionary spans. However, accurate differentiation of operons from spurious gene clusters by genome comparison is a non-trivial task that depends on an underlying model of neutral genomes evolution. Here, we investigate the predictions of a gene clustering based on a recently developed stochastic model of genome rearrangement arising from horizontal gene transfer between evolving species along a phylogenetic tree. We focus on synteny blocks, that is, strings of genes conserved across genomes and derive analytic expressions for the expected number of synteny blocks of a given size (or of maximal size) in terms of the temporal separation between the genomes and the rates of evolutionary events. Our setting is similar to the heavily studied stick breaking problem family, but its discrete structure and the stochastic nature of the underlying process suggest a simple, independent model. We demonstrate the predictive power of this model both in simulations and on real data from the ATGC data base.

Original languageEnglish
Title of host publicationComparative Genomics - 21st International Conference, RECOMB-CG 2024, Proceedings
EditorsCeline Scornavacca, Maribel Hernández-Rosales
PublisherSpringer Science and Business Media Deutschland GmbH
Number of pages16
ISBN (Print)9783031580710
StatePublished - 2024
Event21st RECOMB International Workshop on Comparative Genomics, RECOMB-CG 2024 - Boston, United States
Duration: 27 Apr 202428 Apr 2024

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume14616 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349


Conference21st RECOMB International Workshop on Comparative Genomics, RECOMB-CG 2024
Country/TerritoryUnited States

Bibliographical note

Publisher Copyright:
© The Author(s), under exclusive license to Springer Nature Switzerland AG 2024.


  • Bacterial evolution
  • lateral gene transfer
  • stochastic processes
  • synteny blocks
  • the stick breaking model

ASJC Scopus subject areas

  • Theoretical Computer Science
  • General Computer Science


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