BREC: an R package/Shiny app for automatically identifying heterochromatin boundaries and estimating local recombination rates along chromosomes

BMC Bioinformatics

Yasmine Mansour¹  Anna-Sophie Fiston-Lavier²  Annie Chateau³ 

[1] Genomics Department, Institute of Evolution Science of Montpellier (ISEM), Montpellier, France;Informatics Department, Laboratory of Computer Science, Robotics and Microelectronics of Montpellier (LIRMM), Montpellier, France;Genomics Department, Institute of Evolution Science of Montpellier (ISEM), Montpellier, France;Institut Universitaire de France (IUF), Paris, France;Informatics Department, Laboratory of Computer Science, Robotics and Microelectronics of Montpellier (LIRMM), Montpellier, France;

关键词: Heterochromatin regions;    Centromere position;    Recombination rate;    Non-genome-specific;    Data quality control;    Graphical user interface;   

DOI  :  10.1186/s12859-021-04233-1

来源: Springer

【 摘 要 】

BackgroundMeiotic recombination is a vital biological process playing an essential role in genome's structural and functional dynamics. Genomes exhibit highly various recombination profiles along chromosomes associated with several chromatin states. However, eu-heterochromatin boundaries are not available nor easily provided for non-model organisms, especially for newly sequenced ones. Hence, we miss accurate local recombination rates necessary to address evolutionary questions.ResultsHere, we propose an automated computational tool, based on the Marey maps method, allowing to identify heterochromatin boundaries along chromosomes and estimating local recombination rates. Our method, called BREC (heterochromatin Boundaries and RECombination rate estimates) is non-genome-specific, running even on non-model genomes as long as genetic and physical maps are available. BREC is based on pure statistics and is data-driven, implying that good input data quality remains a strong requirement. Therefore, a data pre-processing module (data quality control and cleaning) is provided. Experiments show that BREC handles different markers' density and distribution issues.ConclusionsBREC's heterochromatin boundaries have been validated with cytological equivalents experimentally generated on the fruit fly Drosophila melanogaster genome, for which BREC returns congruent corresponding values. Also, BREC's recombination rates have been compared with previously reported estimates. Based on the promising results, we believe our tool has the potential to help bring data science into the service of genome biology and evolution. We introduce BREC within an R-package and a Shiny web-based user-friendly application yielding a fast, easy-to-use, and broadly accessible resource. The BREC R-package is available at the GitHub repository https://github.com/GenomeStructureOrganization.

【 授权许可】

CC BY