BYSY_Replication

Laurent Lacroix (laurent.lacroix@inserm.fr)

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About this repository

To see this text in browser, go there https://lacroixlaurent.github.io/BYSY_Replication/, otherwise this repository can be viewed in RStudio.
This repository contains the scripts used for all the analysis in the one-chromosome yeast replication manuscript Pellet et al., 2025.

Raw data are available from ENA repository under accession number PRJEB89792.

This repository documents the bioinformatics workflows used to compare the replication program of a yeast strain with all 16 chromosomes fused (strain SY14, Shao et al) to the standard 16-chromosome reference strain BY4742.
Genome sequences for SY14 and BY4742 have been downloaded from public database using the accession number from the original SY14 strain publication PRJNA429985.

NFS and nanoTiming experiments have been conducted as in Theulot et al, 2022 and Theulot et al, 2024 respectively (see BYSY publication for more details). NFS and nanoTiming data have been processed with matching reference genome. Please note that these reference genomes do not contain the sequence of the plasmid used to enable BrdU usage (pBL-hsvTKCO-hENT1CO).

The procedure are explained in separate notebooks corresponding to the following processes:

1. Data transposition

2. Genomes annotations

3. Generating RFD profiles

4. Defining active replication origins in SY and/or BY strain

5. Importing bibliographic data

6. Computing OEM

7. Testing RFD data

8. Testing Initiation data

9. Testing nanoTiming data

10. Generating master table

11. Generating and testing speed map

The scripts starting with BYSY_FiguresArticle are the one used to generate the figures.
The file Helper_function.R contains accessory R functions used during the analysis.

• the Data_raw folder contains the raw data used to generate the figures and analysis.
• the Data folder contains the data produced by the analysis scripts.
• the BigWig folder contain the genomic track generated during the analysis.
• the Genome_annotations folder contains the genomic annotation tracks generated during the analysis.
• the FigArticle folder contains the figures generated during the analysis. The figures with mod in their name have been manually modified with Inkscape to adjust ARS name positions for readability.
• the BigFiles folder should contain BigWig, Data_raw and Data files too big for github and that have to be downloaded from the Zenodo repository https://doi.org/10.5281/zenodo.15462552 and unzip into the directory BigFiles. This directory has to be created upon cloning this repository.

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Code to generate the session info:
library(sessioninfo)
session_info() %>% capture.output(file=”BYSY_Replication_processing_session_info.txt”)

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