Evolutionary Dynamics of G-Quadruplexes in Human and Other Great Ape Telomere-to-Telomere Genomes

This repository contains all the code and data generated for the paper.

Saswat K. Mohanty, Francesca Chiaromonte, Kateryna D. Makova*

Department of Biology, Penn State University, University Park, PA 16802
Department of Statistics, Penn State University, University Park, PA 16802
*Correspondence to Kateryna D. Makova (kdm16@psu.edu)

Directory Structure

This repository contains the following directories:

• src: Includes all Python and Bash scripts necessary for analyzing data, generating datasets, or creating plots as required for this manuscript.

• jupyterNotebooks: Contains Python-based Jupyter notebooks for analyzing data and generating plots or datasets relevant to the manuscript.

• datasets: Hosts all datasets used or generated during the analyses described in this manuscript.

• plots: Stores all plots generated as part of the manuscript’s analyses.

Some key dependencies required for the analyses in this manuscript are:

• mapsea: A general-purpose repository containing scripts for mapping short elements stored in .BED files (e.g., G-quadruplex intervals) to .MAF (alignment) files.

• g4Discovery: A general-purpose repository with scripts for predicting and annotating G-quadruplexes (G4s) in genome sequences, combining pqsfinder and G4Hunter.

Predicted G4s with Evolutionary Information

For downloading pG4s across the six great ape species—Homo sapiens, Pan paniscus, Pan troglodytes, Gorilla gorilla, Pongo abelii, and Pongo pygmaeus—navigate to the datasets/pG4s/ directory. Each species subdirectory contains a file named: wholeGenome.pG4s.withSharingInfo.bed. This file uses a custom .BED format that includes additional evolutionary and sequence information. The columns in this file are as follows:

- CHR: chromosome
- START: pG4 start
- END: pG4 end
- ID: #unique 10-digit ID assigned to this pG4, other species sharing this pG4 will have same ID
- PQSSCORE: pqsfinder score
- STRAND: strand in which pG4 is present
- G4HUNTERSCORE: G4Hunter score
- SHARED: shared pG4(S), aligned (ASS) or unaligned species-specific (USS) pG4
- WITH: with which species it is shared 
	{B: Bonobo, C: Chimpanzee, H: Human, G: Gorilla, 
	Bo: Bornean Orangutan, So: Sumatran Orangutan}
- DUPLICATED: If it is shared with the same chromosome in the same species (>1 indicates duplicated)
- SEQ: pG4 sequence in positive-strand
- MOTIF: standard (S) or bulged (B) pG4 motif

Using the file as a standard BED file: To convert the file into a standard 6-column .BED format (removing evolutionary and sequence details), use the following command:

cut -f 1-6 wholeGenome.pG4s.withSharingInfo.bed > wholeGenome.pG4s.bed

Citation

If you use any of this data or tool in your research, please cite the following paper:

Mohanty, S. K., Chiaromonte, F., & Makova, K. (2024). "Evolutionary Dynamics of G-Quadruplexes in Human and Other Great Ape Telomere-to-Telomere Genomes. bioRxiv, 2024-11. doi: 10.1101/2024.11.05.621973