This repository contains scripts used in

Aharonoff A, Kim J, Washington A, Ercan S. 2025. Parallel evolution of X chromosome-specific SMC complexes in two nematode lineages. Wittkopp P, editor. Molecular Biology and Evolution:msaf270.

as well as a rescaffolded genome for Pristionchus pacificus (PS312), lifted over annotations for protein coding genes, and detailed collection protocols for each species of worm used in this study.

Update to P. pacificus chromosome scale assembly
We used the genome PRJNA12644 (WBPS16), and rescaffolded using YaHS (version 1.1) with our Hi-C data. YaHS placed pbcontig517 on the left arm of chromosome X (see Figure S4). Via manual curation in Juicebox Assembly Tools, we fixed several misjoins and inversions on chromosomes V and X (see Figure S4). As it stands, we have provided the 6 chromosomes of the rescaffolded and curated genome. For the lifted over annotations, we provide a lift over of the protein coding genes only. We were able to lift all but 8 protein coding genes using the LiftOff (version 1.6.3). The genes that were not lifted over are provided in unmapped_features.txt.

Enter scripts directory for code used in this study
phylogenetic_analysis contains scripts used to generate trees in Figures 1C, S2, S3, and S10 as well as Figures 1B and 1C. RNA-seq contains scripts used for Figures 4, and S11-S14. Hi-C contains scripts for Figures 2, 3 and S4-S9. ChIP-seq contains scripts used for Figures 5, S15-S18.

Detailed protocols for sample collection can be found in the sample_collection directory

This page is a work in progress. If you need something that is not up yet, feel free to contact me at avramiaharonoff@gmail.com.