Functional monocentricity with holocentric characteristics and chromosome-specific centromeres in a stick insect

Centromeres are essential for chromosome segregation in eukaryotes, yet their specification is surprisingly diverse among species, and can involve major transitions such as those from localized to chromosome-wide centromeres between monocentric and holocentric species. How this diversity evolves remains elusive. We discovered within-cell variation in the recruitment of the major centromere protein CenH3, reminiscent of variation typically observed among species. While CenH3-containing nucleosomes are distributed in a monocentric fashion on autosomes and bind tandem repeat sequences specific to individual or groups of chromosomes, they show a longitudinal distribution and broad intergenic binding on the X chromosome, which partially recapitulates phenotypes known from holocentric species. Despite this variable CenH3 distribution among chromosomes, all chromosomes are functionally monocentric, marking the first instance of a monocentric species with chromosome-wide CenH3 deposition. Toget..., , , # Centromere sequence identification in *Timema douglasi*

This repository contains the codes used for analysing centromere sequences in the \"Functional monocentricity with holocentric characteristics and chromosome-specific centromeres in a stick insect\" article.

Input data files for executing the codes are available upon request.

## Documentation

script_chip_tdi_paper_final.sh describes the general pipeline to analyse the centromere sequences in *T. douglasi*.

The separated folders include the different scripts used in the overall pipeline:

### TE\_annotation

script_transposable_element_annotation.Rmd: annotates transposable elements in the *T. douglasi* genome assembly.

### TR annotation and minimal rotations

script_tandem-repeat_annotation.sh: annotates tandem repeat sequences in the *T. douglasi* genome assembly.

script_minimal_rotation_parse.pl: orders every repeated motif sequence alphabetically.

### kmer\_approach

config_xla_merge_final_SE_v9_yf_genome10.2.yaml: confi...