DOI: 10.5061/dryad.hx3ffbgph
title: Data from: Functional monocentricity with holocentric characteristics and chromosome-specific centromeres in a stick insect

description: 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. Together, our findings illustrate a potential transitional
 state between mono- and holocentricity or towards CenH3-independent
 centromere determination, and help to understand the rapid centromere
 sequence divergence between species.
description: # 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: configuration file for
 the kmer approach snakefile_v9_genomev10PRE_SE.py: python script to
 identify CenH3-enriched k-mer motifs. ### Levenshtein distances
 script_levenshtein_rotations_F-F_inputFiles.py: computes pair-wise
 levenstein distances between motif sequences.
 script_levenshtein_rotations_F-R_inputFiles.py: computes pair-wise
 levenstein distances between motif sequences and their reverse
 complements. ### Rscripts TRF_parsing.R: parses gff3 file obtained from
 tandem repeat annotation (see script_tandem-repeat_annotation.sh)
 Proportion_categories.R: estimates proportion and enrichment of sequence
 categories annotated in the *T. douglasi* genome assembly.
 Enriched_windows.R: selects 10kb windows based on coverage ratio of
 CenH3-ChIP to input Enriched_minimal_rotation_TR_motifs.R: extract and
 duplicates motif sequences with minimal rotations to compute Levenshtein
 distances Levenstein_network.R: builds network of sequence similarities
 among tandem repeat motifs identified in the genome assembly.
 kmer_minimal_rotation_TR_motifs.R: extract and duplicates motif sequences
 identified in the de novo contigs with minimal rotations to compute
 Levenshtein distances. Levenstein_network_contigs.R: builds network of
 sequence similarities among tandem repeat motifs identified in the de novo
 contigs (k-mer approach). Heatmap_TRF-based.R: creates a heatmap with
 hierarchical clustering based on total array length inferred by summing
 Tandem Repeat Finder array lengths per repeat family
 Heatmap_blast-based.R: creates a heatmap with hierarchical clustering
 based on total array length inferred by summing the lengths of sequence
 motif blast hits with 80% sequence similarity and 80% query coverage. ###
 Genome\_assembly Genome assembly pipeline for *T. douglasi*. ###
 Sex\_chr\_ID Scripts to ID the X chromosome in *T. douglasi*. ###
 Gene\_annotation Gene annotation scripts for the *T. douglasi* genome.