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...着丝粒（Centromeres）是真核生物（eukaryotes）染色体分离（chromosome segregation）过程中的必需结构，但其在不同物种间的特化模式却呈现出惊人的多样性，甚至会发生重大转型：例如单着丝粒（monocentric）与全着丝粒（holocentric）物种之间，着丝粒的定位模式可从局部化转变为染色体全域分布。这类多样性的演化机制至今仍未被阐明。 我们在研究中发现，主要着丝粒蛋白CenH3的招募过程存在细胞内异质性，这与物种间常见的变异特征高度相似。含CenH3的核小体（nucleosomes）在常染色体上以单着丝粒模式分布，并结合特定染色体或染色体组的特异性串联重复序列（tandem repeat sequences）；而在X染色体（X chromosome）上，这类核小体却呈现纵向分布且广泛结合基因间区域，这部分重现了全着丝粒物种中已知的表型特征。尽管不同染色体间的CenH3分布存在上述差异，但所有染色体均表现为功能上单着丝粒，这是首个被报道的、存在染色体全域CenH3沉积的单着丝粒物种。[原文此处存在内容截断，后续未完整显示] # 道格拉斯竹节虫（*Timema douglasi*）着丝粒序列鉴定 本仓库包含发表于论文《竹节虫兼具全着丝粒特征与染色体特异性着丝粒的功能单着丝粒特性》（*Functional monocentricity with holocentric characteristics and chromosome-specific centromeres in a stick insect*）中，用于分析着丝粒序列的代码。 运行代码所需的输入数据文件可按需申请获取。 ## 文档说明 `script_chip_tdi_paper_final.sh` 描述了分析道格拉斯竹节虫（*T. douglasi*）基因组着丝粒序列的整体分析流程。 各独立子文件夹包含了整体流程中使用的细分脚本： ### 转座元件注释（TE_annotation） `script_transposable_element_annotation.Rmd`：用于注释道格拉斯竹节虫基因组组装结果中的转座元件（transposable elements）。 ### 串联重复序列注释与最小旋转分析（TR annotation and minimal rotations） `script_tandem-repeat_annotation.sh`：用于注释道格拉斯竹节虫基因组组装结果中的串联重复序列。 `script_minimal_rotation_parse.pl`：将所有重复基序序列按字母顺序排序。 ### k-mer分析方法（kmer_approach） `config_xla_merge_final_SE_v9_yf_genome10.2.yaml`：配置[原文此处内容未完整显示]