HiCAT: a tool for automatic annotation of centromere structure

Shenghan Gao; Xiaofei Yang; Hongtao Guo; Xixi Zhao; Bo Wang; Kai Ye

doi:10.1186/s13059-023-02900-5

HiCAT: a tool for automatic annotation of centromere structure

Genome Biol. 2023 Mar 28;24(1):58. doi: 10.1186/s13059-023-02900-5.

Authors

Shenghan Gao^#^{1

2}, Xiaofei Yang^#^{3

4

5}, Hongtao Guo⁶, Xixi Zhao⁷, Bo Wang^{1

2}, Kai Ye^{8

9

10

11

12}

Affiliations

¹ School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China.
² MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China.
³ MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China. xfyang@xjtu.edu.cn.
⁴ School of Computer Science and Technology, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China. xfyang@xjtu.edu.cn.
⁵ Genome Institute, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China. xfyang@xjtu.edu.cn.
⁶ School of Computer Science and Technology, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China.
⁷ Genome Institute, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China.
⁸ School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China. kaiye@xjtu.edu.cn.
⁹ MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China. kaiye@xjtu.edu.cn.
¹⁰ Genome Institute, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China. kaiye@xjtu.edu.cn.
¹¹ School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China. kaiye@xjtu.edu.cn.
¹² Faculty of Science, Leiden University, Leiden, The Netherlands. kaiye@xjtu.edu.cn.

^# Contributed equally.

Abstract

Significant improvements in long-read sequencing technologies have unlocked complex genomic areas, such as centromeres, in the genome and introduced the centromere annotation problem. Currently, centromeres are annotated in a semi-manual way. Here, we propose HiCAT, a generalizable automatic centromere annotation tool, based on hierarchical tandem repeat mining to facilitate decoding of centromere architecture. We apply HiCAT to simulated datasets, human CHM13-T2T and gapless Arabidopsis thaliana genomes. Our results are generally consistent with previous inferences but also greatly improve annotation continuity and reveal additional fine structures, demonstrating HiCAT's performance and general applicability.

Keywords: Centromere annotation; Gapless genomes; HiCAT; Long-read sequencing technologies.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Arabidopsis* / genetics
Centromere*
Genomics / methods
Humans
Tandem Repeat Sequences