HiCAT: a tool for automatic annotation of centromere structure

Genome biology, vol. 24, pp. 58

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.

Authors 6

1. Shenghan Gao

   Xi'an Jiaotong University

   Affiliation as printed

   MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China

   School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China

2. Xiaofei Yang corresponding

   First Affiliated Hospital of Xi'an Jiaotong University · Xi'an Jiaotong University

   Affiliation as printed

   Genome Institute, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China. xfyang@xjtu.edu.cn

   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

   School of Computer Science and Technology, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China. xfyang@xjtu.edu.cn

   MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China

3. Hongtao Guo

   Xi'an Jiaotong University

   Affiliation as printed

   School of Computer Science and Technology, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China

4. Xixi Zhao

   First Affiliated Hospital of Xi'an Jiaotong University

   Affiliation as printed

   Genome Institute, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China

5. Bo Wang

   Xi'an Jiaotong University

   Affiliation as printed

   MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China

   School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China

6. Kai Ye corresponding Aachen Faculty of Science, Leiden University

   Leiden University · First Affiliated Hospital of Xi'an Jiaotong University · Xi'an Jiaotong University

   Affiliation as printed

   Faculty of Science, Leiden University, Leiden, The Netherlands. kaiye@xjtu.edu.cn

   Genome Institute, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China. kaiye@xjtu.edu.cn

   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

   School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China. kaiye@xjtu.edu.cn

   School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China. kaiye@xjtu.edu.cn

   MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China