HiCAT: A tool for automatic annotation of centromere structure

bioRxiv (Cold Spring Harbor Laboratory)

Abstract

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 and maximization of tandem repeat coverage to facilitate decoding of centromere architecture. We applied HiCAT to human CHM13-T2T and gapless Arabidopsis thaliana genomes. Our results not only were generally consistent with previous inferences but also greatly improved annotation continuity and revealed additional fine structures, demonstrating HiCAT’s performance and general applicability.

Authors 5

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

   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

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

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

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

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

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

3. 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

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

4. 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

   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

5. 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

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

   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

   School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, Shaanxi, China

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

   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

   School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China