High-quality Arabidopsis thaliana Genome Assembly with Nanopore and HiFi Long Reads

Bo Wang; Xiaofei Yang; Yanyan Jia; Yu Xu; Peng Jia; Ningxin Dang; Songbo Wang; Tun Xu; Xixi Zhao; Shenghan Gao; Quanbin Dong; Kai Ye

doi:10.1016/j.gpb.2021.08.003

High-quality Arabidopsis thaliana Genome Assembly with Nanopore and HiFi Long Reads

Genomics Proteomics Bioinformatics. 2022 Feb;20(1):4-13. doi: 10.1016/j.gpb.2021.08.003. Epub 2021 Sep 3.

Authors

Bo Wang¹, Xiaofei Yang², Yanyan Jia¹, Yu Xu³, Peng Jia⁴, Ningxin Dang⁵, Songbo Wang⁴, Tun Xu⁴, Xixi Zhao⁶, Shenghan Gao⁴, Quanbin Dong⁶, Kai Ye⁷

Affiliations

¹ MOE Key Laboratory for Intelligent Networks & Network Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China.
² School of Computer Science and Technology, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China. Electronic address: xfyang@xjtu.edu.cn.
³ School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China.
⁴ MOE Key Laboratory for Intelligent Networks & Network Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China; School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China.
⁵ MOE Key Laboratory for Intelligent Networks & Network Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China; School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China; Genome Institute, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China.
⁶ Genome Institute, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China.
⁷ MOE Key Laboratory for Intelligent Networks & Network Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China; School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China; School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China; Genome Institute, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China. Electronic address: kaiye@xjtu.edu.cn.

Abstract

Arabidopsis thaliana is an important and long-established model species for plant molecular biology, genetics, epigenetics, and genomics. However, the latest version of reference genome still contains a significant number of missing segments. Here, we reported a high-quality and almost complete Col-0 genome assembly with two gaps (named Col-XJTU) by combining the Oxford Nanopore Technologies ultra-long reads, Pacific Biosciences high-fidelity long reads, and Hi-C data. The total genome assembly size is 133,725,193 bp, introducing 14.6 Mb of novel sequences compared to the TAIR10.1 reference genome. All five chromosomes of the Col-XJTU assembly are highly accurate with consensus quality (QV) scores > 60 (ranging from 62 to 68), which are higher than those of the TAIR10.1 reference (ranging from 45 to 52). We completely resolved chromosome (Chr) 3 and Chr5 in a telomere-to-telomere manner. Chr4 was completely resolved except the nucleolar organizing regions, which comprise long repetitive DNA fragments. The Chr1 centromere (CEN1), reportedly around 9 Mb in length, is particularly challenging to assemble due to the presence of tens of thousands of CEN180 satellite repeats. Using the cutting-edge sequencing data and novel computational approaches, we assembled a 3.8-Mb-long CEN1 and a 3.5-Mb-long CEN2. We also investigated the structure and epigenetics of centromeres. Four clusters of CEN180 monomers were detected, and the centromere-specific histone H3-like protein (CENH3) exhibited a strong preference for CEN180 Cluster 3. Moreover, we observed hypomethylation patterns in CENH3-enriched regions. We believe that this high-quality genome assembly, Col-XJTU, would serve as a valuable reference to better understand the global pattern of centromeric polymorphisms, as well as the genetic and epigenetic features in plants.

Keywords: Bacterial artificial chromosome; CENH3; Centromere architecture; Model plant; Telomere-to-telomere.

Publication types

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

MeSH terms

Arabidopsis* / genetics
Arabidopsis* / metabolism
Centromere / genetics
Centromere / metabolism
DNA
Histones / metabolism
Nanopores*
Sequence Analysis, DNA

Substances

Histones
DNA