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

Genomics, Proteomics & Bioinformatics (Feb 2022)

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

Affiliations

Bo Wang: MOE Key Laboratory for Intelligent Networks & Network Security, Faculty of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an 710049, China
Xiaofei Yang: School of Computer Science and Technology, Faculty of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an 710049, China; Corresponding authors.
Yanyan Jia: MOE Key Laboratory for Intelligent Networks & Network Security, Faculty of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an 710049, China
Yu Xu: School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, China
Peng Jia: 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
Ningxin Dang: 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
Songbo Wang: 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
Tun Xu: 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
Xixi Zhao: Genome Institute, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China
Shenghan Gao: 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
Quanbin Dong: Genome Institute, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China
Kai Ye: 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; Corresponding authors.

Journal volume & issue: Vol. 20, no. 1
pp. 4 – 13

Abstract

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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.

Published in Genomics, Proteomics & Bioinformatics

ISSN: 1672-0229 (Print); 2210-3244 (Online)
Publisher: Oxford University Press
Country of publisher: United Kingdom
LCC subjects: Science: Biology (General)
Website: https://academic.oup.com/gpb

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