Improving the genome assembly of rabbits with long-read sequencing

Yiqin Bai; Weili Lin; Jie Xu; Jun Song; Dongshan Yang; Y Eugene Chen; Lin Li; Yixue Li; Zhen Wang; Jifeng Zhang

doi:10.1016/j.ygeno.2021.05.031

Improving the genome assembly of rabbits with long-read sequencing

Genomics. 2021 Sep;113(5):3216-3223. doi: 10.1016/j.ygeno.2021.05.031. Epub 2021 May 27.

Authors

Yiqin Bai¹, Weili Lin², Jie Xu³, Jun Song³, Dongshan Yang³, Y Eugene Chen³, Lin Li⁴, Yixue Li⁵, Zhen Wang⁶, Jifeng Zhang⁷

Affiliations

¹ State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China.
² Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
³ Center for Advanced Models for Translational Sciences and Therapeutics, University of Michigan Medical Center, Ann Arbor, MI, USA.
⁴ State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China; School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.
⁵ Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China; School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China; Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China. Electronic address: yxli@sibs.ac.cn.
⁶ Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China. Electronic address: zwang01@sibs.ac.cn.
⁷ Center for Advanced Models for Translational Sciences and Therapeutics, University of Michigan Medical Center, Ann Arbor, MI, USA. Electronic address: jifengz@umich.edu.

PMID: 34051323
DOI: 10.1016/j.ygeno.2021.05.031

Abstract

The European rabbit (Oryctolagus cuniculus) is important as a biomedical model given its unique features in immunity and metabolism. The current reference genome OryCun2.0 established with whole-genome shotgun sequencing was quite fragmented and had not been updated for ten years. In this work, we provided a new rabbit genome assembly UM_NZW_1.0 to improve OryCun2.0 by leveraging the contig lengths based on long-read sequencing and a wealth of available Illumina paired-end sequence data. UM_NZW_1.0 showed a remarkable increase of continuity compared with OryCun2.0, with 5 times longer contig N50 and approximately 75% gaps closed. Many of the closed gaps were overlapped with protein-coding genes or transcriptional features, resulting in an enhancement of gene annotations. In particular, UM_NZW_1.0 presented a more complete landscape of the MHC region and the IGH locus, therefore provided a valuable resource for future researches on rabbits.

Keywords: Gap closing; Long-read sequencing; Rabbit genomes; Reference assembly.

Publication types

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

MeSH terms

Animals
High-Throughput Nucleotide Sequencing*
Molecular Sequence Annotation
Rabbits
Sequence Analysis, DNA
Whole Genome Sequencing