Improving the genome assembly of rabbits with long-read sequencing

2022/10/05 by Bai, Y, Lin, W, Xu, J +7
#Animals #DNA #Gap closing #High-Throughput Nucleotide Sequencing #Long-read sequencing #Molecular Sequence Annotation #Rabbit genomes #Rabbits #Reference assembly #Sequence Analysis #Whole Genome Sequencing

paper · doi:10.7302/6511

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_NZW₁.0 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_NZW₁.0 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_NZW₁.0 presented a more complete landscape of the MHC region and the IGH locus, therefore provided a valuable resource for future researches on rabbits.

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