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Assembly of chromosome-scale contigs by efficiently resolving repetitive sequences with long reads

Author

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  • Huilong Du

    (State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Chengzhi Liang

    (State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

Abstract

The abundant repetitive sequences in complex eukaryotic genomes cause fragmented assemblies, which lose value as reference genomes, often due to incomplete gene sequences and unanchored or mispositioned contigs on chromosomes. Here we report a genome assembly method HERA, which resolves repeats efficiently by constructing a connection graph from an overlap graph. We test HERA on the genomes of rice, maize, human, and Tartary buckwheat with single-molecule sequencing and mapping data. HERA correctly assembles most of the previously unassembled regions, resulting in dramatically improved, highly contiguous genome assemblies with newly assembled gene sequences. For example, the maize contig N50 size reaches 61.2 Mb and the Tartary buckwheat genome comprises only 20 contigs. HERA can also be used to fill gaps and fix errors in reference genomes. The application of HERA will greatly improve the quality of new or existing assemblies of complex genomes.

Suggested Citation

  • Huilong Du & Chengzhi Liang, 2019. "Assembly of chromosome-scale contigs by efficiently resolving repetitive sequences with long reads," Nature Communications, Nature, vol. 10(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-019-13355-3
    DOI: 10.1038/s41467-019-13355-3
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    Cited by:

    1. Jinquan Chao & Shaohua Wu & Minjing Shi & Xia Xu & Qiang Gao & Huilong Du & Bin Gao & Dong Guo & Shuguang Yang & Shixin Zhang & Yan Li & Xiuli Fan & Chunyan Hai & Liquan Kou & Jiao Zhang & Zhiwei Wang, 2023. "Genomic insight into domestication of rubber tree," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    2. Gabriel E. Rech & Santiago Radío & Sara Guirao-Rico & Laura Aguilera & Vivien Horvath & Llewellyn Green & Hannah Lindstadt & Véronique Jamilloux & Hadi Quesneville & Josefa González, 2022. "Population-scale long-read sequencing uncovers transposable elements associated with gene expression variation and adaptive signatures in Drosophila," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    3. Jiantao Guan & Jintao Zhang & Dan Gong & Zhengquan Zhang & Yang Yu & Gaoling Luo & Prakit Somta & Zheng Hu & Suhua Wang & Xingxing Yuan & Yaowen Zhang & Yanlan Wang & Yanhua Chen & Kularb Laosatit & X, 2022. "Genomic analyses of rice bean landraces reveal adaptation and yield related loci to accelerate breeding," Nature Communications, Nature, vol. 13(1), pages 1-16, December.

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