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Assembly of allele-aware, chromosomal-scale autopolyploid genomes based on Hi-C data


Construction of chromosome-level assembly is a vital step in achieving the goal of a ‘Platinum’ genome, but it remains a major challenge to assemble and anchor sequences to chromosomes in autopolyploid or highly heterozygous genomes. High-throughput chromosome conformation capture (Hi-C) technology serves as a robust tool to dramatically advance chromosome scaffolding; however, existing approaches are mostly designed for diploid genomes and often with the aim of reconstructing a haploid representation, thereby having limited power to reconstruct chromosomes for autopolyploid genomes. We developed a novel algorithm (ALLHiC) that is capable of building allele-aware, chromosomal-scale assembly for autopolyploid genomes using Hi-C paired-end reads with innovative ‘prune’ and ‘optimize’ steps. Application on simulated data showed that ALLHiC can phase allelic contigs and substantially improve ordering and orientation when compared to other mainstream Hi-C assemblers. We applied ALLHiC on an autotetraploid and an autooctoploid sugar-cane genome and successfully constructed the phased chromosomal-level assemblies, revealing allelic variations present in these two genomes. The ALLHiC pipeline enables de novo chromosome-level assembly of autopolyploid genomes, separating each allele. Haplotype chromosome-level assembly of allopolyploid and heterozygous diploid genomes can be achieved using ALLHiC, overcoming obstacles in assembling complex genomes.

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Fig. 1: Overview of major steps in the ALLHiC algorithm.
Fig. 2: Description of Hi-C scaffolding problem in the autopolyploid genome and application of the pruning approach for haplotype phasing.
Fig. 3: Network graph of Hi-C links based on a synthetic genome by combing the genome sequences of rice subspecies O. sativa spp. japonica (green dots) and O. sativa spp. indica (orange dots).
Fig. 4: Validation of partitioning on five simulations derived from the rice Nipponbare genome.
Fig. 5: Comparison of four Hi-C scaffolding algorithms, ALLHiC, LACHESIS, SALSA2 and 3D-DNA.
Fig. 6: Hi-C scaffolding of the autotetraploid sugar cane genome S. spontaneum AP85-441.

Data availability

The Hi-C data (O. sativa L. japonica cv. Nipponbare, O. sativa L. indica cv. 93-11 and S. spontaneum L. AP85-441) generated in this study have been deposited in the GSA database ( under BioProject No. PRJCA001420 and accession No. CRA001597. Other published datasets used for ALLHiC testing are listed in Supplementary Table 1.


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This work was supported by the National Key Research and Development Program of China (No. 2016YFD0100305 to H.T.), a National Natural Science Foundation of China grant (No. 31701874 to X.Z.) and the Fuzhou Science and Technology project (No. 2017-N-33 to X.Z). We also thank the Fujian provincial government for a Fujian ‘100 Talent Plan’ award (to H.T.).

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Authors and Affiliations



H.T. and X.Z. designed and implemented the ALLHiC software. X.Z., H.T., S.Z. and Q.Z. tested the software on various datasets. X.Z., H.T. and R.M. wrote the manuscript. All authors read and approved the final manuscript.

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Correspondence to Haibao Tang.

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The authors declare no competing interests.

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Peer review information: Nature Plants thanks Jean Marc Aury, Jay Ghurye and Yves van de Peer for their contribution to the peer review of this work.

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Supplementary Information

Supplementary Notes 1–5, Supplementary Tables 1–6 and Supplementary Figs. 1–36.

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Zhang, X., Zhang, S., Zhao, Q. et al. Assembly of allele-aware, chromosomal-scale autopolyploid genomes based on Hi-C data. Nat. Plants 5, 833–845 (2019).

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