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

Nature Plants
Xingtan ZhangHaibao Tang

Abstract

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 o...Continue Reading

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Citations

May 24, 2020·Molecular Ecology Resources·Jianping DuanXiangwei Wu
Aug 14, 2020·Molecular Ecology Resources·Jianmei YinPeitong Zhang
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Methods Mentioned

BETA
genotyping
Hi-C
PCR
whole-genome shotgun sequencing

Software Mentioned

HiRise
mathop
SALSA
Pro
Hi
BLAST
Juicer
ALLHiC
HiC
Linux

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