Accession PRJCA001420
Title ALLHiC: assembly of allele-aware, chromosomal scale autopolyploid genomes based on Hi-C data
Relevance Genomics
Data Types High throughput chromosome conformation capture
Organisms Saccharum spontaneum
Oryza sativa Indica Group
Oryza sativa Japonica Group
Description Construction of chromosome-level assembly is a vital step to achieve the goal of'Platinum'genome, but it remains a great challenge to 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 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; https://github.com/tangerzhang/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 reveals that ALLHiC has significant effect to phase allelic contigs and improves ordering and orientation when compared to other mainstream Hi-C assemblers. We applied ALLHiC on an auto-tetraploid and an auto-octoploid sugarcane 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 alleles. Haplotype chromosome level assembly of allopolyploid and heterozygous diploid genomes can be achieved using ALLHiC, overcoming obstacles in assembling complex genomes.
Sample scope Multispecies
Release date 2019-05-31
Grants
Agency program Grant ID Grant title
National Key Research and Development Program of China 2016YFD0100305
National Natural Science Foundation of China 31701874
Fuzhou Science and Technology projects 2017N33
Submitter Jing    Lin  (lolyemily@163.com)
Organization Fujian Agriculture and Forestry University cs, Chinese Academy of Sciences
Submission date 2019-05-07

Project Data

Resource name Description
BioSample (6) -
SAMC069969 Hi-C of rice Niponbare: leaves
SAMC069968 Hi-C of rice 93-11: leaves
SAMC069967 Hi-C of sugarcane: leaves
SAMC069966 Hi-C of sugarcane: leaves
SAMC069965 Hi-C of sugarcane: leaves
SAMC069964 Hi-C of sugarcane: leaves
GSA (1) -
CRA001597 ALLHiC: assembly of allele-aware, chromosomal scale autopolyploid genomes based on Hi-C data
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