| 项目编号 | PRJCA001420 | ||||||||||||||||
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| 项目标题 | ALLHiC: assembly of allele-aware, chromosomal scale autopolyploid genomes based on Hi-C data | ||||||||||||||||
| 涉及领域 | Genomics | ||||||||||||||||
| 数据类型 | High throughput chromosome conformation capture | ||||||||||||||||
| 物种名称 |
Oryza sativa Japonica Group
Saccharum spontaneum Oryza sativa Indica Group |
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| 描述信息 | 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. | ||||||||||||||||
| 样品范围 | Multispecies | ||||||||||||||||
| 发布日期 | 2019-05-31 | ||||||||||||||||
| 项目资金来源 |
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| 提交者 | Jing Lin (lolyemily@163.com) | ||||||||||||||||
| 提交单位 | Fujian Agriculture and Forestry University cs, Chinese Academy of Sciences | ||||||||||||||||
| 提交日期 | 2019-05-07 |