Phased diploid genome assembly with single-molecule real-time sequencing
Phased diploid genome assembly with single-molecule real-time sequencing
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DOI：
10.1038/nmeth.4035
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发表时间：
2016-12-01
期刊：
影响因子：
48
通讯作者：
Schatz, Michael C.
中科院分区：
文献类型：
--
作者：
Chin, Chen-Shan;Peluso, Paul;Schatz, Michael C.
虽然基因组组装项目已经在许多单倍体和近交物种中取得了成功，但非近交或重排杂合基因组的组装仍然是一个重大挑战。为了应对这一挑战，我们引入了开源的RISKCON和RISKCON-Unzip算法（https：//github.com/PacificBiosciences/RISKCON/），将长读段测序数据组装成高度准确、连续和正确定相的二倍体基因组。我们产生新的参考序列的杂合样品，包括F1杂交拟南芥，广泛种植的葡萄属葡萄品种。赤霞珠和珊瑚真菌Clavicorona pyxidata，这些样本挑战了短读组装方法。与交替的短读或长读方法相比，基于DCOM的程序集基本上更加连续和完整。定相二倍体组装使得能够研究同源染色体之间的单倍型结构和杂合性，包括鉴定编码序列内广泛的杂合结构变异。
While genome assembly projects have been successful in many haploid and inbred species, the assembly of noninbred or rearranged heterozygous genomes remains a major challenge. To address this challenge, we introduce the open-source FALCON and FALCON-Unzip algorithms (https://github.com/PacificBiosciences/FALCON/) to assemble long-read sequencing data into highly accurate, contiguous, and correctly phased diploid genomes. We generate new reference sequences for heterozygous samples including an F1 hybrid of Arabidopsis thaliana, the widely cultivated Vitis vinifera cv. Cabernet Sauvignon, and the coral fungus Clavicorona pyxidata, samples that have challenged short-read assembly approaches. The FALCON-based assemblies are substantially more contiguous and complete than alternate short-or long-read approaches. The phased diploid assembly enabled the study of haplotype structure and heterozygosities between homologous chromosomes, including the identification of widespread heterozygous structural variation within coding sequences.