Chromosome-scale assemblies of plant genomes using nanopore long reads and optical maps

First author: Caroline Belser; Affiliations: Université Paris-Saclay (巴黎-萨克雷大学): Evry, France

Corresponding author: Jean-Marc Aury

Plant genomes are often characterized by a high level of repetitiveness and polyploid nature. Consequently, creating genome assemblies for plant genomes is challenging. The introduction of short-read technologies 10 years ago substantially increased the number of available plant genomes. Generally, these assemblies are incomplete and fragmented, and only a few are at the chromosome scale. Recently, Pacific Biosciences and Oxford Nanopore sequencing technologies were commercialized that can sequence long DNA fragments (kilobases to megabase) and, using efficient algorithms, provide high-quality assemblies in terms of contiguity and completeness of repetitive regions. However, even though genome assemblies based on long reads exhibit high contig N50s (>1 Mb), these methods are still insufficient to decipher genome organization at the chromosome level. Here, we describe a strategy based on long reads (MinION or PromethION sequencers) and optical maps (Saphyr system) that can produce chromosome-level assemblies and demonstrate applicability by generating high-quality genome sequences for two new dicotyledon morphotypes, Brassica rapa Z1 (yellow sarson) and Brassica oleracea HDEM (broccoli), and one new monocotyledon, Musa schizocarpa (banana). All three assemblies show contig N50s of >5 Mb and contain scaffolds that represent entire chromosomes or chromosome arms.

植物基因组通常含重复序列和多倍化水平较高。因此，植物基因组组装是具有挑战性的。自从10年前短read测序技术出现以来，越来越多的植物基因组被报道。然而，这些基因组并非完整的，是片段化的，仅仅有少数几个植物获得了染色体水平的组装结果。近来，PacBio和Oxford Nanopore测序技术获得了商业化，这两项技术可以对长read进行测序，数千bp到数兆的长度不等，而且通过高效的算法，研究人员可以获得在重复区域连续性和完整性都表现完好的高质量基因组组装结果。然而，即使基于长read获得的基因组组装在contig水平的参数表现较好（N50 长度大于1 Mb），这些方法仍然不能将组装好的基因组序列拼装到染色体水平。本文，作者基于长read技术和光学图谱开发了一套策略用以将基因组组装到染色体水平，并且通过两个双子叶植物大白菜和芸苔及一个单子叶植物芭蕉属物种用作示例。这三个新组装的植物基因组contig N50长度均达到了5Mb，并且scaffold达到了染色体或染色体臂水平。

doi: https://doi.org/10.1038/s41477-018-0289-4

Journal: Nature Plants

First Published: 02 November, 2018

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