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首页> 美国卫生研究院文献>DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes >Multiple hybrid de novo genome assembly of finger millet an orphan allotetraploid crop
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Multiple hybrid de novo genome assembly of finger millet an orphan allotetraploid crop

机译：孤小异源四倍体作物小米的多重杂交从头基因组装配

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Finger millet (Eleusine coracana (L.) Gaertn) is an important crop for food security because of its tolerance to drought, which is expected to be exacerbated by global climate changes. Nevertheless, it is often classified as an orphan/underutilized crop because of the paucity of scientific attention. Among several small millets, finger millet is considered as an excellent source of essential nutrient elements, such as iron and zinc; hence, it has potential as an alternate coarse cereal. However, high-quality genome sequence data of finger millet are currently not available. One of the major problems encountered in the genome assembly of this species was its polyploidy, which hampers genome assembly compared with a diploid genome. To overcome this problem, we sequenced its genome using diverse technologies with sufficient coverage and assembled it via a novel multiple hybrid assembly workflow that combines next-generation with single-molecule sequencing, followed by whole-genome optical mapping using the Bionano Irys® system. The total number of scaffolds was 1,897 with an N50 length >2.6 Mb and detection of 96% of the universal single-copy orthologs. The majority of the homeologs were assembled separately. This indicates that the proposed workflow is applicable to the assembly of other allotetraploid genomes.
机译：手指小米（Eleusine coracana（L.）Gaertn）是粮食安全的重要作物，因为它对干旱具有耐受性，预计全球气候变化会加剧干旱。然而，由于缺乏科学关注，它经常被归类为孤儿/未充分利用的作物。在几个小米中，手指小米被认为是必需营养元素（如铁和锌）的极好来源。因此，它有可能作为替代粗粮。但是，目前尚无法获得小米的高质量基因组序列数据。该物种的基因组组装中遇到的主要问题之一是其多倍性，与二倍体基因组相比，它阻碍了基因组组装。为了解决这个问题，我们使用了覆盖范围广泛的多种技术对它的基因组进行了测序，并通过新颖的多重杂交组装工作流程将其组装，该工作流程将下一代与单分子测序相结合，然后使用BionanoIrys®系统进行全基因组光学定位。支架总数为1897，N50长度> 2.6 Mb，可检测到96％的通用单拷贝直系同源物。大多数同源物是分开组装的。这表明所提出的工作流程适用于其他异源四倍体基因组的组装。

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