Assembling the genome of the African wild rice Oryza longistaminata by exploiting synteny in closely related Oryza species

First author: Stefan Reuscher; Affiliations: Nagoya University (名古屋大学): Nagoya, Japan

Corresponding author: Motoyuki Ashikari

The African wild rice species Oryza longistaminata has several beneficial traits compared to cultivated rice species, such as resistance to biotic stresses, clonal propagation via rhizomes (根茎), and increased biomass production. To facilitate breeding efforts and functional genomics studies, we de-novoassembled a high-quality, haploid-phased genome. Here, we present our assembly, with a total length of 351 Mb, of which 92.2% was anchored onto 12 chromosomes. We detected 34,389 genes and 38.1% of the genome consisted of repetitive content. We validated our assembly by a comparative linkage analysis and by examining well-characterized gene families. This genome assembly will be a useful resource to exploit beneficial alleles found in O. longistaminata. Our results also show that it is possible to generate a high-quality, functionally complete rice genome assembly from moderate SMRT read coverage by exploiting synteny in a closely related Oryza species.

非洲长雄野生稻相比于栽培种水稻具有一些有益的性状，比如说对于生物胁迫的抗性、可直接通过根茎直接无性繁殖、生物量较大等。为加速水稻的育种及功能基因组学的研究，作者从头组装了一个高质量的、单倍体长雄野生稻基因组。本文报道的长雄野生稻基因组总长度351 Mb，且92.2%的序列能够锚定到12个染色体上。作者预测到了34,389个基因，基因组的38.1%为重复序列。作者进一步通过比较连锁分析和基因家族分析验证了基因组组装的质量。该基因组将有助于挖掘长雄野生稻中的有益等位基因。本文的结果显示通过与已报道的近缘水稻物种的共线性比对，利用适当深度的SMRT测序数据即可获得高质量、注释良好的水稻基因组。

p.s. 2015年中国科学院昆明动物所王文（现为西北工业大学生态与环境保护研究中心研究员）研究组就已经在Molecular Plant上以letter的形式报道了长雄野生稻的基因组（https://www.cell.com/molecular-plant/fulltext/S1674-2052(15)00352-4）。

doi: https://doi.org/10.1038/s42003-018-0171-y

Journal: Communications Biology

First Published: 05 October, 2018

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