African wild rice Oryza longistaminata, one of the eight AA‐ genome species in the genus Oryza, possesses highly valued traits, such as the rhizomatousness for perennial rice breeding, strong tolerance to biotic and abiotic stresses, and high biomass production on poor soils. To obtain the high‐quality reference genome for O. longistaminata we employed a hybrid assembly approach through incorporating Illumina and PacBio sequencing datasets. The final genome assembly comprised only 107 scaffolds and was approximately ∼363.5 Mb, representing ∼92.7% of the estimated African wild rice genome (∼392 Mb). The N50 lengths of the assembled contigs and scaffolds were ∼46.49 Kb and ∼6.83 Mb, indicating ∼3.72‐fold and ∼18.8‐fold improvement in length compared to the earlier released assembly (∼12.5 Kb and 364 Kb, respectively). Aided with Hi‐C data and syntenic relationship with O. sativa, these assembled scaffolds were anchored into 12 pseudo‐chromosomes. Genome annotation and comparative genomic analysis reveal that lineage‐specific expansion of gene families that respond to biotic‐ and abiotic stresses are of great potential for mining novel alleles to overcome major diseases and abiotic adaptation in rice breeding programs. This reference genome of African wild rice will greatly enlarge the existing database of rice genome resources and unquestionably form a solid base to understand genomic basis underlying highly valued phenotypic traits and search for novel gene sources in O. longistaminata for the future rice breeding programs.

中文翻译：

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从Illumina和PacBio测序读取非洲野生稻长稻Oryza longistaminata的改良杂交从头基因组装配和注释

非洲野生稻Oryza longistaminata是Oryza属的8个AA基因组物种之一，具有极高价值的特性，例如多年生水稻育种的根茎性，对生物和非生物胁迫的强耐受性以及在贫瘠土壤上的高生物量生产。为了获得长寿稻的高质量参考基因组我们通过结合Illumina和PacBio测序数据集采用了一种混合装配方法。最终的基因组组装仅包含107个支架，大约为〜363.5 Mb，占估计的非洲野生稻基因组（〜392 Mb）的〜92.7％。组装的重叠群和支架的N50长度分别为〜46.49 Kb和〜6.83 Mb，这表明与早先发布的组件（分别为〜12.5 Kb和364 Kb）相比，其长度增加了〜3.72倍和〜18.8倍。借助Hi-C数据以及与稻的协同关系，将这些组装好的支架锚定在12个假染色体中。基因组注释和比较基因组分析表明，响应生物和非生物胁迫的基因家族的谱系特异性扩展对于挖掘新等位基因来克服水稻育种计划中的主要疾病和非生物适应性具有巨大潜力。非洲野生稻的参考基因组将大大扩大现有的水稻基因组资源数据库，并且毫无疑问将为了解高度有价值的表型性状的基因组基础以及为将来的水稻育种计划寻找长寿稻中的新基因来源奠定坚实的基础。