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

作者：Stefan Reuscher, Tomoyuki Furuta, Kanako Bessho‐Uehara, Michele Cosi, Kshirod K. Jena, Atsushi Toyoda, Asao Fujiyama, Nori Kurata, Motoyuki Ashikari · 发表于：Communications Biology · 年份：2018 · DOI：10.1038/s42003-018-0171-y · 被引用次数：64 · 研究领域：Rice Cultivation and Yield Improvement、Genetic Mapping and Diversity in Plants and Animals、GABA and Rice Research

Abstract 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, and increased biomass production. To facilitate breeding efforts and functional genomics studies, we de-novo assembled 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.