September 22, 2019  |  

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

Authors: Reuscher, Stefan and Furuta, Tomoyuki and Bessho-Uehara, Kanako and Cosi, Michele and Jena, Kshirod K and Toyoda, Atsushi and Fujiyama, Asao and Kurata, Nori and Ashikari, Motoyuki

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.

Journal: Communications biology
DOI: 10.1038/s42003-018-0171-y
Year: 2018

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