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

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

doi:10.1038/s42003-018-0171-y

Stefan Reuscher, Michele Cosi + Show 7 more

Open Access

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

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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.

Highlights

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
Genome types range from diploid AA to tetraploid KKLL, with both commercially used species (O. sativa and O. glabberima) belonging to the AA type
It is found in tropical regions of western Africa near fresh water and in swampy areas[1]. It is rarely used for human consumption, but holds a number of beneficial traits, such as resistance to bacterial blight linked to the Xa21 locus[11], perennial growth, and a high biomass production

Summary

Introduction

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. The wild rice Oryza longistaminata is of the AA genome type It is found in tropical regions of western Africa near fresh water and in swampy areas[1]. It is rarely used for human consumption, but holds a number of beneficial traits, such as resistance to bacterial blight linked to the Xa21 locus[11], perennial growth, and a high biomass production. The latter two are likely associated with the ability of O. longistaminata to propagate clonally via rhizomes. The same technologies can be used, due to the smaller genome size, sequencing efforts should require less extensive resources

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