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

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.

The Mitochondrial Iron Regulated (MIR) gene is Oryza genus-specific and evolved before the speciation of major AA-genome lineages

“…Chromosomes 4 and 6 sequences are more closely related to each other than to MIR genes, indicating that they are products of a duplication event, which likely took place after O. glumaepatula speciation, as only the sequence in chromosome 6 is observed in the O. glumaepatula genome ( Figure 6 and Figure 7). However, we did not find these sequences in chromosomes 4 and 6 of O. meridionalis or O. longistaminata, a result that can be derived from genome gaps in the draft sequence (Reuscher, et al 2018;Stein, et al 2018 longistaminata shares the chromosome 4 and 6 duplication event, and the confirmation that O. meridionalis has only the chromosome 6 sequence will need further inspection of a more complete genomic sequence. Although it seems that these non-coding sequences were the source of origin for functional MIR genes, it remains to be explored if they have any function in the genome.…”

“…Considering the genomes available, we only found MIR-like sequences in AA species, glumaepatula (Reuscher, et al 2018) ( Figure 6A). Since the split between these two lineages occurred right after O. glumaepatula speciation, functional MIR origination can be timed to less than 1 MYA.…”

“…Our work aimed at identifying genes orthologous to MIR in closely related wild Oryza species and understanding the MIR gene evolution, using the available Oryza species genome data (Reuscher, et al 2018;Stein, et al 2018). Our findings suggest that MIR originated before the split of major AA genome lineages, and that MIR is not an P orphan gene specific to O. sativa, but an evolutionary novelty generated within the last one million years in the Oryza AA genome lineage.…”

Novel allelic variation in the Phospholipase D alpha1 gene (OsPLDα1) of wild Oryza species implies to its low expression in rice bran

“…These features are not present in any other Oryza species which support to the data we obtained [55][56][57] . Further, haplotype diversity and feature-specific variation has been reported in O. longistaminata which the authors attributed to out-crossing nature of this species 58 . The other explanation could be the long distance dispersal of the seeds by animals, birds or any other way followed by ecological differentiation making this species different.…”

Evolutionary genomics of structural variation in Asian rice (Oryza sativa) and its wild progenitor (O. rufipogon)

“…We collected three kinds of data to detect SVs: whole-genome assemblies, PacBio SMRT reads, and paired-end short-read (Illumina) data. For the first, we downloaded 15 assemblies from previous publications (Table S2), including outgroups assemblies of O. glaberrima (55) and O. longistaminata (56) that were used as to infer the ancestral state of structural variants. For the second dataset, we gathered SMRT reads for ten accessions that were a subset of the wholegenome dataset (Table S2) and included data from 6 indica, 3 japonica, and one O. longistaminata accession.…”