A chromosome scale assembly of Eragrostis curvula genome identify a region linked to apomixis

Abstract

Eragrostis curvula is a grass species that is being studied in order to identify the genes and genomic regions involved in apomixis, an asexual mode of reproduction that avoid meiosis (apomeiosis) and fertilization of the egg cell and develops an embryo by parthenogenesis. Transferring apomixis to economically important crops will revolutionize the agriculture as we know it today since it can fix the hybrid vigor for generations. The identification of genomic regions associated to this trait and its regulatory components is central to transfer apomixis to other crops. In this way, we already sequenced a sexual diploid genotype, however, more complex apomictic tetraploids are necessary to perform comparative analyses. The tetraploid genome of the apomictic genotype Don Walter (2n=4x=40, ~1200 Mb) was sequenced using a combination of technologies to obtain a chromosome scale assembly. We used 10x genomic reads that were assembled with supernova software. Then, 20x of nanopore long reads were added with DGB2OLC software. Finally, Omni-C, the latest proximity ligation technology was used for scaffolding. The assembly has 1,171 Mb distributed in 3037 scaffolds. The N50 was 96 Mb and the number of genes was 133,619. The completeness of the genome was assessed using the BUSCO software finding 96,6% of complete genes. Performing a syntenic analysis with the diploid assembly we could get fully covered the 10 basic chromosomes of E. curvula. Through this analyses we could find regions that are only present in the apomictic genotype. Interestingly, SNPs markers linked to apomixis and candidates genes previously identified were mapped on a single region, togheter with other genes related to reproduction. Since the genome is collapsed in 10 chromosomes we could not distinguish if this region is present in all the haplotypes. More nanopore reads will be added in order to obtain an haplotype resolved assembly.