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

CARBALLO J; ZAPPACOSTA D; SELVA JP; BELLIDO A; CACCAMO M; ALBERTINI E; ECHENIQUE V

Praga

Conferencia; The 26th International Conference on Sexual Plant Reproduction; 2022

Eragrostis curvula is a grass species that is being studied in order toidentify the genes and genomic regions involved in apomixis, an asexualmode of reproduction that avoid meiosis (apomeiosis) and fertilization ofthe egg cell and develops an embryo by parthenogenesis. Transferringapomixis to economically important crops will revolutionize the agricultureas we know it today since it can fix the hybrid vigor for generations. Theidentification of genomic regions associated to this trait and its regulatorycomponents is central to transfer apomixis to other crops. In this way, wealready sequenced a sexual diploid genotype, however, more complexapomictic 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 obtaina chromosome scale assembly. We used 10x genomic reads that wereassembled with supernova software. Then, 20x of nanopore long readswere added with DGB2OLC software. Finally, Omni-C, the latestproximity ligation technology was used for scaffolding. The assembly has1,171 Mb distributed in 3037 scaffolds. The N50 was 96 Mb and thenumber of genes was 133,619. The completeness of the genome wasassessed using the BUSCO software finding 96,6% of complete genes.Performing a syntenic analysis with the diploid assembly we could getfully covered the 10 basic chromosomes of E. curvula. Through thisanalyses we could find regions that are only present in the apomicticgenotype. Interestingly, SNPs markers linked to apomixis and candidatesgenes previously identified were mapped on a single region, togheter withother genes related to reproduction. Since the genome is collapsed in 10chromosomes we could not distinguish if this region is present in all thehaplotypes. More nanopore reads will be added in order to obtain anhaplotype resolved assembly.