Developing a Pan-Genome of the diplosporous grass Eragrostis curvula

Abstract

As large-scale genomic studies have progressed, it has been revealed that a single reference genome patterncannot represent the genetic diversity present at the species level. The pangenome can complement themissing genetic information based on the analysis of a single reference genome, exhibit hidden geneticvariations, and demonstrate the true genetic diversity at the species level. The progress of pangenomeresearch in different species has allowed the identification of large structural variants related to importantagronomic traits. Weeping lovegrass (Eragrostis curvula [Schrad.] Nees) is a forage grass that reproduces bysexuality and by facultative and obligate apomixis. It presents distinctive variants with different ploidy levels(2x – 8x) and a basic chromosome number of 10. The recent availability of the genome assembly of cv.Victoria has provided a valuable resource for identifying specific genomic regions linked to significant traits,for instance, forage quality. However, it is worth noting that the regions that control apomixis and othersrelated with ploidy are typically hosted by genotypes with higher ploidy levels. In this work, we focused on constructing a pan-genome of Eragrostis curvula to detect genomic variation,establish phylogenetic relationships, and analyze the effects of ploidy in genome evolution and reproductivemode. To do that, we used the genome assembly of cv. Victoria and genomic data, obtained by Illumina reads,of nine genetically diverse accessions of E. curvula. The construction of the pan-genome employed an iterativemapping and assembly approach involving the mapping of reads from different genotypes to the referencegenome assembly. The mapped reads were used for variant calling, while the unmapped reads wereassembled into new genomic fragments to annotate genes absent in the reference genome. These newlyassembled sequences were subsequently integrated into the reference genome, and the process was repeatediteratively for other genotypes. When all the accessions were processed, the final pan-genome comprised thereference genome and the newly assembled sequences. This approach proved to be highly efficient forconstructing a pan-genome exploiting the reference genome and the assembly of genetically distantgenotypes of E. curvula. Ultimately, the genomic resources generated were employed to gain a comprehensiveunderstanding of the genetic mechanisms underlying apomixis and related processes.