From tetraploid to diploid, a pangenomic approach to identify genes lost during synthetic diploidization of Eragrostis curvula

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

Frontiers in Plant Science

Frontiers

Año: 2023 vol. 14

1664-462X

In Eragrostis curvula, commonly known as weeping lovegrass, asynthetic diploidization event of the facultative apomictic tetraploidTanganyika INTA cv. originated the sexual diploid Victoria cv. Apomixis is anasexual reproduction by seeds in which the progeny is genetically identical tothe maternal plant. To assess the genomic changes related to ploidy and to thereproductive mode occurred during diploidization, a mapping approach wasfollowed to obtain the first E. curvula pangenome assembly. In this way,gDNA of Tanganyika INTA was extracted and sequenced in 2x250 Illumina pair endreads and mapped against the Victoria genome assembly. The un-mapped reads wereused to do the variant calling while the mapped reads were assembled usingMasurca software. The length of the assembly was 28,982,419 bp distributed in 18,032contigs and the variable genes annotated in these contigs rendered 3,952 genemodels. Functional annotation of the genes showed that the reproductive pathwaywas differentially enriched. PCR amplification in gDNA and cDNA of TanganyikaINTA and Victoria was conducted to validate the presence/absence variation offive genes related to reproduction and ploidy. The polyploid nature of theTanganyika INTA genome was also evaluated through the variant calling analysisshowing the SNP coverage and allele frequency distribution a segmentalallotetraploid pairing behavior. The results presented here suggest that thegenes lost in Tanganyika INTA during the diploidization process conducted to thesuppression of the apomictic pathway, affecting severely the fertility ofVictoria cv.