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

CARBALLO, JOSE; BELLIDO, ANDRÉS MARTIN; SELVA, JUAN PABLO; ZAPPACOSTA, DIEGO; GALLO, CRISTIAN ANDRES; ALBERTINI, EMIDIO; CACCAMO, MARIO; ECHENIQUE, VIVIANA

Frontiers in Plant Science

Frontiers Media S.A.

Lugar: Lausana; Año: 2023 vol. 14 p. 1 - 11

Introduction: In Eragrostis curvula, commonly known as weeping lovegrass, asynthetic diploidization event of the facultative apomictic tetraploid TanganyikaINTA cv. originated from the sexual diploid Victoria cv. Apomixis is an asexualreproduction by seeds in which the progeny is genetically identical to thematernal plant.Methods: To assess the genomic changes related to ploidy and to thereproductive mode occurring during diploidization, a mapping approach wasfollowed to obtain the first E. curvula pangenome assembly. In this way, gDNA ofTanganyika INTA was extracted and sequenced in 2x250 Illumina pair-end readsand mapped against the Victoria genome assembly. The unmapped reads wereused for variant calling, while the mapped reads were assembled usingMasurca software.Results: 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 reproductivepathway was differentially enriched. PCR amplification in gDNA and cDNA ofTanganyika INTA and Victoria was conducted to validate the presence/absencevariation in five genes related to reproduction and ploidy. The polyploid nature ofthe Tanganyika INTA genome was also evaluated through the variant callinganalysis showing the single nucleotide polymorphism (SNP) coverage and allelefrequency distribution with a segmental allotetraploid pairing behavior.