Sequencing Paspalum Genomes

LEBLANC O; PUPILLI F; ALBERTINI E; ESPINOZA F; PESSINO SC; ORTIZ JPA

Rosario

Workshop; Proceedings of the 7th Series of Seminars on Advances in Apomixis Research; 2021

PaspalumnotatumisaforagegrassfromSouthAmericansubtropicalregions. Diploidindividuals (2n = 20) are sexual plants, while polyploid individuals reproduce through aposporous apomixis. In grasses, apomixis is genetically controlled by a single nonrecombinant heterochromatic genomic region, the Apomixis Controlling Region (ACR) which nature and function remain elusive. Our objective is to generate genomic sequences of sexual and apomictic P. notatum individuals to understand ACR emergence and evolution; to identify genes governing important agronomical traits, including apomixis; and to improve genomic selection in breeding programs. To achieve this, we selected one diploid genotype(R1)andtwotetraploidgenotypesreproducingthroughobligate(Q4188)andfacultative (Q3664) apomixis. Genomic DNA was sequenced using Illumina (R1) and Oxford Nanopore (R1, 32 Gb; Q4188, 22 Gb; Q3664, 21 Gb) technologies. K-mer analyses using short reads confirmed flow cytometrical analyses for R1 genome size (~600 Mbp) and high heterogozigosity. HerewereportonthequalitymetricsofR1genomicassembliesgenerated by combining the output of several long-read assemblers (wtdbg2, Shasta, Flye, miniasm, and smartdenovo) and Bionano optical maps: size, N50, contiguity, BUSCO completeness, coverage distribution. The best hybrid scaffolding using a 2300-contig smartdenovo assembly rendered 53 scaffolds (795.27 Mbp, N50 33.54 Mbp, >95% BUSCO completeness). However, a partial representation of heterozygous regions and numerous, dispersed gaps still hinder structural variation analyses. We anticipate that a new set of ONT sequences and the use of tools for detecting and purging haplotypes will allow in a short time the completion of the assembly of R1 genome haplotypes.