Producción CyT
XIII Argentine Congress of Bioinformatics and Computational Biology (XIII CAB2C) XIII International Conference of the Iberoamerican Society of Bioinformatics (XIII SoIBio) III Annual Meeting of the Ibero-American Artificial Intelligence Network for Big Bi - Assembly and annotation of diploid and tetraploid genomes of Bahiagrass (Paspalum notatum Flügge)
Congreso
Autoría:
Vega, Juan Manuel ; PODIO, MARICEL ; Orjuela, Julie ; Siena, Lorena Adelina ; Mariac, Cedric ; Leblanc, Olivier ; Ortiz, Juan Pablo AmelioFecha:
2023Editorial y Lugar de Edición:
ICB2C Rosario 2023Resumen *
Paspalum notatum is a subtropical forage grass native of South America. The species forms a multiploid complex, composed of sexual self-sterile diploids (var. saurae) and pseudogamous apomictic self-fertile tetraploids (var. notatum). It is currently one of the most important grasses for pastures and lawns in the southeastern USA. P. notatum is considered one of the models for the study of apomixis in grasses because of the large amount of information on the reproductive biology, genetics and breeding that has been generated over the last 50 years. The objective of this work was to generate a high quality, fully characterized genome assembly of the species at the diploid level, to be used as a reference for disclosing the genomic structure of the apomictic tetraploid cytotypes. A natural biotype (#R1) from the center of origin and diversity of the species was used as plant material. Using more than 200x Oxford Nanopore long reads and 100x Illumina short reads, we generated a new chromosome level 564 Mb genome assembly (N50 = 56.1 Mb) of the species with high completeness (BUSCO score = 98.73%). The genome heterozygosity estimated with GenomeScope resulted of 1.73% while the repetitive elements detected by Repeatmaker, accounted for 57.86 % of the total genome. Gene annotation carried out using the MAKER pipeline predicted 45,074 gene models of which 32,101 were classified as high confidence due to their homology hits in InterProScan databases and having start and stop codons in appropriate positions. Overall, a higher gene density was found in distal chromosome regions, while a higher frequency of transposable elements was found in pericentromeric regions. Alignment of the #R1 assembly with the reference and other grass genomes revealed a high degree of sequence conservation. Despite some large structural variations compared to rice and Setaria italica were found. Genome characterization included the identification of 59 miRNA precursors together with their putative targets and the generation of a set of 4,774 SSRs useful for breeding. Moreover, a preliminary assembly of the natural apomictic tetraploid genotype Q4117 was constructed using 80x Oxford Nanopore Technology long reads and 70x Illumina short reads. This assembly focused on preserving haplotype information, resulted in 5,500 contigs, spanning 2,345. Reference based annotation of this assembly identified 170,000 gene models exhibiting homology with #R1 gene models. Mapping the Q4117 assembly against the #R1 reference demonstrated an average coverage of 4.1 ± 2.1. The present work provides a comprehensive genomic resource for analyzing the structure and evolution of the P. notatum agamic complex and the apomixis locus as well as a framework for stablishing molecular breeding strategies. Información suministrada por el agente en SIGEVAPalabras Clave
Paspalum notatumNanoporeGenomeapomixis