De novo genome assembly of Texas wintergrass [Nassella leucotricha {Trin. & Rupr.} Pohl] supports diagnostic marker development and phylogenetic analysis of species within the family Poaceae

Abstract

Abstract Texas wintergrass is a cool-season perennial bunchgrass native to North America with ecological and agronomic importance as a winter forage species, yet genomic resources for this species remain limited. Here, we present the first de novo genome assembly of Nassella leucotricha generated using PacBio HiFi sequencing. Assembly with hifiasm produced a 959.92-Mb genome with 8× coverage, comprising 2,394 contigs with an N50 of 530.6 kb. Assembly completeness was high, with 99.6% of Benchmarking Universal Single-Copy Orthologs identified, although a substantial proportion were duplicated. Genome size estimates based on flow cytometry and k-mer analysis, together with assembly metrics, indicate a repeat-rich and structurally complex genome. Repeat annotation revealed that 64.42% of the genome consists of repetitive elements, predominantly long terminal repeat retrotransposons, including Ty1/Copia and Gypsy/DIRS1. Gene prediction using the homology-based pipeline GeMoMa identified 54,132 high-confidence genes, of which 53,868 were functionally annotated and 26,346 were assigned to KEGG pathways. Mining for genome-wide simple sequence repeats identified over 38,000 markers, with a validated subset demonstrating use for genetic diversity analysis. Reference-guided alignment and scaffolding using Brachypodium distachyon and Oryza sativa provided comparative frameworks for evaluating conserved sequence relationships between Texas wintergrass and representative grass genomes. Our results establish a genomic resource for Texas wintergrass, supporting future studies in comparative genomics and molecular breeding.