Genomes ofAegilops umbellulataprovide new insights into unique structural variations and genetic diversity in the U-genome for wheat improvement

Abstract

AbstractAegilopsspp. serve as an important reservoir for novel sources of resistance or tolerance to biotic and abiotic stresses. To harness this reservoir, we have generated a high-quality chromosome-level genome assembly of anAe.umbellulataaccession PI 554389 using a combination of PacBio HiFi, Oxford nanopore, and chromosome conformation capture (Hi-C) sequencing technologies and resequenced 20Ae. umbellulatagenomes using Illumina sequencing. We assembled a 4.20 Gb genome spanned over seven chromosomes, rich in repetitive elements (∼84%), achieving a QV of 59.54 with 98.14% completeness. The phylogenetic analysis places the U-genome with D-lineage, but major and distinct rearrangements were revealed in the U-genome. Unique transposon landscape of diploid U-genome and complex chromosomal rearrangements, most prominently in 4U and 6U chromosomes uncovered a distinct evolutionary trajectory ofAe. umbellulata. Additionally, the resequencing of geographically and morphologically diverseAe. umbellulataaccessions revealed three distinctive evolutionary sub-populations. Resequencing also identified six new haplotypes forLr9, the first leaf rust resistance gene introgressed and cloned fromAe. umbellulata.These genomics resources along with high levels of resistance in the resequenced accessions against five devastating wheat diseases affirmed the genetic potential ofAe. umbellulatafor wheat improvement.