Unveiling centromeric retrotransposon dynamics through a near-complete rye genome assembly

Rye (Secale cereale L.) is an important cereal crop known for its high yield potential and tolerance to biotic and abiotic stresses. However, its large, repeat-rich, and heterozygous genome has posed challenges for assembly compared to related species such as wheat and barley. Here, we present a high-quality, chromosome-scale genome assembly of the inbred line Lo7, generated using PacBio HiFi, Oxford Nanopore, Hi-C, and BioNano technologies using the TRITEX pipeline. The resulting Lo7_V3 assembly spans 6.76 Gb with a contig N50 of 128 Mb, correcting previous misorientations and achieving complete centromere assemblies across all seven chromosomes. Repetitive clusters containing rye-specific satellite sequences (pSc200 and pSc250) were contiguously assembled. Their chromosomal positions were validated using FISH. Centromeric retrotransposon analysis highlighted RLG_Abia as a prominent element in rye, showing signs of recent activity and high abundance, unlike in wheat. Collectively, the new Lo7_V3 genome assembly provides a highly improved resource that will support future genomic research and crop improvement efforts in rye and related cereal species.