Unveiling centromeric retrotransposon dynamics through a high-quality rye genome assembly
TL;DR
An improved rye genome assembly is presented and unique retrotransposon organizations within its centromeres are uncovered, revealing RLG_Abia and RLG_Abigail as abundant, recently active elements, unlike in wheat.
Abstract
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 with the TRITEX pipeline. The resulting Lo7_V3 assembly spans 6.76 Gb with a contig N50 of 128 Mb, correcting previous misorientations and fully assembling all seven centromeres. Repetitive clusters containing rye-specific satellite sequences (pSc200 and pSc250) are contiguously assembled. Their chromosomal positions are validated using FISH. Centromeric retrotransposon analysis reveals RLG_Abia and RLG_Abigail as abundant, recently active elements, unlike in wheat. Collectively, the Lo7_V3 genome assembly provides an improved genomic resource for future genomic research in rye and related cereal species. The large, repeat-rich, and highly heterozygous rye (Secale cereale L.) genome has posed significant challenges for genome assembly. Here, the authors present an improved rye genome assembly and uncover unique retrotransposon organizations within its centromeres.