Unveiling centromeric retrotransposon dynamics through a high-quality rye genome assembly
- Erwang Chen
- Carlotta Marie Wehrkamp
- Srijan Jhingan
- Thomas Lux
- Zihao Zhu
- Jianyong Chen
- Zuzana Tulpová
- Axel Himmelbach
- Jörg Fuchs
- Jia-Wu Feng
- M. Timothy Rabanus-Wallace
- Hana Šimková
- Manuel Spannagl
- Martin Mascher
- Thomas Wicker
- Andreas Houben
- Nils Stein
2026-08-15
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.