Carlotta Marie Wehrkamp

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.

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.

Background: Recent advances in assemblies of nearly gap-free, high-quality genomes have enabled detailed analysis of centromeres in large and highly repetitive crop genomes. Here, we analyse the hexaploid Avena sativa genome and its tetraploid ( A. insularis ) and diploid relatives ( A. longiglumis , A. atlantica and A. eriantha ). Results: Avena centromeres are largely composed of retrotransposons belonging to three families, RLG_Ava , RLG_Cereba and RLG_Beth . Analysis of retrotransposon populations revealed striking differences in the centromere architecture between the A, C and D genome lineages. We identified distinct profiles of transposable element bursts for these lineages which include the emergence and disappearance of retrotransposon families and subfamilies. We identified multiple centromere shifts which occurred in the C genome lineage within the past ∼ 4 myrs and retraced species divergences and polyploidization events in the Avena genus. Although the studied species are closely related, our data show that their centromeres have rapidly evolved different and distinct centromere architectures, for example through the spread of novel satellite repeats or activity bursts of different retrotransposon families and subfamilies. Additionally, we found that RLG_Ava and RLG_Cereba retrotransposons have been coexisting while simultaneously competing for the centromeric “niche” since the emergence of the Poaceae (grasses). Conclusions: Our comparative analyses provided detailed insight into centromere evolution across the Avena genus and revealed that composition and architecture of centromeres can vary greatly even between closely related species and different ploidy levels. Our findings emphasize the need for extended analyses of large genome species to improve our understanding of centromere evolution.

Summary: ● Lichens are an ancient symbiosis comprising the thalli of lichen-forming fungi, their photoautotrophic partners and their microbiome. So far, they were poorly studied at the genome sequence level. Here, we present a reference metagenome for the holobiont of Cladonia rangiformis . ● Using long read sequences from an entire symbiotic complex, plus short read libraries from 28 additional diverse European lichen samples, we were able to separate genome sequences of 20 individual species. ● We constructed chromosome-scale assemblies of the C. rangiformis fungus and its trebouxioid green algal photobiont Asterochloris mediterranea . The genome of the fungus comprises ∼22% transposable elements and is highly compartmentalized into genic regions and large TE-derived segments which show extensive signatures of repeat-induced point mutations (RIP). We found that A. mediterranea centromeres are predominantly derived from two interacting retrotransposon families. We also identified strong candidates for genes that were horizontally transferred from bacteria to both alga and fungus. Furthermore, we isolated 18 near-complete bacterial genomes, of which 13 are enriched in the lichen compared to surrounding soil. ● Our study revealed that the thalli of C. rangiformis have a highly complex microbiome, comprising a mix of species that may include opportunists, ecologically obligate symbionts and possibly even lichen-beneficial bacteria.