Aug 2026· Nature Communications· Vol 17· 0 citations· 90 references
Medicine
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.
Aegilops peregrina is a wild allotetraploid wheat wild relative and an important source of genetic diversity for stress tolerance and agronomic traits. Here, we report a subgenome-resolved, chromosome-scale reference genome assembly of a drought tolerant and stem rust resistant Ae. peregrina accession PI 604178 generated using PacBio HiFi and Hi-C sequencing. The 10.13 Gb assembly contains 98.81% of sequence anchored to 14 pseudomolecules representing the seven Sᵖ and seven Uᵖ chromosomes, with contig and scaffold N50 values of 25.84 and 746.48 Mb, respectively. The assembly achieved a consensus quality value of 74.61, 97.83% k-mers completeness, and 99.9% BUSCO completeness. LTR Assembly Index values of 20.43 and 18.79 for the Sᵖ and Uᵖ subgenomes, respectively, further supported high continuity across repeat-rich regions. Repetitive elements comprise 85.93% of chromosome-anchored assembly. We annotated 59,910 high-confidence protein-coding genes, with comparable gene representation across the two subgenomes. This reference genome provides a high-quality genomic framework for comparative analyses, characterization of important loci regulating agronomic and resilience related traits, and sequence-guided exploitation of Ae. peregrina allelic diversity for wheat improvement.
Jatinder Singh, Santosh Gudi, P. Maughan et al.· bioRxiv· 0 citations
The adzuki bean (Vigna angularis) is an economically and nutritionally significant legume species. Using a multi-strategy sequencing approach, a gapless, telomere-to-telomere (T2T) genome assembly of an elite cultivar, Jihong 16 (JH16), was generated. The genome size was 514.85 Mb, with a Contig N50 of 48.72 Mb, 3x longer than previous published genome. The centromeres of adzuki bean were revealed for the first time and found to be composed of ~ 9-bp minisatellites — a distinct departure from the much longer satellites typically found in other plants. Low sequence conservation between the centromeres of adzuki bean and mung bean further highlights the highly active evolutionary dynamics of centromeric sequences in Vigna species. Whole-genome resequencing of 706 adzuki bean accessions was performed and three major phylogenetic groups were identified. Among these, the Southern China group exhibited the highest genetic diversity and the most rapid linkage disequilibrium (LD) decay. A set of 112 core accessions was selected to represent the global germplasm, and 12 barcode SNPs were identified for DNA fingerprinting. Leveraging high-quality phenotypic data for 39 agronomic traits collected across seven locations over two years, a genome-wide association study (GWAS) identified 9613 significant marker-trait associations (MTAs) and thousands of candidate genes, including 40 MTAs located in the centromere regions. Several genes were experimentally validated, including the flowering-time gene Vigan07G000670, overexpression of which in Arabidopsis led to early flowering phenotype and altered FT/FLC expression. Finally, genomic selection (GS) evaluations demonstrated that even a small set (500 ~ 1000) of trait-associated markers achieved high prediction accuracy (>0.8) for key agronomy traits such as seed weight, flowering date and plant height. The genomic resources and insights generated in this study provide a robust foundation for genetic improvement of adzuki bean and related legume crops.
Italian ryegrass (Lolium multiflorum) is a key temperate forage species underpinning livestock production in Europe. Genomic resources remain limited by its large (2.2 Gb), repetitive, and highly heterozygous genome. Here, we present a high-quality chromosome-scale genome assembly of the Swiss L. multiflorum ecotype Tremona, collected in 2008 in Ticino, Switzerland, and subsequently incorporated into recurrent breeding cycles in the Swiss breeding program. To address systematic assembly artefacts caused by unresolved haplotypes in our initial PacBio HiFi assembly, we developed ParaLies, a post-assembly tool that identifies and removes artefactual duplications based on sequence divergence while preserving true paralogous gene copies. ParaLies reduced the duplicated BUSCO rate from 16.91% to 6.72% without loss of bona fide genomic content. The resulting assembly has a contig N50 of 15.69 Mb and captures 94% of the expected 2.2-Gb genome size. We further analyzed whole-genome resequencing data from Tremona, additional Swiss ecotypes, and publicly available North American germplasm. Tremona was genetically homogeneous, with no evidence of pronounced recent bottlenecks or substantial within-population structure, and was genetically distinct from the other Swiss ecotypes analyzed. Together, the Tremona genome and ParaLies provide valuable resources for L. multiflorum genomics and breeding and demonstrate a scalable approach for reducing haplotype-induced redundancy in highly heterozygous genomes.
L. Piat, Gerhard Herren, C. Grieder et al.· bioRxiv· 0 citations
We report a near telomere-to-telomere high quality genome assembly of the historically important spring wheat cultivar, Timstein, generated using PacBio HiFi long-read sequencing data followed by Hi-C scaffolding. The assembly spanned 14.76 Gb, accounting for all 21 chromosomes of the A, B, and D subgenomes. Gene annotations identified around 105 K high-confidence (HC) gene models. The genome was comprised of ~85% transposable elements, primarily from the Gypsy, Copia, and CACTA families. For each subgenome, the BUSCO completeness score ranging from 97.4 to 99.6% and LTR Assembly Index (LAI) values surpassing 13 indicated the assembly quality was reference grade. Synteny analysis with IWGSC Chinese Spring (CS) RefSeq v2.1 revealed strong chromosomal collinearity between two genomes. Timstein has been extensively studied in classical genetics research for stem and leaf rust resistance and septoria nodorum blotch (SNB) susceptibility. This high-quality genome assembly provides cultivar-resolved references that can expand the wheat pangenome, supports structural and functional genomics studies, and enables fine mapping of disease resistance/susceptibility loci for their utilization in wheat genetics and breeding programs.
Jatinder Singh, Santosh Gudi, P. Maughan et al.· Scientific Data· 1 citation· ⚡1
Conifers, which comprise nearly two-thirds of extant gymnosperm species, are ecologically and economically important but remain genomically understudied because of their exceptionally large, repeat-rich genomes. Here, we report a chromosome-level assembly of the haploid genome of Cupressus sempervirens generated using PacBio HiFi reads and scaffolded with optical and genetic maps. The 10 Gb assembly shows exceptional contiguity for a conifer genome (contig N50 = 29.8 Mb) and was organized into 11 pseudomolecules. Iso-Seq-supported annotation identified 42,980 protein-coding genes. Repetitive elements account for over 80% of the genome, with LTR retrotransposons alone representing 52.5%. Transposable elements (TE) are pervasive in both intergenic and genic regions and have a major impact on gene architecture: TE insertions within introns generate ultra-long introns, often exceeding 100 kb, and drive gene size expansion. Analyses of LTR retrotransposon dynamics indicate that genome enlargement in C. sempervirens was driven not by recent transpositional bursts, but by the long-term accumulation and incomplete removal of ancient LTR retrotransposons. Consistent with this pattern, paleogenomic reconstruction across representative gymnosperms found no evidence of whole-genome duplication in the Cupressus lineage. This reference genome provides a valuable resource for studying conifer genome evolution, gene structure, and traits of agronomic and ecological interest, including cypress pollinosis.
Cravero Charlotte, L. Isabelle, Choisne Nathalie et al.· bioRxiv· 0 citations
A pangenome of tetraploid wheat constructed from 12 de novo genome assemblies spanning all 10 recognized tetraploid wheat subspecies, integrating with whole-genome sequencing data, highlights genetic variation associated with agricultural traits.
