Jia-Wu Feng

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.

Grain yield in wheat is frequently driven by pre-anthesis growth and how carbon is directed to reproductive parts, determining the potential size of the grain-producing sink. However, the genetic mechanisms controlling this carbon allocation remain unclear. In this study we discovered a series of loci in tetraploid and hexaploid wheats that, when combined, confer an average grain yield advantage in hexaploid winter wheat of approx. 5-7% under high-input farming while approx. 10-15% under low-input conditions. The responsible gene is GRAIN NUMBER INCREASE 2 ( GNI2 ), ancestral to its duplicate GNI1 , and represented by the homoeo-allelic series GNI-A2 , GNI-B2 , and GNI-D2 . GNI1 and all GNI2 copies additively affect floral growth and fertility by modulating reproductive allocation and harvest index. Herewith, we describe a series of grain yield-relevant GNI2 homoeo-alleles with a proven track record for being beneficial in both high- and low-input environments. Their deployment offers a sustainable pathway to raise global grain yields in the future.

Summary: Wild crop relatives are valuable genetic resources for improving stress adaptation in cultivated species, but their effective use depends on high‐quality reference genomes integrated with phenotypic and molecular datasets. Hordeum erectifolium , a wild relative of barley ( H. vulgare ), is adapted to intermittent and prolonged drought and saline soils, making it an excellent species for stress‐adaptation research. We assembled a chromosome‐scale, annotated reference genome of H. erectifolium comprising 3.85 Gbp, and identified 71 475 genes supported by a tissue‐specific gene expression atlas. Comparative morphological, physiological and transcriptomic analyses under water limitation were conducted with H. erectifolium , and cultivated and wild barley. Hordeum erectifolium displayed a greater density of leaf veins and sclerenchyma cells, alongside rapid leaf rolling upon dehydration. Genomic comparisons revealed structural variations, independent transposon‐driven evolution and copy number expansions of desiccation‐responsive gene families relative to barley. The transcriptional responses of H. erectifolium and barley to water limitation suggested contrasting drought‐adaptation strategies: metabolic downregulation and survival prioritization in H. erectifolium vs maintenance of metabolic activity and competitiveness in barley. Our data suggest that H. erectifolium is genetically primed for survival under drought through anatomical adaptations, gene family expansion, efficient shutdown of growth‐related metabolism and rapid recovery upon rehydration.

The genus Hordeum, which includes cultivated barley and its wild relatives, represents a diverse group of grasses with agricultural, ecological, and evolutionary importance. Here, we present a genus-wide pangenome based on 25 chromosome-scale genome sequences encompassing all known diploid Hordeum species and selected tetraploids. Comparative analysis reveals extensive structural variations, including large-scale inversions and chromosomal rearrangements, which disrupt proximal chromosomal collinearity and reflect lineage-specific genome remodeling. Using single-copy gene phylogenies, we identify multiple deep interspecific hybridization events, segmental exchanges, and introgressions, particularly in regions enriched for conserved inversions. We also uncover widespread horizontal gene transfer from Panicoideae grasses into Hordeum, with functional integration of transferred genes. Transposable element dynamics, especially retrotransposon proliferation, account for much of the observed genome size variation and offer insights into polyploid genome evolution. Whole-genome alignments reveal contrasting evolutionary patterns: while coding genes remain highly conserved, regulatory elements show rapid turnover, providing a substrate for phenotypic diversification. Case studies of vernalization and glume development demonstrate how natural variation in regulatory and coding sequences contributes to flowering time and floral morphology. This comprehensive pangenomic framework establishes Hordeum as a model for studying genome evolution, structural variation, and the genetic basis of adaptive traits, offering new avenues for barley improvement.

Summary: Wild crop relatives are valuable genetic resources for improving stress adaptation in cultivated species, but their effective use depends on high-quality reference genomes integrated with phenotypic and molecular datasets. Hordeum erectifolium , a wild relative of barley ( H. vulgare ), is adapted to intermittent and prolonged drought and saline soils, making it an excellent model for stress-adaptation research. We assembled a chromosome-scale, annotated reference genome of H. erectifolium comprising 3.85 Gbp, and identified 71,475 genes supported by a tissue-specific gene expression atlas. Comparative morphological, physiological, and transcriptomic analyses under water limitation were conducted with cultivated and wild barley. H. erectifolium displayed a greater density of leaf veins and sclerenchyma cells, alongside rapid leaf rolling upon dehydration. Genomic comparisons revealed structural variations, independent transposon-driven evolution, and copy number expansions of desiccation-responsive gene families relative to barley. The transcriptional responses of H. erectifolium and barley to water limitation suggested contrasting drought-adaptation strategies: metabolic down-regulation and survival prioritization in H. erectifolium versus maintenance of metabolic activity and competitiveness in barley. Our data suggest that H. erectifolium is genetically primed for survival under drought through anatomical adaptations, gene family expansion, efficient shutdown of growth-related metabolism, and rapid recovery upon rehydration.

Wild plants can contribute valuable genes to their domesticated relatives ¹ . Fertility barriers and a lack of genomic resources have hindered the effective use of crop–wild introgressions. Decades of research into barley’s closest wild relative, Hordeum bulbosum , a grass native to the Mediterranean basin and Western Asia, have yet to manifest themselves in the release of a cultivar bearing alien genes ² . Here we construct a pangenome of bulbous barley comprising 10 phased genome sequence assemblies amounting to 32 distinct haplotypes. Autotetraploid cytotypes, among which the donors of resistance-conferring introgressions are found, arose at least twice, and are connected among each other and to diploid forms through gene flow. The differential amplification of transposable elements after barley and H. bulbosum diverged from each other is responsible for genome size differences between them. We illustrate the translational value of our resource by mapping non-host resistance to a viral pathogen to a structurally diverse multigene cluster that has been implicated in diverse immune responses in wheat and barley.

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.

Matricaria chamomilla L. (chamomile) is a medicinal plant that is widely used for treating skin infections and respiratory ailments. Chamomile belongs to the Asteraceae family of flowering plants and is a primarily outcrossing species with a heterozygous genome. Despite its extensive use, no reference genome has been available for chamomile until now. We present a chromosome-level genome sequence for chamomile which was assembled with TRITEX pipeline from PacBio accurate long reads and chromosome conformation capture sequencing data. The assembled pseudo-haploid genome has a total size of 2.75 Gb, organized into 9 chromosomes with a scaffold N50 of 285 Mb. This high-quality reference genome has a BUSCO value of 98.8% and includes 47,820 functional genes. Additionally, we assembled a haplotype-resolved genome, taking advantage of the high heterozygosity of chamomile. The haplotype assemblies have total sizes of 2.28 Gb and 2.34 Gb and cover 87.6% and 89.8% of the pseudo-haploid reference genome, respectively. Our assemblies provide a valuable resource for genetics and genomics works for chamomile and related members of the Asteraceae.

Pangenomes are collections of annotated genome sequences of multiple individuals of a species¹. The structural variants uncovered by these datasets are a major asset to genetic analysis in crop plants². Here we report a pangenome of barley comprising long-read sequence assemblies of 76 wild and domesticated genomes and short-read sequence data of 1,315 genotypes. An expanded catalogue of sequence variation in the crop includes structurally complex loci that are rich in gene copy number variation. To demonstrate the utility of the pangenome, we focus on four loci involved in disease resistance, plant architecture, nutrient release and trichome development. Novel allelic variation at a powdery mildew resistance locus and population-specific copy number gains in a regulator of vegetative branching were found. Expansion of a family of starch-cleaving enzymes in elite malting barleys was linked to shifts in enzymatic activity in micro-malting trials. Deletion of an enhancer motif is likely to change the developmental trajectory of the hairy appendages on barley grains. Our findings indicate that allelic diversity at structurally complex loci may have helped crop plants to adapt to new selective regimes in agricultural ecosystems.