This new durum reference genome, enhanced with advanced annotation and an expression atlas linked to QTLome data, is the most comprehensive tool available for durum wheat genomics.
Abstract
ABSTRACT Advancements in plant genome sequencing and assembly have enabled the production of increasingly accurate and contiguous genome sequences. Here, we present the chromosome‐level assembly of the durum wheat ( Triticum turgidum L. ssp. durum, cv. Svevo) reference genome produced using accurate long‐reads, optical mapping and Hi‐C. The new assembly (Svevo Rel.2.0) comprises 263 hybrid scaffolds with an N50 value of 112.3 Mb, arranged into 14 contiguous pseudomolecules spanning 10.4 Gb. The Svevo Rel.2.0 genome assembly was annotated using extensive short‐ and long‐read RNA sequencing data obtained from 60 tissue/treatment combinations. The resulting annotation comprises 68 154 high‐confidence protein‐coding genes, which have been integrated into a comprehensive transcriptome atlas accessible through an eFP browser. Annotation was manually curated for storage protein gene families and for Leucine‐Rich Repeat‐Containing Receptor genes yielding 3763 LRR‐CR loci. The genome assembly's accuracy and completeness were demonstrated by the correct reconstruction of the physical map of Tg1‐B (Tenacious glumes 1), a locus controlling the free threshing trait located on chromosome 2B that was not assembled in the previous genome release (Svevo Rel.1.0). A wealth of 6621 QTLs/MTAs from the literature were mapped onto Svevo Rel.2.0 to identify QTL hotspots and trait‐specific candidate genes. The ancestry of the durum genome to representative wild emmer populations from North‐Eastern and Southern‐Levant Fertile Crescent assessed by tracing haplotype transmission patterns revealed a clear mosaic pattern. This new durum reference genome, enhanced with advanced annotation and an expression atlas linked to QTLome data, is the most comprehensive tool available for durum wheat genomics.
Abstract Fusarium head blight (FHB) is a devastating disease that severely impacts global wheat (Triticum aestivum L.) production. Sumai 3, a wheat cultivar widely used in breeding programs for its strong FHB resistance, has not been fully resolved at the chromosome level. Here, we present a high‐quality chromosome‐scale assembly of Sumai 3 using PacBio HiFi reads and chromosome conformation capture sequencing. The 14.6 Gb assembly consists of 832 contigs, with the longest contig being 245.2 Mb and a contig N50 of 41.90 Mb, which were scaffolded into 21 pseudomolecules. De novo annotation identified 104,620 high‐confidence protein‐coding genes and found 92.67% of the genome to consist of repetitive sequences. Synteny analysis showed strong collinearity between Sumai 3 and the wheat reference sequence Chinese Spring IWGSC RefSeq v2.1 (CS). Structural variant analysis identified chromosome 2A with the highest number of deletions (2773) and insertions (2645), while chromosome 3B had the most inversions (359). Duplications were most frequent on 2A (337), and contractions on 5B (122). The gene content of the major resistance quantitative trait loci on 3B, Fhb1, largely validates previous annotations for CS, although we discovered two new genes at approximately 12.4 Mb, including an additional copy of a terpene synthase, further suggesting homology with CS 3D over 3B. Differential expression analysis highlighted up‐regulation of three genes coding pore‐forming toxin‐like protein, sina superfamily protein, and plastid‐lipid‐associated proteins potentially involved in FHB resistance. This assembly provides critical insights into FHB resistance and offers a valuable genomic resource for wheat breeding programs.
Rubylyn D. Mijan, Bikash Poudel, Sittal Thapa et al.· The Plant Genome· 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
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
A chromosome-scale genome assembly of KD18 generated using Oxford Nanopore long-read and Illumina short-read sequencing is reported, providing a cultivar-specific genomic resource for research involving KD18 and KD18-derived materials.
T. Q. Nguyen, K. Do, T. M. Vu et al.· bioRxiv· 0 citations
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.
Erwang Chen, Carlotta Marie Wehrkamp, Srijan Jhingan et al.· Nature Communications· 0 citations
Cyclamen is an economically important ornamental plant widely cultivated for its diverse floral characteristics and adaptation to cool climates. Despite its horticultural significance, genomic resources for this species remain limited, hindering molecular studies and genomics-assisted breeding. Here, we report the first highly contiguous nuclear genome assembly of C. persicum generated using high-fidelity long-read sequencing. The assembled genome spans 1.48 Gb, consisting of 126 contigs with an N50 length of 52.3 Mb. Telomeric repeat analysis identified eight contigs containing telomeric sequences at both ends, suggesting the presence of near-complete chromosome assemblies. Genome completeness assessment using BUSCO indicated 98.1% completeness. Repetitive sequences occupied 82.9% of the assembly, with long terminal repeat retrotransposons accounting for 42.1% of the genome. A total of 40,223 protein-coding genes were predicted, with a complete BUSCO score of 95.7%. Comparative orthogroup analysis with five representative eudicot species identified 430 orthogroups specific to C. persicum and 363 orthogroups shared exclusively between C. persicum and Primula kwangtungensis, indicating the presence of both lineage-specific and Primulaceae-conserved gene families. These findings provide critical insights into gene family evolution within Primulaceae and establish an essential comparative framework for future genomic studies. The genome resource presented here provides an invaluable foundation for investigating genome evolution, gene function, and trait-associated loci in cyclamen, effectively facilitating molecular breeding and genetic improvement in this ornamental species.
K. Shirasawa, Y. Akita, Y. Mizunoe et al.· bioRxiv· 0 citations
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