Aug 2026· Cell Reports· Vol 45, pp.
117765
· 0 citations· 68 references
Medicine
TL;DR
Haplotype analysis links BnaSCC1Hap2 with lighter seed coat color, higher oil and oleic acid contents, and lower erucic acid content, supporting its use in marker-assisted breeding.
Abstract
Yellow-seeded rapeseed has higher oil content and seed quality than black-seeded varieties, but its genetic basis remains unclear. We report a telomere-to-telomere genome assembly of yellow-seeded rapeseed GH06 (981.18 Mb; contig N50, 56.93 Mb) generated with PacBio HiFi, Oxford Nanopore ultra-long reads, and Hi-C sequencing. The GH06_SWU assembly shows high completeness, accuracy, and continuity, with 110,096 annotated protein-coding genes. Using GH06_SWU, GWAS of seed coat color in 504 accessions identifies a seed coat color-associated BnaSCC1 on chromosome A10. CRISPR-Cas9 knockout of BnaSCC1 inhibits seed coat pigmentation and increases seed oil content (SOC) by 3.37 percentage points on average. Multi-omics analyses show that BnaSCC1 disruption is associated with reduced flavanol glycoside accumulation, elevated triacylglycerol levels, and increased oil body number. Haplotype analysis links BnaSCC1Hap2 with lighter seed coat color, higher oil and oleic acid contents, and lower erucic acid content, supporting its use in marker-assisted breeding.
A T2T rapeseed resource and a BnaWRKY44-BnaVPT1 module for breeding high-oil, yellow-seeded rapeseed are provided for breeding high-oil, yellow-seeded rapeseed.
Haijiang Liu, Yongheng Yuan, Kaijie Ye et al.· Cell Reports· 0 citations
Wild soybean (
Glycine soja
), the progenitor of cultivated soybean (
Glycine max
), represents an important reservoir of genetic diversity crucial for soybean improvement. However, the limited availability of high-quality reference genomes for wild soybean has constrained its comprehensive genomic characterization. Here, we present a telomere-to-telomere (T2T) genome assembly of a wild soybean (
G. soja
) accession HAAS216 with a size of 1,018.17 Mb, generated using PacBio HiFi, ultra-long Oxford Nanopore sequencing, and Hi-C data. The assembly spans all 20 chromosomes and captures 20 centromeric and 40 telomeric regions, forming a gap-free T2T genome assembly. This assembly exhibits superior quality regarding completeness (BUSCO: 99.6%), contiguity (contig N50: 51 Mb), and base-level accuracy (QV: 55.53). Repetitive sequences make up 55.84% (568.57 Mb) of the genome, and 48,390 protein-coding genes were predicted, of which 47,567 (98.30%) were functionally annotated. This genome assembly provides a genomic resource for comparative genomics and facilitates genetic research and crop improvement in soybean.
M. Asad, Sui Wang, Jing Zhang et al.· Scientific Data· 0 citations
The mangrove red snapper (Lutjanus argentimaculatus) is a commercially important marine fish species in the Indo-Pacific region. Despite its significant economic value for aquaculture, existing genomic resources remain fragmented, limiting the advancement of molecular breeding and functional genomic studies. Here, we present a gap-free, telomere-to-telomere (T2T) genome assembly of L. argentimaculatus, generated using a hybrid approach combining PacBio HiFi, Oxford Nanopore ultra-long reads and Hi-C technology. The resulting assembly comprises exactly 24 scaffolds spanning 1.03 Gb, perfectly matching the haploid chromosome number with a contig N50 of 46.17 Mb. Notably, this assembly resolves all physical gaps present in previous versions, achieving a BUSCO completeness score of 98.2%. Comprehensive genome annotation successfully predicted 23,167 protein-coding genes. Among these, 22,067 genes (95.25%) were functionally annotated across major public databases, including eggNOG, InterPro, and Swiss-Prot. Furthermore, structural analysis successfully identified 19 telomeres and 20 centromeres, validating the chromosomal integrity. This high-fidelity, gap-free reference genome provides a robust foundation for comparative genomics, population genetics, and the genetic improvement of Lutjanidae species.
Yang Xiang, Zhen-Cheng Lu, Hao-Ling Jiang et al.· Scientific Data· 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
