This annotated genome assembly for C. kousa provides insight into the genomic composition of the species and will enhance the understanding of the genetic control of traits of interest in breeding programs and the evolutionary history of the Cornus genus.
Abstract
Kousa dogwood (Cornus kousa Hance) is a popular flowering ornamental tree in the United States (U.S.), largely due to its pest and disease tolerance. Here, we present the first chromosome-scale, diploid genome assembly of C. kousa K2, a foundational breeding parent. The final chromosome-scale genome assemblies are 1602.739 Mb for Hap 1 and 1598.929 Mb for Hap 2. The complete Benchmarking Universal Single-Copy Ortholog (BUSCO) for Hap 1 and 2 were 98.8% and 98.4%, respectively. Between the two haplotypes, 98.97% of the genome is placed into chromosomes. 30,799 and 31,044 genes were annotated in Hap 1 and Hap 2, respectively. This annotated genome assembly for C. kousa provides insight into the genomic composition of the species and will enhance our understanding of the genetic control of traits of interest in breeding programs and the evolutionary history of the Cornus genus.
Tea (
Camellia sinensis
) is a globally important economic crop. Among elite cultivars, ‘Fuding Dahao’ is particularly prized for its superior agronomic traits and its central role in premium white tea production. However, the lack of a high-quality chromosome-level genome for this regionally adapted cultivar has hindered molecular breeding efforts. Here, we present the first chromosome-level reference genome of ‘Fuding Dahao’ assembled using PacBio HiFi long-read sequencing and Hi-C chromatin interaction mapping. The final 3.30 Gb assembly is highly contiguous, with 90% of the sequences anchored to 15 pseudochromosomes. A total of 54,345 protein-coding genes were predicted, representing a substantial improvement in both assembly contiguity and annotation completeness compared with previously published tea genomes. This high quality genome provides a critical resource for dissecting the genetic basis of white tea quality traits and accelerating molecular breeding programs. Our results fill a major gap in tea genomics and lay a solid foundation for the development of superior, locally adapted tea cultivars.
Yang Chen, Lizhong Wang, Deng-Feng Shen et al.· Scientific Data· 0 citations
White star apple (Gambeya albida) is native to the lowland rainforests of Central, East, and West Africa. This species is highly valued for its nutritious fruits and offers medicinal, socio-cultural, and economic benefits. In West Africa, it contributes to food security for rural and urban communities alike. However, no genomic resources are available to untap the agronomic and medicinal traits of the white star apple. Here, we present its first chromosome-scale genome, generated using PacBio HiFi and Omni-C sequencing. The white star apple genome is highly homozygous, and we assembled 98.9% of the estimated haploid genome size (822 Mbp) into 13 pseudochromosomes. It has a base-level accuracy (QV) of 58.14, an N50 of 57 Mbp, and 97.5% BUSCO completeness, representing a reference-quality assembly. About 58.5% of the genome constitutes repetitive sequences, and ab initio gene prediction identified 33,602 gene models. This reference-quality genome of the white star apple will serve as a valuable resource to enhance our understanding of its nutritional and pharmacological traits and facilitate improvement research.
Michael Landi, S. Muzemil, Adedapo Adediji et al.· Scientific Data· 0 citations
This genome provides a foundational resource for investigating the molecular basis of evolutionary mechanisms, genetic breeding, and conservation genomics of male Andinoacara rivulatus, with direct implications for sustainable aquaculture and the global ornamental fish trade.
Zhen Yuan, Qi Liu, Hong-Wei Yan et al.· Scientific Data· 0 citations
This chromosome-scale genome assembly and annotation of anise hyssop provides a foundational genomic resource for comparative and functional genomics within the genus Agastache and the Lamiaceae family.
This high-quality chromosome-level genome assembly of C. Saxicola will serve as a valuable resource for understanding the ecology, genetics, and evolution of the endangered herbaceous plant and will help towards its cultivation.
Ming Lei, Jing Wang, S. Sooranna et al.· Scientific Data· 0 citations
Horsenettle (Solanum carolinense L.) is a noxious weed widely distributed across North America and increasingly invasive in other regions. Its strong environmental adaptability, complex defense strategies, and distinctive reproductive traits make it an important model for studying plant–herbivore coevolution. However, the absence of high-quality genomic resources has limited deeper investigation into its adaptive evolutionary mechanisms. In this study, we generated a chromosome-level reference genome assembly for S. carolinense using an integrated approach combining PacBio HiFi long-read sequencing, Illumina second-generation sequencing, and Hi-C chromatin interaction scaffolding. The final genome assembly had a total length of 915.40 Mb, with a contig N50 of 51.06 Mb and a scaffold N50 of 73.17 Mb; 96.05% of the sequences were successfully anchored onto 12 pseudochromosomes. The genome was characterized by a high proportion of repetitive sequences (73.64%) and substantial heterozygosity (1.13%), consistent with a highly repetitive and moderately high heterozygous genome. BUSCO analysis indicated that the chromosome-level genome assembly of S. carolinense reached a completeness score of 94.8%. A total of 32,206 protein-coding genes were annotated, of which 97.95% received functional annotations. The evaluation of the annotated protein-coding gene set returned a completeness value of 94.9%. This reference genome provides a valuable resource for advancing research on the adaptive evolution of weedy Solanaceae species, supports the development of more effective management strategies for this troublesome species, and offers a technical reference for assembling other highly heterozygous weed genomes.
Luyue Shan, Xiao-Ling Song, Jian-Guo Fu et al.· Plants· 0 citations
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