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
The family Cichlidae, exemplified by
Andinoacara rivulatus
, is a widely recognized model system for studying adaptive radiation and phenotypic diversity in freshwater fishes. Furthermore,
A. rivulatus
is an important ornamental fish species exhibiting significant sexual dimorphism, monosex fish breeding and has important application prospects for aquaculture. Here, we present the first high-contiguity chromosome-level genome assembly of male
A. rivulatus
, constructed using a multi-platform approach combining PacBio HiFi long-read sequencing, MGI paired-end short reads, and Hi-C data. The assembly spans 778.79 Mb with a contig N50 of 27.16 Mb and scaffold N50 of 32.80 Mb, anchored to 24 chromosomes (99.33% anchoring rate). Repeat annotation revealed that 32.60% of the genome consists of repetitive elements, including 20.51% known transposable elements. We predicted 24,838 protein-coding genes with an average of 10.22 exons per gene, and functional annotation identified evolutionarily conserved domains and key metabolic pathways. BUSCO assessment demonstrated 99.23% completeness, confirming the assembly’s high quality. This genome provides a foundational resource for investigating the molecular basis of evolutionary mechanisms, genetic breeding, and conservation genomics of
A. 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
We present a chromosome-scale genome assembly and annotation of anise hyssop (Agastache foeniculum), an aromatic perennial herb widely used for medicinal, horticultural, and ornamental purposes. The genome was assembled using PacBio HiFi long-read sequencing, Illumina short-read sequencing, and Omni-C proximity ligation data, with gene annotation supported by RNA-seq data from leaf tissue. The final assembly spans 482.39 Mb, of which 434.47 Mb (90.06%) were anchored into nine chromosome-scale pseudomolecules. Structural annotation identified 28,193 protein-coding genes. Genome completeness was assessed using BUSCO, yielding scores of 98.0% (embryophyta_odb10, genome mode) and 95.5% (protein mode). This chromosome-scale genome assembly provides a foundational genomic resource for comparative and functional genomics within the genus Agastache and the Lamiaceae family.
Corydalis saxicola
, an endangered herbaceous plant belonging to the Papaveraceae family and used traditionally as folk medicine, is exclusively endemic to karst habitats. However, the lack of a reference genome limits the implementation of molecular techniques in its breeding, pharmacology and domestication. Here, we present a high-quality chromosome-level genome assembly of
C. saxicola
based on PacBio HiFi and Hi-C data. The assembled genome size is 240.94 Mb with a contig N50 of 29.21 Mb and BUSCO completeness of 97.71%. Approximately 93.26% of the assembled sequences could be anchored to eight pseudo-chromosomes. A total of 74.29 Mb repeat sequences were identified, which account for 32.33% of the genome. In addition, 24,203 protein-coding genes were identified with a BUSCO completeness of 97.89%. This high-quality genome assembly will serve as a valuable resource for understanding the ecology, genetics, and evolution of
C. Saxicola
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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