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.
Abstract
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.
Oxyria digyna
is a perennial herb widely distributed across Arctic and Alpine regions, representing one of the oldest extant Arctic plant lineages. Despite its ecological and evolutionary importance, no chromosome-scale reference genome has been published as a research paper to date. Here, we present two high-quality chromosome-level genome assemblies of
O. digyna
generated using high-fidelity long-read sequencing data and long-read–based chromatin conformation capture sequencing data. Our final phased genome assemblies span 548.60 Mb and 540.00 Mb with scaffold N50 values of 77.17 Mb and 76.59 Mb, respectively. Karyotyping confirmed a chromosome number of 2n = 14, which matches the number of chromosome-scale scaffolds in our final genome assemblies. Also, Telomere-to-telomere continuity was achieved for three chromosomes in one haplotype. The assemblies exhibit high completeness and accuracy, with BUSCO scores exceeding 95% and QV values above 57. Gene annotation identified 20,794 genes, including 19,500 protein-coding genes. Pan-genome analysis incorporating publicly available assemblies revealed 3.17 million variant loci, including 84,360 structural variants. This chromosome-level genome provides a valuable resource for studying Arctic plant adaptation, genome evolution, and genetic mechanisms underlying environmental resilience.
Jeongwoen Shin, Moonkyo Kim, Misun Moon 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 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
The comprehensive genomic and transcriptomic resources developed in this study will facilitate the domestication and aquaculture development of C. heberi, as well as support research on its nutritional potential, ecological adaptations, and evolutionary biology.
M. Shekhar, V. K. Katneni, Sudheesh K. Prabhudas et al.· Scientific Data· 0 citations
We present a genome assembly of Hypericum pulchrum (slender St John’s-wort; Streptophyta; Magnoliopsida; Malpighiales; Hypericaceae). The assembly consists of two haplotypes with total lengths of 373.14 megabases and 367.88 megabases. Most of haplotype 1 (94.8%) is scaffolded into 9 chromosomal pseudomolecules. Haplotype 2 was assembled to scaffold level. The mitochondrial sequences have lengths of 217.84 and 276.52 kilobases and the plastid genome assembly has a length of 149.16 kilobases. Gene annotation of this assembly on Ensembl identified 29 497 protein-coding genes. This assembly was generated as part of the Darwin Tree of Life project, which produces reference genomes for eukaryotic species found in Britain and Ireland.
Raj Whitlock, Robert N. L. Fitt· Wellcome Open Research· 0 citations
The Malabar red snapper (Lutjanus malabaricus) is a high-value marine food fish of growing economic and aquaculture importance across the Indo-Pacific. Despite its significance, genomic resources for this species have remained scarce, hindering the application of genomic tools for selective breeding. Here, we present the first chromosome-level genome assemblies and full-length transcriptome of L. malabaricus. Using PacBio HiFi long-read sequencing and Hi-C scaffolding, we generated high-quality assemblies for unsexed, male, and female individuals, each approximately 1.0 Gb in size and anchored to 24 chromosomes. The assemblies exhibited exceptional contiguity (N50 ≈ 42 Mb) and completeness (BUSCO > 99%), with karyotyping confirming 2n = 48 telocentric chromosomes. Genome annotation identified ~25,000 protein-coding genes, and repeat sequences accounted for almost half of the genome, comparable to other reef-associated teleosts. Comparative analyses of the male and female assemblies revealed strong chromosomal synteny and localized sex-associated regions, suggesting a polygenic or complex mechanism of sex determination. The accompanying multi-tissue full-length transcriptome supports functional and developmental studies. Together, these genomic and transcriptomic datasets provide a comprehensive molecular foundation for population genetics, comparative genomics, and selective breeding in L. malabaricus.
Shubha Vij, V. Nguyen, Kathiresan Purushothaman et al.· Scientific Data· 0 citations
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