This high-quality, chromosome-level reference genome provides a foundational resource for understanding the population genetic structure, adaptive evolution and speciation mechanisms of C. appendiculata, thereby offering valuable insights into its evolutionary history and conservation.
Abstract
Cremastra appendiculata (D. Don) Makino, an endangered terrestrial orchid with significant medicinal value, lacks comprehensive genomic resources to elucidate its evolution and conservation genetics. Here, we present a chromosome-level genome assembly for C. appendiculata, generated by integrating PacBio circular consensus sequencing and Hi-C technologies. The final genome assembly totals 2.40 Gb, achieving contig and scaffold N50 values of 27.47 Mb and 98.06 Mb, respectively. Hi-C scaffolding anchored 98.66% of the assembly to 24 chromosomes, with repetitive elements comprising 83.85% of the genome and a total of 31,703 protein-coding genes predicted, of which 29,094 (91.77%) were functionally annotated. This high-quality, chromosome-level reference genome provides a foundational resource for understanding the population genetic structure, adaptive evolution and speciation mechanisms of C. appendiculata, thereby offering valuable insights into its evolutionary history and conservation.
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.
M. Lei, Jing Wang, S. Sooranna et al.· Scientific Data· 0 citations
The Chinese lizard gudgeon (Saurogobio dabryi) is an economically important freshwater species within the Cyprinidae family, abundant in the middle and lower reaches of the Yangtze River and its adjacent basins. As a promising species suitable for aquaculture in China, the lack of genomic resources has rendered the genetic breeding and conservation research. Here, we present the first chromosome-level genome assembly of S. dabryi using PacBio HiFi long reads, short reads, and Hi-C sequencing data. The final assembly reaches a total size of 1.09 Gb and Hi-C scaffolding anchors 99.55% of the assembled contigs onto 25 chromosomes, with a scaffold N50 reaching 43.15 Mb. The final genome assembly shows a BUSCO completeness of 98.39%. We annotated 659.55 Mb repetitive sequences and 26,036 protein-coding genes, 99.47% of which are functionally annotated. Comparative phylogenomic analysis clarifies the phylogenetic position of Saurogobio within Gobioninae. This high-quality genome provides a critical genetic basis for exploring cyprinid phylogeny, benthic adaptive evolution, genetic improvement, and conservation efforts of S. dabryi.
Lei Fang, Xin Liu, Yi-Ming Huang et al.· Animals· 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, Hongwei Yan et al.· Scientific Data· 0 citations
Caranx heberi (Bennett, 1830) commonly known as the blacktip trevally belongs to the family Carangidae and is a potential brackishwater aquaculture species. However, the limited genomic resources are hindering the efforts to study its genetic traits and their molecular basis. To bridge this gap, we generated a high-quality reference genome employing multiple sequencing strategies including PacBio Hifi reads (135x), Illumina short reads (150x), and Hi-C chromosome conformation capturing (180x). The high-quality genome assembly consisted of 159 scaffolds summing to 618.71 Mb and an N50 value of 26.72 Mb. Among these, 24 chromosome level scaffolds covered 97.5% of the total assembly. The genome contained 20.94% of repeat elements and 30,354 protein encoding genes. In addition, full-length transcriptomes were generated using the PacBio IsoSeq approach from seven tissues (gill, kidney, liver, muscle, heart, spleen, and intestine). 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. S. Shekhar, V. K. Katneni, Sudheesh K. Prabhudas 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.
Corizus hyoscyami (Heteroptera: Rhopalidae) is a widely distributed and highly polyphagous insect, making it a relevant species for understanding the evolution of herbivory and host adaptation in true bugs. However, the genome of Corizus hyoscyami has not yet been sequenced, limiting investigations into its biological characteristics. In this study, a high-quality chromosome-level genome assembly was generated by integrating MGI DNBSEQ-T7 short-read, PacBio Sequel II long-read, and Hi-C scaffolding technologies. The assembly was assessed to be 97.6% complete by BUSCO. The final genome was assembled into a size of 1.47 Gb, with a contig N50 of 1.61 Mb and a scaffold N50 of 198.34 Mb. The GC content was determined to be 34%, and 94.90% of the sequences were anchored onto 6 chromosome-level scaffolds, representing the major chromosomal elements of the genome. Repetitive sequences accounted for 69.79% of the genome, and 18,540 protein-coding genes were annotated. This genome assembly is expected to facilitate research on adaptive evolution in Heteroptera.
Ye Xu, Yuzhou Zhao, Rong Ji et al.· Scientific Data· 0 citations
