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PubMed2025

A chromosome-level reference genome assembly of the Small snakehead (Channa asiatica).

The Small snakehead (Channa asiatica) is an economically important species in both aquaculture and ornamental trade, mainly distributed in South China and Southeast Asia. Despite its significance, limited genomic resources have impeded in-depth genetic studies and breeding programs. In this study, we used PacBio HiFi long-read sequencing, Illumina short-read sequencing, and Hi-C technologies to generate a high-quality chromosome-level genome of the C. asiatica. The final genome spans 659.44 Mb, with an impressive 98.18% anchored to 23 chromosomes. Notably, the contig N50 and scaffold N50 are 23.92 Mb and 29.61 Mb, validated by a BUSCO completeness score of 98.93%. Genome annotation identified 26,603 protein-coding genes, 99.29% of which were confirmed by BUSCO analysis, and 93.68% were functionally annotated. Approximately 27.72% of the genome sequences were classified as repeat elements. This high-fidelity genome assembly provides a robust foundation for advancing molecular breeding, comparative genomics, and evolutionary studies of C. asiatica and related species.

Animals↗

PubMed2025

Chromosome-level genome assembly of Nothapodytes nimmoniana.

Nothapodytes nimmoniana is a plant species belonging to the genus Nothapodytes in the family Icacinaceae. This species holds significant medicinal value due to its camptothecin content. In this study, we present the first chromosome-level genome assembly of N. nimmoniana constructed using NGS, Hi-C, and HiFi sequencing technologies. The assembled genome spans 3.53 Gb across 14 chromosomes, with an N50 length of 248.74 Mb. Genome annotation revealed that repetitive sequences constitute 80.82% of the genome size, and 83,269 protein-coding genes were predicted. Additionally, 4,360,538 bp of non-coding RNA were annotated. This genomic resource provides a foundation for further investigation into camptothecin biosynthesis pathways and plant phylogeny in N. nimmoniana.

Genome, Plant↗

PubMed2025

A chromosome-level genome assembly and annotation of Cercis chuniana (Fabaceae).

The genus Cercis L., at the base of the subfamily Cercidoideae of Fabaceae, is known for its ecological adaptability and significant medicinal, ornamental, and economic value. However, the lack of a high-quality genome hinders the understanding of the evolution of Cercis and Fabaceae. In this study, we present a chromosome-level genome of Cercis chuniana by combining Illumina short reads, PacBio HiFi long reads, and Hi-C data. The final genome size is 355.53 Mb, consisting of 12 contigs with a N50 of 42.34 Mb. Notably, 344.24 Mb, corresponding to 96.82% of the genome, was anchored to seven chromosomes. The assembly comprises 24.83% repetitive sequences, including 19.32% long terminal repeats. Additionally, a total of 33,837 protein-coding genes were predicted in the genome, with 32,709 (96.67%) genes successfully annotated. The high-quality genome assembly of C. chuniana not only bridges the existing gap in genomic data and offers important resources for molecular studies of this species, but also provides essential insights for future studies on speciation, functional and comparative genomics within the Fabaceae family.

Genome, Plant↗

PubMed2025

A chromosomal level genome assembly of Nguni Sheep, Ovis aries.

Nguni sheep (Ovis aries) are indigenous to the Southern Africa region and common within the smallholder and poor resources farming systems. They are well adapted to different agroecological regions. However, limited genomic resources such as high-quality reference genomes have hindered our understanding of its adaptation and establishment of an effective breeding program. To address this, we assembled a chromosomal-level genome of Nguni sheep using a combination of PacBio HiFi reads and Omni-C reads. The genome size was estimated to be 2.9 Gb with a contig/scaffold N50 74 Mb and 99.6 Mb and a genome completeness of 96.1%, as estimated by the Benchmarking Universal Single-Copy Orthologs (BUSCO) program. The final genome encompassed a total of 25,926 protein-coding genes. The findings of this study provide a valuable genomic resource for understanding the adaptability of the Nguni sheep and the establishment of effective breeding programs.

Animals↗

PubMed2025

Chromosome-level genome assembly of starry flounder (Platichthys stellatus).

Starry flounder (Platichthys stellatus) is widely distributed along the coastlines of the North Pacific. As an euryhaline flatfish, it can adapt to a wide range of environmental salinity ranging from freshwater to seawater, and is a promising aquaculture flatfish species in Korea and North China. However, no high-quality starry flounder reference genome has been reported to date, which greatly limits the studies of genetics and functional genomics. Here, we obtained a high-quality chromosome-level starry flounder genome assembly with a length of 643.56 Mb (scaffold N50: 26.19 Mb, contig N50: 10.00 Mb) combining short-reads sequencing, PacBio HiFi sequencing, and Hi-C sequencing. Approximately 94.02% of assembled sequences were anchored into 24 pseudochromosomes, and a total of 18 telomeres were detected. Totally 22,835 protein-coding genes and 227.87 Mb repetitive sequences were identified. In summary, the high-quality chromosome-level genome assembly not only provides valuable resources for genetic research in starry flounder, but also advances the development of molecular breeding technology of starry flounder.

Animals↗

PubMed2025

The chromosome-level genome assembly of Prunus cerasifera 'Atropurpurea'.

Prunus cerasifera 'Atropurpurea' (Purpleleaf Plum), known for its unique purple-red foliage, is an important ornamental plant that enhances the aesthetic value of urban greening. To explore the molecular mechanisms underlying leaf color changes, this study assembled the Purpleleaf Plum genome, providing new insights for related research. We used HiFi sequencing data to assemble its genome. After chromosome anchoring, the final genome size was 244.89 Mb, with a contig N50 of 26.60 Mb, and approximately 97.10% of sequences were anchored to 8 chromosomes. Genome annotation identified 28,231 protein-coding genes, with LTR transposons comprising 27.93% of the genome. BUSCO assessment revealed a genome completeness of 98.9%. Telomeric repeat analysis identified 14 telomeres, with six chromosomes capped by double telomeres and two chromosomes containing a single telomere. This high-quality Purpleleaf Plum genome provides a solid foundation for future gene function analysis, cultivar improvement, and genetic research, offering valuable resources for related fields.

Genome, Plant↗

PubMed2025

Near-complete reference genome assembly of Hoya carnosa.

Hoya R. Br. is the largest genus in the tribe Marsdenieae (Apocynaceae), comprising 350-450 species. Hoya species are popular in horticulture for their distinctive floral traits and fragrances, primarily sourced from domestication and mutation breeding. However, the lack of molecular analysis for floral morphological traits has limited their cultivation and application. In this study, we assembled a near-complete reference genome for H. carnosa, the model species of the genus, using PacBio HiFi reads and Hi-C method. The genome size was approximately 465.7 Mb with a contig N50 of 39.3 Mb. 99.7% of the sequences were anchored to 11 pseudochromosomes, and the assembly achieved a BUSCO score of 98.5%. We predicted 24,309 protein-coding genes, of which 90.2% (21,927) were functionally annotated. This high-quality genome provides a valuable reference for the research of evolution, conservation and molecular breeding in Hoya.

Genome, Plant↗

PubMed2025

Chromosome-level genome assembly of Elaeocarpus petiolatus (Elaeocarpaceae).

Elaeocarpus petiolatus is an ecologically and economically important species in tropical and subtropical forests. Despite its significance, the lack of genomic resources has hindered research on the genetic diversity and adaptive traits of E. petiolatus. To address this gap, we present a comprehensive chromosome-level genome assembly of E. petiolatus generated using advanced PacBio high-fidelity (HiFi) long-read sequencing and Hi-C technology. The assembly spans 322.45 Mb, with a scaffold N50 of 20.58 Mb, indicating that 37.11% of the genome is composed of repetitive elements. We identified 25,295 protein-coding genes, of which 96.74% were functionally annotated. This high-quality genome provides a critical resource for understanding the genetic mechanisms underlying environmental adaptability and biosynthesis of bioactive compounds in E. petiolatus, thereby supporting conservation efforts and sustainable forest management. The assembled genome and associated sequencing data are publicly available, facilitating further evolutionary and functional studies on the Elaeocarpaceae family.

Chromosomes, Plant↗

PubMed2025

A chromosome-level genome assembly of Guimi No. 2 (Actinidia chinensis).

In this study, we report a high-quality chromosome-level genome assembly of Actinidia chinensis var. chinensis 'Guimi No. 2'. This cultivar, discovered in Guizhou karst ecosystems, exhibits resistance to Pseudomonas syringae pv. actinidiae (Psa). Using a combination of MGI short-read sequencing, PacBio HiFi long-read sequencing, and Hi-C technology, we generated a genome assembly of 608.43 Mb with a contig N50 of 20.70 Mb, and 99.70% of the assembly was successfully anchored onto 29 pseudochromosomes. The quality value (QV) and the LTR Assembly Index (LAI) of the assembled genome were 72.23 and 10.10. The BUSCO analysis indicated that the genome assembly and gene model prediction were 98.40% and 96.56% complete, respectively. A total of 251.15 Mb of repetitive sequences and 45,986 protein-coding genes were annotated. This genome assembly provides critical insights into A. chinensis's genomic architecture and serves as a foundational resource for elucidating disease resistance mechanisms against Psa, while enabling comparative phylogenomic studies across the Actinidia genus.

Actinidia↗

PubMed2025

A telomere-to-telomere reference genome assembly of the red silk cotton tree (Bombax ceiba).

Bombax ceiba, an important ornamental tree and potential fiber resource in the textile industry, is widely distributed in tropical and subtropical regions. In this study, we assembled a nearly gap-free telomere-to-telomere (T2T) genome of B. ceiba using Illumina, PacBio High-fidelity (HiFi), ONT ultra-long, and Hi-C sequencing technologies. The genome spanned approximately 807.89 Mb, with a scaffold N50 of 16.58 Mb, and 754.68 Mb (93.41%) of genomic sequences were anchored onto 48 pseudo-chromosomes. Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis revealed a completeness of 99.40%, identifying 1,378 single-copy and 213 duplicated genes out of 1,614. The genome contained 67.72% (547.11 Mb) repeat regions, with 39,708 predicted protein-coding genes. Collectively, our study provides valuable genomic data for investigating the evolutionary history of the Malvaceae family.

Genome, Plant↗

PubMed2025

A chromosomal-level genome assembly of Odontolabis cuvera Hope, 1842 (Coleoptera: Lucanidae).

The stag beetle (Coleoptera: Lucanidae) represents a captivating and evolutionarily significant group, regarded as one of the most basal lineages within the superfamily Scarabaeoidea. Despite their importance for studying beetle evolution and ecology, genomic resources for this family remain scarce. Here, we report a chromosome-level genome assembly of Odontolabis cuvera, generated by integrating PacBio HiFi, Illumina, and Hi-C data. The genome assembly spans 908.07 Mb, comprising 66 scaffolds (scaffold N50: 65.36 Mb) and 147 contigs (contig N50: 16.39 Mb). A total of 99.58% (904.22 Mb) of the assembly was anchored to 14 chromosomes. BUSCO analysis (insecta_odb10 dataset, n = 1,367) demonstrated high completeness, with 99.1% of conserved insect orthologs identified (98.3% single-copy, 0.8% duplicated). Repetitive elements accounted for 53.00% (281.28 Mb) of the genome, and a total of 18,332 protein-coding genes were annotated. This high-contiguity genome provides a critical foundation for uncovering the evolutionary mechanisms and ecological adaptations unique to Lucanidae.

Animals↗

PubMed2025

Chromosome-level genome assembly of Qihe gibel carp.

Qihe gibel carp (Carassius gibelio var. Qihe) is a local population of natural gynogenetic amphitriploid (AAABBB) Carassius gibelio, and has high nutritional and economic value. In this study, we assemble a high-quality chromosome-level genome of Qihe gibel carp through DNBSEQ, PacBio HiFi, and Hi-C sequencing data. The resulting assembly consisted of 350 contigs with the full length of 1.607 Gb and 96.21% (1.515 Gb) of the assembled genome was successfully anchored to 50 chromosomes, with a contig N50 of 28.97 Mb and a scaffold N50 of 29.84 Mb. Repeated sequences accounting for 43.72% (732.494 Mb) of the total were also identified, and gene prediction revealed 46,131 protein-coding genes with an annotation ratio of 96.48%. Furthermore, Benchmarking Universal Single-Copy Orthologue (BUSCO) analysis demonstrated that the genome assembly achieved high completeness, with a score of 97.66%. This high-quality chromosome-level genome lays the foundation for molecular biology research as well as molecular breeding and evolutionary studies of Qihe gibel carp in the future.

Animals↗

PubMed2025

A chromosome-level genome assembly of Coffea arabica L. var. 'Kona Typica'.

Coffea arabica L. var. 'Kona Typica' is renowned for its premium cup quality, but its vulnerability to pests and diseases limits production. To accelerate cultivar improvement, we generated a chromosome-level genome assembly of 'Kona Typica' using PacBio HiFi sequencing and Hi-C scaffolding technology. The final assembly spans 1.13 Gb, with a scaffold N50 of 50.50 Mb, organized into 22 chromosomes. BUSCO assessment indicated a high completeness at 99.1%. We annotated 65,458 protein-coding genes and identified 1,073,545 interspersed repeats, accounting for 65.16% of the genome. Analysis of transposon insertion ages revealed that most long terminal repeat retrotransposons proliferated after the polyploidization event. This high-quality genome assembly of 'Kona Typica' provides a valuable resource for exploring coffee genomic evolution and genetic mechanisms of complex traits, facilitating genomics studies and the development of improved coffee cultivars with enhanced disease resistance and quality traits.

Coffea↗

PubMed2025

Chromosome-level haplotype-resolved genome assembly of the giant honeycomb oyster, Hyotissa hyotis.

The giant honeycomb oyster, Hyotissa hyotis, a common bivalve inhabitant of tropical and subtropical coastal waters, holds significant ecological and economic importance due to its shell characteristics, rapid growth, and high-quality adductor muscle. However, the lack of high-quality genome has impeded the genetic study and artificial breeding of this species. In this study, we provided the first chromosomal-level haplotype-resolved assembly for the H. hyotis (2n = 20) by combining PacBio HiFi long-read and Hi-C sequencing. We obtained a haplotype-resolved assembly of 3.39 Gb in size, of which 96.69% were anchored to 20 chromosomes. The haplotype A and B genome (HapA and HapB) was 1,639.90 and 1,643.23 Mb in size, respectively. Accordingly, a total of 28,720 and 29,003 protein-coding genes were annotated from HapA and HapB. Through the BUSCO evaluation, the assembly and annotation results exhibited the completeness value of 94.65% and 94.03% for HapA, while 94.13% and 92.98% for HapB. This high-quality genome assembly provides valuable resource for further genetic studies and genetic improvement of the group of oysters.

Animals↗

PubMed2026

Chromosomal-level genome assembly of Trypanosoma carassii, the etiologic agent of a recent outbreak of trypanosomiasis in cage-cultured large yellow croaker (Larimichthys crocea) in China.

Trypanosoma carassii, a typical freshwater fish trypanosome, has recently been identified as the etiological agent of a trypanosomiasis outbreak in cage-cultured large yellow croaker (Larimichthys crocea) in China and has been designated as T. c. larimichthys. To date, publicly available genomic data for trypanosomes have been limited to terrestrial species, particularly those of medical importance. Here, we present a chromosome-level genome assembly of T. carassii, the first genome of an aquatic trypanosome, generated using PacBio HiFi long-read sequencing and Hi-C scaffolding technologies. A preliminary genome survey based on Illumina sequencing data estimated the genome size at 56.38 Mb with a heterozygosity of 1.17%. The final assembled genome spans 48.55 Mb, with contig N50 and scaffold N50 values of 139.15 Kb, and achieves 100.00% BUSCO completeness. Hi-C data resolved the assembly into 34 chromosomes and 9 unanchored scaffolds. Repetitive elements account for 53.29% of the genome (approximately 25.87 Mb). A total of 11,584 protein-coding genes were predicted, 95.36% of which were functionally annotated. Synonymous substitution rates analysis of paralogous genes indicates a recent burst of gene duplication, which likely corresponds to a whole-genome duplications. This high-quality genome assembly provides invaluable resources for understanding the evolution and host adaptation of aquatic trypanosomes.

Animals↗

PubMed2026

Chromosome-level genome assembly and annotation of the porcupine fish (Diodon hystrix).

The porcupinefish (Diodon hystrix), a coral reef teleost, is widely distributed in tropical/subtropical waters of the Pacific, Atlantic, Indian Oceans, and Mediterranean Sea. It shares easily recognizable features with pufferfish, such as body inflation and spines. Additionally, its culinary value makes D. hystrix a highly desirable species in many tropical coastal regions, with considerable market potential. However, lack of a high-quality genome hindered further studies on its reproduction, molecular biology, and genomic improvement. Here, we assembled the chromosome-scale genome using PacBio HiFi, ultra-long reads, and Hi-C. Of the 713.62 Mb genome, 98.63% anchored to 23 chromosomes (scaffold N50: 31.52 Mb) with 39.82% repetitive sequences. The assembled genome achieved a BUSCO completeness score of 97.7%, with 23,171 protein-coding genes predicted, 22,221 of which were functionally annotated. Phylogenetic analysis identified D. hystrix's evolutionary relationships with other species in the Tetraodontiformes. In summary, the high-quality genome of D. hystrix sheds light on valuable insights into genome size evolution, and provides a valuable resource for exploiting genomic study and breeding applications in this species.

Animals↗

PubMed2026

Chromosome-level genome assembly of Manglietia pachyphylla.

Manglietia pachyphylla, an endangered evergreen tree within the Magnoliaceae family, is renowned for its exceptional ornamental value in landscape horticulture. Despite its classification as a Category II nationally protected plant species in China, the genetic basis of its adaptive traits and conservation priorities remains poorly understood. To address this, we present the first chromosome-scale genome assembly of M. pachyphylla utilizing an integrated approach combining PacBio HiFi long-read and Hi-C chromosome conformation capture sequencing technologies. The assembled genome spans 2.15 Gb (contig N50 = 43.57 Mb), exhibiting a heterozygosity rate of 0.78% and repeat content of 78.64%, predominantly comprising long terminal repeat (LTR) retrotransposons (52.86%). Hi-C scaffolding anchored 99.57% of the assembly to 19 pseudochromosomes, achieving a BUSCO completeness score of 96.4%. Annotation revealed 42,505 putative protein-coding genes, with 84.46% of predicted genes were functionally annotated. Phylogenomic analysis positioned M. pachyphylla and Oyama sieboldii clustered together in a well-supported group. This high-contiguity genome assembly enables future investigations into adaptive evolution, functional genomics, and evidence-based conservation strategies for this endangered species.

Chromosomes, Plant↗

PubMed2026

High-Resolution Chromosome-Level Genome Assembly and Annotation of Triplophysa stewarti, an Endemic Plateau Loach from the Qinghai-Tibet Plateau.

The bottom-dwelling fish Triplophysa stewarti, endemic to the Qinghai-Tibet Plateau, is a valuable model for studying high-altitude adaptation in aquatic ecosystems. However, the lack of a high-quality reference genome has hindered comparative genomic and evolutionary studies within this genus. Here, we present a chromosome-level genome assembly for T. stewarti, generated using PacBio HiFi long-read sequencing and Hi-C scaffolding. The 697.9 Mb assembly is highly continuous (scaffold N50 of 253.58 Mb) and encompasses 25 chromosomes, representing 92.65% of the genome. BUSCO analysis indicated a 98.4% completeness, supporting the high quality of the assembly. We annotated 28,009 protein-coding genes, with 97.04% being functionally assigned across multiple databases (NR, UniProt, KEGG, GO, Pfam and InterPro). Additionally, repetitive elements constituted 42.47% of the genome, and we identified 52,709 non-coding RNAs. This high-quality reference genome provides a fundamental resource for exploring the adaptive evolution, population structure, and conservation genetics of T. stewarti and related species on the Qinghai-Tibet Plateau.

Animals↗