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PubMed2004

Analysis of the centromeric regions of the human genome assembly.

The sequence of the human genome is not yet complete, and major gaps remain at the centromere region of each chromosome, which is comprised of repetitive alpha satellite DNA. In this article, we describe the sequences in the vicinity of the centromere that are included in the current genome assembly, analyze the approximately 7Mb of alpha satellite that have been assembled thus far and anticipate the nature of the sequences that remain to be accounted for.

Centromere↗
PubMed2004

Odorant and vomeronasal receptor genes in two mouse genome assemblies.

Odorant receptors (ORs) and vomeronasal receptors (V1Rs and V2Rs) are large superfamilies of chemosensory receptors. As an extension of previous research using the 2001 Celera mouse genome assembly, we analyzed OR and V1R genes in the 2002 public mouse genome assembly. We identified 1403 OR genes (1068 potentially intact) and 332 V1R genes (164 potentially intact) in this C57BL/6J mouse genome. This expands the mouse OR and V1R superfamilies by adding approximately 100 OR and approximately 40 V1R potentially intact genes. The description of the genomic distribution of OR genes is more complete and accurate, and two major errors in OR gene distribution in the 2001 Celera assembly were corrected. For the first time, the complete genomic distribution of V1R genes was investigated in detail and placed in context with that of OR genes. V1R genes, like OR genes, tend to form clusters of similar genes in the genome. Comparison between the two genome assemblies revealed a high rate of single-nucleotide polymorphisms (SNPs) in both OR and V1R genes. The high ratio of nonsynonymous SNPs over synonymous SNPs in V1R genes suggests positive selection for these genes, possibly favoring species-specific and strain-specific pheromone detection. In addition, detailed analysis of the SNP rate aided in the identification of key residues in ORs.

Animals↗
PubMed2025

Chromosome-level genome assembly of the longhorn beetle Arhopalus rusticus (Coleoptera: Cerambycidae).

The longhorn beetle Arhopalus rusticus (Coleoptera: Cerambycidae) is a widely distributed wood-boring pest of conifers. Here, we assembled a chromosome-level genome of A. rusticus using Illumina, Oxford Nanopore, and Hi-C sequencing technologies. The assembled genome is 1180.40 Mb, with a scaffold N50 of 125.01 Mb, and BUSCO completeness of 93.6%. All contigs were assembled into ten pseudo-chromosomes. The genome contains 69.87% repeat sequences. We identify 18, 377 protein-coding genes in the genome, of which 11,368 were functionally annotated. This genome provides a valuable resource for understanding the ecology, genetics, and evolution of A. rusticus, as well as for controlling wood-boring pests.

Animals↗
PubMed2026

Chromosome-Level Genome Assembly of Solanum carolinense.

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.

Solanum carolinense↗
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↗
PubMed2025

First chromosome-level genome assembly of the colonial chordate model Botryllus schlosseri (Tunicata).

BACKGROUND: Botryllus schlosseri (Tunicata) is a colonial, laboratory model tunicate recognized for its remarkable developmental diversity, its regenerative abilities, and its peculiar genetically determined allorecognition system governed by a polymorphic locus controlling chimerism and cell parasitism. RESULTS: We report the first chromosome-level genome assembly of B. schlosseri subclade A1. By integrating long and short reads with Hi-C scaffolding, we produced both a phased diploid genome assembly and a conventional collapsed consensus sequence of 533 Mb. Of this total length, 96% belonged to 16 chromosome-scale scaffolds, with a BUSCO completeness score of 91.4%. We then compared our assembly with other high-quality tunicate genomes, revealing some synteny conservation but also extensive genomic rearrangements and a general loss of colinearity. CONCLUSIONS: The chromosome-level resolution of this assembly enhances our understanding of genome organization in colonial modular organisms. Comparative analyses highlight the dynamic nature of tunicate genomes, with conserved macrosynteny yet extensive microsyntenic rearrangements and scrambling, underscoring their rapid evolutionary trajectory. This high-quality genome assembly provides a valuable resource for exploring the unique biological features of colonial chordates, including their exceptional regenerative abilities and complex allorecognition system.

Animals↗
PubMed2003

PCAP: a whole-genome assembly program.

We describe a whole-genome assembly program named PCAP for processing tens of millions of reads. The PCAP program has several features to address efficiency and accuracy issues in assembly. Multiple processors are used to perform most time-consuming computations in assembly. A more sensitive method is used to avoid missing overlaps caused by sequencing errors. Repetitive regions of reads are detected on the basis of many overlaps with other reads, instead of many shorter word matches with other reads. Contaminated end regions of reads are identified and removed. Generation of a consensus sequence for a contig is based on an alignment of reads in the contig, in which both base quality values and coverage information are used to determine every consensus base. The PCAP program was tested on a mouse whole-genome data set of 30 million reads and a human Chromosome 20 data set of 1.7 million reads. The program is freely available for academic use.

Algorithms↗
PubMed2026

Annotated genome assemblies of two temperate North American dung beetles, Canthon chalcites and Phanaeus vindex.

Dung beetles serve as cultivators of their natural habitats, improving soil health and functions in both natural and anthropogenic environments. Despite their ecological importance, whole genome sequences for Scarabaeinae are limited. Here, we present the draft annotated genome assemblies for 2 temperate species of North American dung beetles collected from eastern Tennessee: Canthon chalcites and Phanaeus vindex. Both genome assemblies were generated from PacBio long reads and have high completeness, with BUSCO scores of 98.1% and 98.6% for C. chalcites and P. vindex, respectively. For C. chalcites, the BRAKER3 pipeline predicted 12,799 genes, and the gene set was 93.7% complete. For P. vindex, the BRAKER3 predicted 12,252 genes, and the gene set was 94.9% complete. From the annotated gene sets, orthologous protein sequence analyses among C. chalcites, P. vindex, the dung beetle species Onthophagus taurus, and the more evolutionarily distant beetle Tribolium castaneum indicated that there are 260 unique protein clusters for C. chalcites and 210 unique protein clusters for P. vindex. These 2 draft genomes provide valuable data for comparative genomics, evolution, and phylogenic studies for dung beetle species.

Animals↗
PubMed2026

Chromosome-Level Genome Assembly and Annotation of the Chinese Lizard Gudgeon (Saurogobio dabryi).

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.

Saurogobio dabryi↗
PubMed2026

De novo genome assemblies of threatened Asian hornbills (Bucerotidae) reveal declining population trajectories during the late Pleistocene.

BACKGROUND: Asian hornbills are flagship species of the wet tropics that face significant threats from hunting, habitat loss, and fragmentation. Despite being conservation flagships, whole genome information is available for only two of the 32 Asian hornbill species. In this study, we provide the first de novo genome assemblies for four hornbill species (Bucerotidae) in Asia. METHODS: We used a combination of long-read and short-read sequencing data to assemble and annotate de novo hybrid genomes of four species of hornbills. We also assembled and compared mitochondrial genomes of these species. Using a comparative genomics approach, we performed orthology assignment and gene evolution analyses to identify unique gene families in Asian hornbills, gene families that showed significant expansion, their functions and structural variation. Furthermore, using the Pairwise Sequentially Markov Coalescent (PSMC) method, we reconstructed demographic histories of hornbill species to examine changes in their population trajectories in the past. RESULTS: We present hybrid genome assemblies for Great Hornbill (B. bicornis - GH), Rufous-necked Hornbill (A. nipalensis- RNH), Malabar Pied Hornbill (A. coronatus- MPH) and Wreathed Hornbill (R. undulatus- WH). The genome sizes of these hornbills range from 1.1 Gb to 1.3 Gb, with over 95.9% completeness and gene prediction BUSCO. We reported 10,525 orthogroups shared among four Asian hornbill species and identified significant expansion in gene families associated with structural keratin development in Asian hornbills compared to their ancestors. We also provide annotated mitogenomes for each of these species. Furthermore, we found that the WH, a more abundant, widely distributed, and migratory species, showed a higher Ne than the other three hornbill species. However, an overall decline in Ne for all species was recorded during the Pleistocene climatic fluctuations. CONCLUSIONS: We present the first-ever, high-quality reference genomes for the threatened hornbill species from Asia. Hornbills have shown significant expansion in genes involved in structural keratin development. Our results indicate that Pleistocene climatic fluctuations have led to dramatic population declines in all four species. We believe that this study provides robust genomic resources to support future comparative and conservation genomics efforts for hornbills.

Animals↗
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↗
PubMed2024

Haplotype-resolved genome assembly and implementation of VitExpress, an open interactive transcriptomic platform for grapevine.

Haplotype-resolved genome assemblies were produced for Chasselas and Ugni Blanc, two heterozygous Vitis vinifera cultivars by combining high-fidelity long-read sequencing and high-throughput chromosome conformation capture (Hi-C). The telomere-to-telomere full coverage of the chromosomes allowed us to assemble separately the two haplo-genomes of both cultivars and revealed structural variations between the two haplotypes of a given cultivar. The deletions/insertions, inversions, translocations, and duplications provide insight into the evolutionary history and parental relationship among grape varieties. Integration of de novo single long-read sequencing of full-length transcript isoforms (Iso-Seq) yielded a highly improved genome annotation. Given its higher contiguity, and the robustness of the IsoSeq-based annotation, the Chasselas assembly meets the standard to become the annotated reference genome for V. vinifera. Building on these resources, we developed VitExpress, an open interactive transcriptomic platform, that provides a genome browser and integrated web tools for expression profiling, and a set of statistical tools (StatTools) for the identification of highly correlated genes. Implementation of the correlation finder tool for MybA1, a major regulator of the anthocyanin pathway, identified candidate genes associated with anthocyanin metabolism, whose expression patterns were experimentally validated as discriminating between black and white grapes. These resources and innovative tools for mining genome-related data are anticipated to foster advances in several areas of grapevine research.

Vitis↗
PubMed2026

Complete telomere-to-telomere genome assembly of Guazuma ulmifolia uncovers evolutionary mechanisms, drought adaptation, and flavonoid biosynthesis.

The first T2T reference genome of Guazuma ulmifolia is reported, which serves as a core genomic resource for stress adaptation research and stress-tolerant breeding in cacao wild relatives. Climate change, particularly increased incidence of drought, poses a major threat to food security. Understanding the genomic basis of environmental adaptation in crop wild relatives can provide valuable resources for improving stress resilience. Guazuma ulmifolia, a wild relative of Theobroma cacao with important ecological and medicinal value, lacks high-quality reference genomic resources. Here, we report the first telomere-to-telomere (T2T) chromosome-level genome assembly of G. ulmifolia, with a genome size of 311.31 Mb, contig N50 of 35.19 Mb, and 98.70% BUSCO completeness. Repetitive sequences constitute 27.43% of the G. ulmifolia genome, with LTR retrotransposons as the predominant class. Comparative genomic analyses revealed that genome-size variation among Malvaceae species is associated with differences in polyploidization history and TE dynamics. Ancestral karyotype reconstruction identified five lineage-specific chromosome fusion events distinguishing G. ulmifolia from T. cacao. Comparative analyses further identified tandem duplication-associated expansion of stress-related LEA and GST gene families, suggesting potential genomic features associated with stress responses. Flavonoid biosynthesis genes were largely conserved in copy number but showed tissue-specific expression patterns, providing candidate genes for investigating secondary metabolism. Together, this study establishes a high-quality T2T genome resource for exploring genome evolution, chromosome organization, and stress-related genomic features in Malvaceae.

Genome, Plant↗
PubMed2025

Chromosome-level genome assembly of the large carpenter bee Xylocopa dejeanii Lepeletier, 1841 (Hymenoptera: Apidae).

Xylocopinae, a diverse bee subfamily comprising over 1,000 bee species, and also a major model system for studying the pollination and evolution of sociality. The lack of chromosome-level genome assembly resources for the Xylocopinae limits our research of their biology and evolution. Here, we provided the first pseudo-chromosomes genome assembly of the Xylocopa dejeanii combined PacBio CLR long reads, Illumina sequences, and Hi-C data. The final genome is 194.44 Mb located in 16 chromosomes. Our assembly includes 141 scaffolds, with a scaffold N50 length of 13.15 Mb. BUSCO analysis revealed 99.00% completeness. Genome annotation identified 28.27 Mb of repetitive elements, 10,970 protein-coding genes, and 432 ncRNAs. This high-quality X. dejeanii assembly advances our understanding of Xylocopinae genomics and provides new insights into bee evolution.

Animals↗
PubMed2025

Chromosomal level genome assembly of medicinal plant Chrysosplenium macrophyllum.

Chrysosplenium macrophyllum Oliv., a perennial herb native to China, is widely used in traditional medicine for its notable therapeutic properties. However, the absence of a reference genome has constrained its full potential for research and application. This study presents the first chromosome-level de novo genome assembly of C. macrophyllum, constructed by integrating long reads from Oxford Nanopore Technologies (ONT), short reads from BGI, and Hi-C data. The final assembly spans 2.55 Gb, with a scaffold N50 of 93.38 Mb, and 83.70% of the genome has been assigned to 22 chromosomes. The mapping rate of the BGI short reads to the genome is approximately 97.94%, and BUSCO analysis reveals that 97.94% of the predicted genes are complete. A total of 62,921 protein-coding genes were predicted, with functional annotations for 93.67% of them. This chromosome-level genome assembly represents an important resource for expanding our understanding of Chrysosplenium species and supports future genomic studies and applications.

Genome, Plant↗
PubMed2025

Chromosomal genome assembly resolves drug resistance loci in the parasitic nematode Teladorsagia circumcincta.

The parasitic nematode Teladorsagia circumcincta is one of the most important pathogens of sheep and goats in temperate climates worldwide and can rapidly evolve resistance to drugs used to control it. To understand the genetics of drug resistance, we have generated a highly contiguous genome assembly for the UK T. circumcincta isolate, MTci2. Assembly using PacBio long-reads and Hi-C long-molecule scaffolding together with manual curation resulted in a 573 Mb assembly (N50 = 84 Mb, total scaffolds = 1,286) with five autosomal and one sex-linked chromosomal-scale scaffolds consistent with its karyotype. The genome resource was further improved via annotation of 22,948 genes, with manual curation of over 3,200 of these, resulting in a robust and near complete resource (96.3% complete protein BUSCOs) to support basic and applied research on this important veterinary pathogen. Genome-wide analyses of drug resistance, combining evidence from three distinct experiments, identified selection around known candidate genes for benzimidazole, levamisole and ivermectin resistance, as well as novel regions associated with ivermectin and moxidectin resistance. These insights into contemporary and historic genetic selection further emphasise the importance of contiguous genome assemblies in interpreting genome-wide genetic variation associated with drug resistance and identifying key loci to prioritise in developing diagnostic markers of anthelmintic resistance to support parasite control.

Animals↗
PubMed2026

De novo haplotype-resolved genome assembly of the endemic kiwifruit Actinidia hubeiensis.

The genus Actinidia, which encompasses the widely cultivated kiwifruit, is characterized by its rich species diversity. Wild Actinidia species serve as invaluable germplasm reservoirs for crop improvement. As an important kiwifruit species, Actinidia hubeiensis represents a unique taxonomic group endemic to Hubei Province, contributing valuable genetic diversity to the genus Actinidia. Here, we present a haplotype-resolved genome assembly for A. hubeiensis. The two haplotype assemblies (Hap1 and Hap2) spanned 658.03 Mb (N50 = 23.16 Mb) and 597.19 Mb (N50 = 20.89 Mb), encoding 35,741 and 36,647 high-confidence protein-coding genes, respectively. Based on comprehensive assessments, both haplotypes demonstrated high completeness (BUSCO completeness > 99%), excellent continuity (LAI up to 21.67), low base-error rates (QV > 40), and nearly complete read mapping rates (> 98%). This genome assembly provides crucial genomic resources for the genus, enriching our understanding of kiwifruit biodiversity and offering new insights into the genetic background and evolutionary characteristics of this distinctive species.

Actinidia↗