Hi-C Technology Research Articles

A high-quality genome assembly of the Spectacled Fulvetta (Fulvetta ruficapilla) endemic to China

The Spectacled Fulvetta (Fulvetta ruficapilla) is the type species of Fulvetta, an evolutionarily distinct group whose species show a high degree of sympatry in distribution and phenotypic convergence. To pave the way for insights into their adaptive evolution and speciation, we have assembled the first high quality reference genome for F. ruficapilla using high-fidelity (HiFi) long-read and Hi-C sequencing technologies. The resulting assembly spans a total of ~1.21 Gb with a contig N50 of 18.8 Mb and scaffold N50 of 75.9 Mb, and has a BUSCO completeness of 97.0%. The quality assessment suggests a high standard in base accuracy, continuity, and completeness of the assembly, comparable or close to that of Vertebrate Genomes Project. On this basis, we have annotated 23,774 protein-coding genes, of which 18,832 are functionally identified. The availability of this high-quality genome provides a solid foundation for the future studies of evolution and local adaptation in birds.

Chromosome scale genome assembly and annotation of coconut cultivar Chowghat Green Dwarf

The high-quality genome of coconut (Cocos nucifera L.) is a crucial resource for enhancing agronomic traits and studying genome evolution within the Arecaceae family. We sequenced the Chowghat Green Dwarf cultivar, which is resistant to the root (wilt) disease, utilizing Illumina, PacBio, ONT, and Hi-C technologies to produce a chromosome-level genome of ~ 2.68 Gb with a scaffold N50 of 174 Mb; approximately 97% of the genome could be anchored to 16 pseudo-molecules (2.62 Gb). In total, 34,483 protein-coding genes were annotated; the BUSCO completeness score was 96.80%, while the k-mer completeness was ~ 87%. The assembled genome includes 2.19 Gb (81.64%) of repetitive sequences, with long terminal repeats (LTRs) constituting the most abundant class at 53.76%. Additionally, our analysis confirms two whole-genome duplication (WGD) events in the C. nucifera lineage. A genome-wide analysis of LTR insertion time revealed ancient divergence and proliferation of copia and gypsy elements. In addition, 1368 RGAs were discovered in the CGD genome. We also developed a web server ‘Kalpa Genome Resource’ (http://210.89.54.198:3000/), to manage and store a comprehensive array of genomic data, including genome sequences, genetic markers, structural and functional annotations like metabolic pathways, and transcriptomic profiles. The web server has an embedded genome browser to analyze and visualize the genome, its genomics elements, and transcriptome data. The in-built BLAST server allows sequence homology searches against genome, annotated transcriptome & proteome sequences. The genomic dataset and the database will support comparative genome analysis and can expedite genome-driven breeding and enhancement efforts for tapping genetic gains in coconut.

A chromosome-level genome assembly of the heteronomous hyperparasitoid wasp Encarsia sophia.

Encarsia sophia, a heteronomous hyperparasitoid wasp, is a well-known biological control agent, but its genomic information is limited, hindering molecular investigations and understanding of multitrophic interactions. In this study, we present a chromosome-level genome assembly for E. sophia using Illumina, PacBio HiFi, and Hi-C technologies. The assembled genome size is 398.3 Mb, with a contig N50 of 1.0 Mb and a scaffold N50 of 74.0 Mb. The BUSCO completeness score is 97.1%, and genome coverage reaches 99.1%. Utilizing Hi-C assisted assembly, the genome was organized into five chromosomes, with a mounting rate of 95.1%. Repetitive sequences make up 54.6% of the genome, and 14,914 protein-coding genes were predicted, with 95.5% functionally annotated. The high-quality genome assembly of E. sophia is a significant achievement, marking the first complete genome for a heteronomous hyperparasitoid wasp. This milestone offers valuable insights into the evolution and host interactions of heteronomous hyperparasitoids, laying the foundation for extensive research in biological control.

New genomic resources inform transcriptomic responses to heavy metal toxins in the common Eastern bumble bee Bombus impatiens.

The common Eastern bumble bee Bombus impatiens is native to North America and is the main commercially reared pollinator in the Americas. There has been extensive research on this species related to its social biology, applied pollination, and genetics. The genome of this species was previously sequenced using short-read technology, but recent technological advances provide an opportunity for substantial improvements. This species is common in agricultural and urban environments, and heavy metal contaminants produced by industrial processes can negatively impact it. To begin to identify possible mechanisms underlying responses to these toxins, we used RNA-sequencing to examine how exposure to a cocktail of four heavy metals at field-realistic levels from industrial areas affected B. impatiens worker gene expression. PacBio long-read sequencing resulted in 544x coverage of the genome, and HiC technology was used to map chromatin contacts. Using Juicer and manual curation, the genome was scaffolded into 18 main pseudomolecules, representing a high quality, chromosome-level assembly. The sequenced genome size is 266.6Mb and BRAKER3 annotation produced 13,938 annotated genes. The genome and annotation show high completeness, with ≥ 96% of conserved Eukaryota and Hymenoptera genes present in both the assembly and annotated genes. RNA sequencing of heavy metal exposed workers revealed 603 brain and 34 fat body differentially expressed genes. In the brain, differentially expressed genes had biological functions related to chaperone activity and protein folding. Our data represent a large improvement in genomic resources for this important model species-with 10% more genome coverage than previously available, and a high-quality assembly into 18 chromosomes, the expected karyotype for this species. The new gene annotation added 777 new genes. Altered gene expression in response to heavy metal exposure suggests a possible mechanism for how these urban toxins are negatively impacting bee health, specifically by altering protein folding in the brain. Overall, these data are useful as a general high quality genomic resource for this species, and provide insight into mechanisms underlying tissue-specific toxicological responses of bumble bees to heavy metals.

Chromosome-level genome assembly of the mud carp (Cirrhinus molitorella) using PacBio HiFi and Hi-C sequencing

The mud carp (Cirrhinus molitorella) is an important economic farmed fish, mainly distributed in South China and Southeast Asia due to its strong adaptability and high yield. Despite its economic importance, the paucity of genomic information has constrained detailed genetic research and breeding efforts. In this study, we utilized PacBio HiFi long-read sequencing and Hi-C technologies to generate a meticulously assembled chromosome-level genome of the mud carp. This assembly spans 1,033.41 Mb, with an impressive 99.82% distributed across 25 chromosomes. The contig N50 and scaffold N50 are 33.29 Mb and 39.86 Mb, respectively. The completeness of the mud carp genome assembly is highlighted by a BUSCO score of 98.05%. We predict 25,865 protein-coding genes, with a BUSCO score of 96.54%, and functional annotations for 91.83% of these genes. Approximately 52.21% of the genome consists of repeat elements. This high-fidelity genome assembly is a vital resource for advancing molecular breeding, comparative genomics, and evolutionary studies of the mud carp and related species.

Chromosome-level genome assembly of the smallscale yellowfin (Plagiognathops microlepis)

The small-scale yellowfin (Plagiognathops microlepis) is a highly valued species in East Asian aquaculture due to its adaptability and high yield. However, the lack of genomic data has impeded genetic research and breeding efforts. In this study, we utilize PacBio Hifi long-read sequencing and Hi-C technologies to construct a highly detailed genome of P. microlepis at the chromosomal level. The assembly encompasses 976.41 Mb, with an exceptional 99.84% distribution across 24 chromosomes. Notably, the contig N50 was 34.41 Mb and scaffold N50 was 38.38 Mb. The completeness of the P. microlepis genome assembly is underscored by a BUSCO score of 98.08%. A total of 25,389 protein-coding genes were identified, with a BUSCO score of 96.98%, and 99.85% of these genes were functionally annotated. Synteny relationships at the chromosome level with Danio rerio and Chanodichthys erythropterus genomes uncover small-scale chromosomal rearrangements. This high-fidelity genome assembly serves as a pivotal resource for forthcoming endeavors such as the genome structure, functional elements, comparative genomics, and evolutionary characteristics of P. microlepis and its relative species.

The chromosome-level genome assembly and annotation of an invasive forest pest Obolodiplosis robiniae

Biological invasion is a major global problem, leading to the loss of biodiversity and species extinction, and causing huge economic losses to countries. Obolodiplosis robiniae is a major invasive forest pest that has caused economic losses in Asia and Europe. Here, the chromosome- level genome of O. robiniae was assembled using the PacBio platform and Hi-C technology. A contig-level genome with a length of 199.49 Mb and a contig N50 of 4.66 Mb was assembled. Approximately 98.05% of contigs were successfully anchored to four chromosomes using Hi-C assisted genome assembly. The genome integrity was assessed to be 90.3% based on BUSCOs analysis. The high-quality genome provides valuable data for the study of invasive species, and a foundation for the understanding the biology and ecology of O. robiniae.

Modification of the hi-c technology for molecular genetic analysis of formalin-fixed paraffin-embedded sections of tumor tissues

Molecular genetic analysis of tumor tissues is the most important step towards understanding the mechanisms of cancer development, and it is also necessary for the choice of targeted therapy. Hi-C (high-throughput chromatin conformation capture) technology can be used to detect various types of genomic variants, including balanced chromosomal rearrangements: inversions and translocations. In this work, we propose a modification of the Hi-C method for the analysis of chromatin contacts in formalin-fixed paraffin-embedded (FFPE) sections of tumor tissues. Our results demonstrate that this protocol allow to generate high-quality Hi-C data and detect all types of chromosomal rearrangements. We have analyzed various databases to compile a comprehensive list of translocations that hold clinical importance for targeted therapy selection. The practical value of molecular genetic testing is its ability to influence patient treatment strategies and provide prognostic insights. Detecting specific chromosomal rearrangements can guide the choice of targeted therapies, which is a critical aspect of personalized medicine in oncology.

Chromosome-scale genome assembly of Codonopsis pilosula and comparative genomic analyses shed light on its genome evolution.

Codonopsis pilosula is a significant plant in traditional Chinese medicine, valued for its edible and medicinal properties. However, the lack of available genomic resources has hindered further research. This study presents the first chromosome-scale genome assembly of C. pilosula using PacBio CLR reads and Hi-C scaffolding technology. Additionally, Ks analysis and syntenic depth analysis were performed to elucidate its evolutionary history. The final assembly yielded a high-quality genome of 679.20 Mb, which was anchored to 8 pseudo-chromosomes with an anchoring rate of 96.5% and a scaffold N50 of 80.50 Mb. The genome assembly showed a high completeness of 97.6% based on Benchmarking with Universal Single-Copy Orthologs (BUSCO) analysis. Repetitive elements constituted approximately 76.8% of the genome, with long terminal repeat retrotransposons (LTRs) accounting for about 39.17%. Ks and syntenic depth analyses revealed that the polyploidization history of three platycodonoid clade species involved only the γ-WGT event. Karyotype evolutionary analysis identified an ancestral karyotype with 9 protochromosomes for the three platycodonoid clade species. Moreover, non-WGD genes, particularly those arising from tandem duplications, were found to contribute significantly to gene family expansion. These findings provide essential insights into the genetic diversity and evolutionary biology of C. pilosula, aiding its conservation and sustainable use.

Chromosome-level genome of Osmia excavata (Hymenoptera: Megachilidae) provides insights into low-temperature tolerance of Osmia pollinator.

The solitary bee Osmia excavata (Hymenoptera: Megachilidae) is a key pollinator managed on a large scale. It has been widely used for commercial pollination of fruit trees, vegetables, and other crops with high efficiency in increasing the crop seeding rate, yield, and seed quality in Northern hemisphere. Here, a high-quality chromosome-level genome of O. excavata was generated using PacBio sequencing along with Hi-C technology. The genome size was 207.02Mb, of which 90.25% of assembled sequences were anchored to 16 chromosomes with a contig N50 of 9,485kb. Approximately 186.83Mb, accounting for 27.93% of the genome, was identified as repeat sequences. The genome comprises 12,259 protein-coding genes, 96.24% of which were functionally annotated. Comparative genomics analysis suggested that the common ancestor of O. excavata and Osmia bicornis (Hymenoptera: Megachilidae) lived 8.54 million years ago. Furthermore, cytochrome P450 family might be involved in the responses of O. excavata to low-temperature stress. Taken together, the chromosome-level genome assembly of O. excavata provides in-depth knowledge and will be a helpful resource for the pollination biology research.

Chromosome-level genome assembly of Cyamophila willieti (Hemiptera: Psyllidae)

Cyamophila willieti (Hemiptera: Psyllidae) is a significant pest that adversely affects the growth of Styphnolobium japonicum and its variant, Styphnolobium japonicum f. pendula. Despite its impact, research on this species remains limited. In this study, we successfully assembled a chromosome-level genome for Cyamophila willieti using a comprehensive approach that integrated Illumina sequencing, PacBio sequencing, and Hi-C technology. The genome size was determined to be 361.61 Mb, with a scaffold N50 length of 28.90 Mb. Additionally, the genome was mapped to 13 chromosomes (N = 12 A + X), and a total of 15,841 genes were predicted, with 90.38% of them functionally annotated. In summary, the high-quality genome of Cyamophila willieti provides valuable data to support further research, including pest management strategies.

Chromosome-level genome assembly of two cultivated Jujubes

Jujube (Ziziphus jujuba Mill.) is a valuable tree species with economic, edible, medicinal, and ecological conservation benefits. In this study, we used PacBio HiFi sequencing and Hi-C technology to assemble chromosome-level genomes of two cultivated Jujubes, namely ‘Lingwuchangzao’ and ‘Shiguang’. The genome sizes of ‘Lingwuchangzao’ and ‘Shiguang’ were 385.66 Mb and 394.12 Mb, respectively, with contig N50 sizes of 30.62 Mb and 4.30 Mb. These genomes contained 31,082 and 31,015 protein-coding genes, with repeat element contents of 42.11% and 42.33%, respectively. Phylogenetic analysis revealed that ‘Lingwuchangzao’ was sister to ‘Shiguang’ and followed by ‘Dongzao’. Additionally, comparative analysis of gene families among ‘Lingwuchangzao’, ‘Shiguang’, ‘Dongzao’, ‘Junzao’, and ‘Suanzao’ identified 15,988 (57.98%) core gene families, 11,191 (40.59%) disposable gene families, and 394 (1.43%) private gene families. Overall, the assembly of the genomes of these two cultivated Jujube varieties provides valuable genetic information for Jujube evolution, functional genomics research, and molecular breeding.

Chromosome-level genome assembly of the cashmere goat

The goat, an early domesticated ruminant, is a reliable source of cashmere, meat and milk in global agricultural production. Despite this, the genome of cashmere-rich goats has yet to be characterized. Here, we assembled the nearly complete genome of a cashmere goat from a highly economically valuable Inner Mongolian Cashmere buck, utilizing a combination of PacBio HiFi, ONT ultra-long reads, and Hi-C technologies. The size of this genome is 2.76 Gb, with a contig N50 of 95.22 Mb. All assembled sequences were anchored onto 29 autosomes and both sex chromosomes, with only two gaps present on the X chromosome. We identified 1,333.29 Mb (48.26%) of repetitive sequences and predicted 22,480 protein-coding genes. Assembly quality assessment of the genome demonstrated that our assembled cashmere goat genome surpasses the continuity, completeness, and accuracy of other published goat genomes. Taken together, we provided the first cashmere goat assembly, bridging the gap in the genome of important economic breeds of domestic goats, and providing a valuable reference resource for goat genetics and genome research.

Chromosome-Scale Genome and Transcriptomic Analyses Reveal Differential Regulation of Terpenoid Secondary Metabolites in Hericium coralloides.

Construction of the genome of Hericium coralloides, a species of edible mushroom, and identification of the genes involved in terpenoid biosynthesis can determine the biology and genetics of terpenoids. The present study describes the assembly of a high-quality chromosome-scale genome of H. coralloides using Pacbio HiFi sequencing and Hi-C technology. This genome consisted of 13 chromosomes, a total size of 43.6 Mb, contigs of N50 3.6 Mb, GC content at 54%, and BUSCOs integrity of 96.9%. Genes associated with terpenoid biosynthesis were predicted by KEGG enrichment analysis and homologous alignment. The Her011461 and Her008335 genes, encoding proteins in the terpenoid backbone synthesis pathway, were found to encode geranylgeranyl pyrophosphate and farnesyl diphosphate synthases, key enzymes in the biosynthesis of geranylgeranyl diphosphate, a precursor of several diterpenoids. Her011463 was found to be involved in regulating diterpene cyclase. The Her005433, Her006724, Her010605, and Her010608 genes were found to encode sesquiterpene synthesis. Most of these genes were more highly expressed in dikaryotic mycelia than in the primordium and fruiting bodies, indicating that terpenoids may be more abundant in dikaryotic mycelia. To our knowledge, this study is the first to assemble the H. coralloides genome at the chromosome scale and to identify the genes involved in terpenoid biosynthesis.

Chromosome genome assembly and annotation of Adzuki Bean (Vigna angularis)

Adzuki bean (Vigna angularis) is a significant dietary legume crop that is prevalent in East Asia. It also holds traditional medicinal importance in China. In this study, we report a high-quality, chromosome-level genome assembly of adzuki bean obtained by employing Illumina short-read sequencing, PacBio long-read sequencing, and Hi-C technology. The assembly spans 447.8 Mb, encompassing 96.32% of the estimated genome, with contig and scaffold N50 values of 16.5 and 41.0 Mb, respectively. More than 98.2% of the 1,614 BUSCO genes were fully identified, and 25,939 genes were annotated, with 98.23% of them being functionally identifiable. Vigna angularis was estimated to diverge successively from Vigna unguiculata and Vigna radiata about 15.3 and 8.7 million years ago (Ma), respectively. This chromosome-level reference genome of Vigna angularis provides a robust foundation for exploring the functional genomics and genome evolution of adzuki bean, thereby facilitating advancements in molecular breeding of adzuki bean.

Chromosome-scale genome assembly of Astragalus membranaceus using PacBio and Hi-C technologies

Astragalus membranaceus (Fisch.) Bge (AM) is a medicinal herb plant belonging to the Leguminosae family. In this study, we present a chromosome-scale genome assembly of AM, aiming to enhance the molecular biology and functional studies of Astragali Radix. The genome size of AM is about 1.43 Gb, with a contig N50 value of 1.67 Mb. A total of 98.16% of the assembly anchored to 9 pseudochromosomes using Hi-C technology. The assembly completeness was estimated to be 97.27% using BUSCO with the long terminal repeat assembly index (LAI) of 16.22 and quality value (QV) of 48.58. Additionally, the genome contained 67.98% repetitive sequences. Genome annotation predicted 29,914 protein-coding genes, including 73 genes involved in the flavonoid biosynthetic pathway and 2,048 transcription factors. The high-quality genome assembly and gene annotation resources will greatly facilitate future functional genomic studies in Leguminosae species.

Chromosome-level genome assembly of Huai pig (Sus scrofa)

Although advances in long-read sequencing technology and genome assembly techniques have facilitated the study of genomes, little is known about the genomes of unique Chinese indigenous breeds, including the Huai pig. Huai pig is an ancient domestic pig breed and is well-documented for its redder meat color and high forage tolerance compared to European domestic pigs. In the present study, we sequenced and assembled the Huai pig genome using PacBio, Hi-C, and Illumina sequencing technologies. The final highly contiguous chromosome-level Huai pig genome spans 2.53 Gb with a scaffold N50 of 138.92 Mb. The Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness score for the assembled genome was 95.33%. Remarkably, 23,389 protein-coding genes were annotated in the Huai-pig genome, along with 45.87% repetitive sequences. Overall, this study provided new foundational resources for future genetic research on Chinese domestic pigs.

Chromosome-Level Genome Assembly for the Chinese Serow (Capricornis milneedwardsii) Provides Insights Into Its Taxonomic Status and Evolution.

Chinese serow (Capricornis milneedwardsii) is mainly distributed in the south of Yellow River in China, which has been listed as vulnerable by the International Union for Conservation of Nature (IUCN). However, the reference genome of serow has not been reported and its taxonomic status is still unclear. Here, we first constructed a high-quality chromosome-level reference genome of C. milneedwardsii using PacBio long HiFi reads combined with Hi-C technology. The assembled genome was ~2.83 Gb in size, with a contig N50 of 100.96 Mb and scaffold N50 of 112.75 Mb, which were anchored onto 24 chromosomes. Furthermore, we found that the Chinese serow was more closely related to muskox, which diverged from ~4.85 million years ago (Mya). Compared to the karyotype of goat (2n = 60), we found the Chinese serow (2n = 48) experienced six chromosome fusions, which resulted in the formation of six central centromere chromosomes. We also identified two positively selected genes (MYH6 and DCSTAMP) specific to Chinese serow, which were involved in 'viral myocarditis' and 'Cardiac muscle contraction'. Interestingly, compared to other Caprinae animals, the MYH6 protein of Chinese serow occurred two mutations (E1520S and G1521S), which might be related to hypoxia tolerance. The high-quality reference genome of C. milneedwardsii provides a valuable information for protection of serows and insights into its evolution.

Chromosome-level genome assembly and annotation of Clanis bilineata tsingtauica Mell (Lepidoptera: Sphingidae).

The soybean hawkmoth Clanis bilineata tsingtauica Mell (Lepidoptera, Sphingidae; CBT), as one of the main leaf-chewing pests of soybeans, has gained popularity as an edible insect in China recently due to its high nutritional value. However, high-quality genome of CBT remains unclear, which greatly limits further research. In the present study, we assembled a high-quality chromosome-level genome of CBT using PacBio HiFi reads and Hi-C technologies for the first time. The size of the assembled genome is 477.45 Mb with a contig N50 length of 17.43 Mb. After Hi-C scaffolding, the contigs were anchored to 29 chromosomes with a mapping rate of 99.61%. Benchmarking Universal Single-Copy Orthologues (BUSCO) completeness value is 99.49%. The genome contains 252.16 Mb of repeat elements and 14,214 protein-coding genes. In addition, chromosomal synteny analysis showed that the genome of CBT has a strong synteny with that of Manduca sexta. In conclusion, this high-quality genome provides an important resource for future studies of CBT and contributes to the development of integrated pest management strategies.

High-quality chromosome-level genomic insights into molecular adaptation to low-temperature stress in Madhuca longifolia in southern subtropical China

BackgroundMadhuca longifolia, the energy-producing and medicinal tropical tree originally from southern India, faces difficulties in adapting to the low temperatures of late autumn and early winter in subtropical southern China, impacting its usability. Therefore, understanding the molecular mechanisms controlling the ability of this species to adapt to environmental challenges is essential for optimising horticulture efforts. Accordingly, this study aimed to elucidate the molecular responses of M. longifolia to low-temperature stress through genomic and transcriptomic analyses to inform strategies for its effective cultivation and utilisation in colder climates.ResultsHerein, the high-quality reference genome and genomic assembly for M. longifolia are presented for the first time. Using Illumina sequencing, Hi-C technology, and PacBio HiFi sequencing, we assembled a chromosome-level genome approximately 737.92 Mb in size, investigated its genomic features, and conducted an evolutionary analysis of the genus Madhuca. Additionally, using transcriptome sequencing, we identified 17,941 differentially expressed genes related to low-temperature response. Through bioinformatics analysis of the WRKY gene family, 15 genes crucial for M. longifolia low-temperature resistance were identified.ConclusionsThis research not only lays the groundwork for the successful ecological adaptation and cultivation of M. longifolia in China’s southern subtropical regions but also offers valuable insights for the genetic enhancement of cold tolerance in tropical species, contributing to their sustainable horticulture and broader industrial, medicinal, and agricultural use.