Chromosome-level Assembly Research Articles

Dispensable genome and segmental duplications drive the genome plasticity in Fusarium solani

Fusarium solani is a species complex encompassing a large phylogenetic clade with diverse members occupying varied habitats. We recently reported a unique opportunistic F. solani associated with unusual dark galls in sugarbeet. We assembled the chromosome-level genome of the F. solani sugarbeet isolate strain SB1 using Oxford Nanopore and Hi-C sequencing. The average size of F. solani genomes is 54 Mb, whereas SB1 has a larger genome of 59.38 Mb, organized into 15 chromosomes. The genome expansion of strain SB1 is due to the high repeats and segmental duplications within its three potentially accessory chromosomes. These chromosomes are absent in the closest reference genome with chromosome-level assembly, F. vanettenii 77-13-4. Segmental duplications were found in three chromosomes but are most extensive between two specific SB1 chromosomes, suggesting that this isolate may have doubled its accessory genes. Further comparison of the F. solani strain SB1 genome demonstrates inversions and syntenic regions to an accessory chromosome of F. vanettenii 77-13-4. The pan-genome of 12 publicly available F. solani isolates nearly reached gene saturation, with few new genes discovered after the addition of the last genome. Based on orthogroups and average nucleotide identity, F. solani is not grouped by lifestyle or origin. The pan-genome analysis further revealed the enrichment of several enzymes-coding genes within the dispensable (accessory + unique genes) genome, such as hydrolases, transferases, oxidoreductases, lyases, ligases, isomerase, and dehydrogenase. The evidence presented here suggests that genome plasticity, genetic diversity, and adaptive traits in Fusarium solani are driven by the dispensable genome with significant contributions from segmental duplications.

Chromosome-level reference genome assembly of the gyrfalcon (Falco rusticolus) and population genomics offer insights into the falcon population in Mongolia

The taxonomic classification of a falcon population found in the Mongolian Altai region in Asia has been heavily debated for two centuries and previous studies have been inconclusive, hindering a more informed conservation approach. Here, we generated a chromosome-level gyrfalcon reference genome using the Vertebrate Genomes Project (VGP) assembly pipeline. Using whole genome sequences of 49 falcons from different species and populations, including “Altai” falcons, we analyzed their population structure, admixture patterns, and demographic history. We find that the Altai falcons are genomic mosaics of saker and gyrfalcon ancestries, and carry distinct W and mitochondrial haplotypes that cluster with the lanner falcon. The Altai maternally-inherited haplotypes diverged 422,000 years before present (290,000–550,000 YBP) from the ancestor of sakers and gyrfalcons, both of which, in turn, split 109,000 YBP (70,000–150,000 YBP). The Altai W chromosome has 31 coding variants in 29 genes that may possibly influence important structural, behavioral, and reproductive traits. These findings provide insights into the question of Altai falcons as a candidate distinct species.

Chromosome level genome assembly and annotation of Hanseniaspora mollemarum CBS 18055 strain.

Hanseniaspora species gained attention due to the ability of these species to ferment simple sugars and to actively contribute to the development of bouquet aromas in wine and cider fermentations. We present a chromosome-level assembly of an isolate of Hanseniaspora mollemarum that would enhance its potential applications.

Genome sequences of four Ixodes species expands understanding of tick evolution

BackgroundTicks, hematophagous Acari, pose a significant threat by transmitting various pathogens to their vertebrate hosts during feeding. Despite advances in tick genomics, high-quality genomes were lacking until recently, particularly in the genus Ixodes, which includes the main vectors of Lyme disease.ResultsHere, we present the genome sequences of four tick species, derived from a single female individual, with a particular focus on the European species Ixodes ricinus, achieving a chromosome-level assembly. Additionally, draft assemblies were generated for the three other Ixodes species, I. persulcatus, I. pacificus, and I. hexagonus. The quality of the four genomes and extensive annotation of several important gene families have allowed us to study the evolution of gene repertoires at the level of the genus Ixodes and of the tick group. We have determined gene families that have undergone major amplifications during the evolution of ticks, while an expression atlas obtained for I. ricinus reveals striking patterns of specialization both between and within gene families. Notably, several gene family amplifications are associated with a proliferation of single-exon genes—most strikingly for fatty acid elongases and sulfotransferases.ConclusionsThe integration of our data with existing genomes establishes a solid framework for the study of gene evolution, improving our understanding of tick biology. In addition, our work lays the foundations for applied research and innovative control targeting these organisms.

Chromosome-level genome assembly of the pine wood nematode carrier Arhopalus unicolor

Arhopalus unicolor is a carrier of the pine wood nematode (PWN), which causes pine wilt disease, killing pine trees and causing considerable economic and environmental losses. While the A. unicolor mitochondrial genome has been published, a high-quality genome assembly and annotation of A. unicolor is not yet available. To address this, we assembled a chromosome-level reference genome assembly of A. unicolor with a combination of Illumina, PacBio, and Hi-C sequencing technologies. The final genome size was determined to be 1268.11 Mb, with a GC% of 32.44%, and the scaffold N50 value was 19.30 Mb. A total of 98.77% of the assembled sequences mapped to 10 pseudochromosomes, and BUSCO analysis revealed high completeness, with 97.15% gene coverage. Furthermore, the genome contains 71.74% repeat elements and encompasses 16,450 predicted protein-coding genes. This genome sequence of A. unicolor will be a valuable resource for understanding the genetics and evolutionary history of this species and for developing effective management strategies for this PWN carrier.

A Chromosome level assembly of pomegranate (Punica granatum L.) variety grown in arid environment

The pomegranate (Punica granatum L.) is an ancient fruit-bearing tree known for its nutritional and antioxidant properties. They originated from the Middle East in regions having large farms including mountainous regions of Al-Baha in Saudi Arabia. Pomegranates can tolerate arid climates and are considered among the fruits that will play a major role in food security. However, the genomics resources of pomegranate growing in arid regions are scarce. Here, we present a high-quality chromosome-level reference genome using PacBio HiFi long reads. The final assembly was 384.65 Mb with N50 contig size of 43.11 Mb, with 353.42 Mb being anchored on the eight pseudo chromosomes. Annotation revealed that 48.79% of the genome comprises repetitive elements and contains 21,620 protein-coding genes. The new reference genome will contribute to identifying stress resistance traits in pomegranates thriving in arid environments as well as new dietary antioxidants and antimicrobial peptides with pharmaceutical and therapeutic applications.

Genomic Resources for the Scuttle Fly Megaselia abdita: A Model Organism for Comparative Developmental Studies in Flies.

The order Diptera (true flies) holds promise as a model taxon in evolutionary developmental biology due to the inclusion of the model organism, Drosophila melanogaster, and the ability to cost-effectively rear many species in laboratories. One of them, the scuttle fly Megaselia abdita (Phoridae) has been used in evolutionary developmental biology for 30 years and is an excellent phylogenetic intermediate between fruit flies and mosquitoes but remains underdeveloped in genomic resources. Here, we present a de novo chromosome-level assembly and annotation of M. abdita and transcriptomes of 9 embryonic and 4 postembryonic stages. We also compare 9 stage-matched embryonic transcriptomes between M. abdita and D. melanogaster. Our analysis of these resources reveals extensive chromosomal synteny with D. melanogaster, 28 orphan genes with embryo-specific expression including a novel F-box LRR gene in M. abdita, and conserved and diverged features of gene expression dynamics between M. abdita and D. melanogaster. Collectively, our results provide a new reference for studying the diversification of developmental processes in flies.

The haplotype-resolved and chromosome-level reference genome assembly of Diospyros deyangensis provides insights into the evolution and juvenile growth of persimmon

Abstract The Diospyros genus, which includes both wild and cultivated species such as Diospyros lotus and Diospyros kaki, represents a diverse genetic pool with significant agricultural value. In this study, we present a high-quality, haplotype-resolved, chromosome-level genome assembly for D. deyangensis (hereinafter referred to as “Deyangshi”), an autotetraploid wild species notable for its short juvenile phase, by integrating high-fidelity single-molecule, nanopore sequencing, and high-throughput chromosome conformation capture techniques. The assembled genome size is approximately 3.01 Gb, anchored onto 60 pseudo-chromosomes. Comparative genomic analysis revealed that the D. deyangensis genome underwent an additional whole-genome duplication event following the eudicots shared ancient hexaploidy event. Resequencing and clustering on 63 samples representing 11 geographically diverse Diospyros accessions revealed significant genetic differentiation between D. deyangensis and D. kaki, as well as between D. kaki and other Diospyros species using population genomic analyses, suggesting that D. kaki followed an independent evolutionary pathway. Additionally, we identified DdELF4 (EARLY FLOWERING 4) from the “Deyangshi” backcross population using bulked segregant RNA sequencing (BSR-seq) with 50 early flowering and 50 non-early flowering individuals. Overexpression of DdELF4 in Arabidopsis resulted in delayed flowering and down-regulation of FT gene expression, indicating its role as a flowering repressor. This high-quality genome assembly of “Deyangshi” provides an essential genomic resource for the Diospyros genus, particularly for breeding programs focused on developing early-flowering persimmon varieties.

The vertebrate small leucine-rich proteoglycans: amplification of a clustered gene family and evolution of their transcriptional profile in jawed vertebrates.

Small Leucine-Rich Proteoglycans (SLRPs) are a major family of vertebrate proteoglycans. In bony vertebrates, SLRPs have a variety of functions from structural to signaling and are found in extracellular matrices, notably in skeletal tissues. However, there is little or no data on the diversity, function and expression patterns of SLRPs in cartilaginous fishes, which hinders our understanding of how these genes evolved with the diversification of vertebrates, in particular regarding the early events of whole genome duplications that shaped gnathostome and cyclostome genomes. We used a selection of chromosome-level assemblies of cartilaginous fish and other vertebrate genomes for phylogeny and synteny reconstructions, allowing better resolution and understanding of the evolution of this gene family in vertebrates. Novel SLRP members were uncovered together with specific loss events in different lineages. Our reconstructions support that the canonical SLRPs have originated from different series of tandem duplications that preceded the extant vertebrate last common ancestor, one of them even preceding the extant chordate last common ancestor. They then further expanded with additional tandem and whole-genome duplications during the diversification of extant vertebrates. Finally, we characterized the expression of several SLRP members in the small-spotted catshark Scyliorhinus canicula and from this, inferred conserved and derived SLRP expression in several skeletal and connective tissues in jawed vertebrates.

Chromosome-level assembly of basil genome unveils the genetic variation driving Genovese and Thai aroma types.

Basil, Ocimum basilicum L., is a widely cultivated aromatic herb, prized for its culinary and medicinal uses, predominantly owing to its unique aroma, primarily determined by eugenol for Genovese cultivars or methyl chavicol for Thai cultivars. To date, a comprehensive basil reference genome has been lacking, with only a fragmented draft available. To fill this gap, we employed PacBio HiFi and Hi-C sequencing to construct a homeolog-phased chromosome-level genome for basil. The tetraploid basil genome was assembled into 26 pseudomolecules and further categorized into subgenomes. High levels of synteny were observed between the two basil subgenomes but comparisons to Salvia rosmarinus show collinearity quickly breaks down in near relatives. We utilized a bi-parental population derived from a Genovese × Thai cross to map quantitative trait loci (QTL) for the aroma chemotype. We discovered a single QTL governing the eugenol/methyl chavicol ratio, which encompassed a genomic region with 95 genes, including 15 genes encoding a shikimate O-hydroxycinnamoyltransferase (HCT/CST) enzyme. Of them, only ObHCT1 exhibited significantly higher expression in the Genovese cultivar and showed a trichome-specific expression. ObHCT1 was functionally confirmed as a genuine HCT enzyme using an in vitro assay. The high-quality, contiguous basil reference genome is now publicly accessible at BasilBase, a valuable resource for the scientific community. Combined with insights into cell-type-specific gene expression, it promises to elucidate specialized metabolite biosynthesis pathways at the cellular level.

Genomic features of lichen-associated black fungi.

Lichens are mutualistic associations consisting of a primary fungal host, and one to few primary phototrophic symbiont(s), usually a green alga and/or a cyanobacterium. They form complex thallus structures, which provide unique and stable habitats for many other microorganisms. Frequently isolated from lichens are the so-called black fungi, or black yeasts, which are mainly characterized by melanized cell walls and extremophilic lifestyles. It is presently unclear in which ways these fungi interact with other members of the lichen symbiosis. Genomic resources of lichen-associated black fungi are needed to better understand the physiological potential of these fungi and shed light on the complexity of the lichen consortium. Here, we present high-quality genomes of 14 black fungal lineages, isolated from lichens of the rock-dwelling genus Umbilicaria. Nine of the lineages belong to the Eurotiomycetes (Chaetothyriales), four to the Dothideomycetes, and one to the Arthoniomycetes, representing the first genome of a black fungus in this class. The PacBio-based assemblies are highly contiguous (5-42 contigs per genome, mean coverage of 79-502, N50 of 1.0-7.3 mega-base-pair (Mb), Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness generally ≥95.4%). Most contigs are flanked by a telomere sequence, suggesting we achieved near chromosome-level assemblies. Genome sizes range between 26 and 44 Mb. Transcriptome-based annotations yielded ~11,000-18,000 genes per genome. We analyzed genome content with respect to repetitive elements, biosynthetic genes, and effector genes. Each genome contained a polyketide synthase gene related to the dihydroxynaphthalene-melanin pathway. This research provides insights into genome content and metabolic potential of these relatively unknown, but frequently encountered lichen associates.

A chromosome-level genome assembly of skipjack tuna, Katsuwonus pelamis (Perciformes: Scombridae)

Skipjack tuna (Katsuwonus pelamis), a highly migratory pelagic species widely distributed in tropical and subtropical oceanic regions, has consistently ranked third in global fishery landings from 2015 to 2022 and holds substantial economic significance for the coastal fisheries of Pacific Rim countries. Integrating PacBio and Hi-C data, a chromosome-level assembly of its genome was accomplished. This assembly comprises 24 pseudo-chromosomes, yielding a genome size of 827.9 Mb with a scaffold N50 length of 32.7 Mb, indicative of a highly contiguous assembly. A BUSCO assessment ascertained the comprehensiveness of the genome at 98.7%, indicative of comprehensive genomic representation. A total of 32,001 protein-coding genes were predicted with 31,993 genes (99.98%) annotated. The chromosome-level genome assembly of K. pelamis is key to understanding its evolution and genetics, facilitating targeted conservation and sustainable fishing practices for this economically important species.

Chromosome-level assemblies of the endemic Korean species Abeliophyllum distichum and Forsythia ovata

Abeliophyllum distichum and Forsythia ovata are closely related species endemic to Korea and are highly valued as ornamental shrubs in the Oleaceae family. A combination of PacBio and Illumina sequencing with Hi-C scaffolding technologies was employed to develop chromosome-level genome assemblies of these species. The assembled genome sizes are 795.72 Mb for A. distichum and 1,108.53 Mb for F. ovata. The assemblies exhibit scaffold N50 lengths of 53.12 Mb and 68.97 Mb, with minimal gaps measuring 323.40 kb and 149.00 kb, and 97.71% and 98.82% BUSCO scores for Embryophyta single-copy orthologs, respectively, indicating high contiguity and completeness. The genomes contain 485.24 Mb and 691.68 Mb of repetitive sequences, 4,926 and 7,175 full-length long terminal repeat retrotransposons, and 49,414 and 57,587 protein-coding genes, respectively. The 14 pseudochromosomes encompass 93.80% of the A. distichum genome and 89.11% of the F. ovata genome, thereby demonstrating one-to-one chromosome-level collinearity. These high-quality genome assemblies serve as invaluable resources for genetic and breeding studies, facilitating a deeper understanding of the evolutionary history of these distinctive species.

A new chromosome-level genome assembly and annotation of Cryptosporidium meleagridis

Cryptosporidium spp. are medically and scientifically relevant protozoan parasites that cause severe diarrheal illness in infants, immunosuppressed populations and many animals. Although most human Cryptosporidium infections are caused by C. parvum and C. hominis, there are several other human-infecting species including C. meleagridis, which are commonly observed in developing countries. Here, we annotated a hybrid long-read Oxford Nanopore Technologies and short-read Illumina genome assembly for C. meleagridis (CmTU1867) with DNA generated using multiple displacement amplification. The assembly was then compared to the previous C. meleagridis (CmUKMEL1) assembly and annotation and a recent telomere-to-telomere C. parvum genome assembly. The chromosome-level assembly is 9.2 Mb with a contig N50 of 1.1 Mb. Annotation revealed 3,919 protein-encoding genes. A BUSCO analysis indicates a completeness of 96.6%. The new annotation contains 166 additional protein-encoding genes and reveals high synteny to C. parvum IOWA II (CpBGF). The new C. meleagridis genome assembly is nearly gap-free and provides a valuable new resource for the Cryptosporidium community and future studies on evolution and host-specificity.

Evaluating data requirements for high-quality haplotype-resolved genomes for creating robust pangenome references

BackgroundLong-read technologies from Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) have transformed genomics research by providing diverse data types like HiFi, Duplex, and ultra-long ONT. Despite recent strides in achieving haplotype-phased gapless genome assemblies using long-read technologies, concerns persist regarding the representation of genetic diversity, prompting the development of pangenome references. However, pangenome studies face challenges related to data types, volumes, and cost considerations for each assembled genome, while striving to maintain sensitivity. The absence of comprehensive guidance on optimal data selection exacerbates these challenges.ResultsOur study evaluates recommended data types and volumes required to establish a robust de novo genome assembly pipeline for population-level pangenome projects, extensively examining performance between ONT’s Duplex and PacBio HiFi datasets in the context of achieving high-quality phased genomes with enhanced contiguity and completeness. The results show that achieving chromosome-level haplotype-resolved assembly requires 20 × high-quality long reads such as PacBio HiFi or ONT Duplex, combined with 15–20 × of ultra-long ONT per haplotype and 10 × of long-range data such as Omni-C or Hi-C. High-quality long reads from both platforms yield assemblies with comparable contiguity, with HiFi excelling in phasing accuracies, while Duplex generates more T2T contigs.ConclusionOur study provides insights into optimal data types and volumes for robust de novo genome assembly in population-level pangenome projects. Reassessing the recommended data types and volumes in this study and aligning them with practical economic limitations are vital to the pangenome research community, contributing to their efforts and pushing genomic studies with broader impacts.

A chromosome-level genome assembly of tropical purple sea urchin Heliocidaris crassispina

Heliocidaris crassispina is a tropical sea urchin that holds both ecological and economic value and serves as an ideal experimental animal. This study first employed a combination of PacBio HiFi and Hi-C sequencing data to present a high-quality, chromosome-level assembly of H. crassispina genome. This assembled genome spanned 709.77 Mb, with a contig N50 length of 4.98 Mb and a scaffold N50 length of 33.23 Mb. The assembly was anchored on 21 pseudo-chromosomes, covering 98.32% of the genome. A total of 18,665 protein-coding genes were identified, and BUSCO analysis revealed a completeness score of 97.1%. Additionally, non-coding RNAs (ncRNAs) were annotated, including miRNAs, rRNAs, tRNAs and snRNAs, providing a more complete functional understanding of the genome. The high-quality reference genome will enrich the current echinoderm genomic resources and provide a solid foundation for future studies on H. crassispina, including resource surveys, genomic breeding, and marine ranch management.

Near-complete telomere-to-telomere de novo genome assembly in Egyptian clover (Trifolium alexandrinum).

Egyptian clover (Trifolium alexandrinum L.), also known as berseem clover, is an important forage crop to Semi-arid conditions that was domesticated in ancient Egypt since 6,000 years BC and introduced and well adapted to numerous countries including India, Pakistan, Turkey, and Mediterranean region. Despite its agricultural importance, genomic research on Egyptian clover has been limited to developing efficient modern breeding programs. In the present study, we constructed near-complete telomere-to-telomere-level genome assemblies for two Egyptian clover cultivars, Helaly and Fahl. Initial assemblies were established by using highly-fidelity long-read technology. To extend sequence contiguity, we developed a gap-targeted sequencing (GAP-Seq) method, in which contig ends are targeted for sequencing to obtain long reads bridging two contigs. The total length of the resultant chromosome-level assemblies was 547.7Mb for Helaly and 536.3Mb for Fahl. These differences in sequence length can be attributed to the expansion of DNA transposons. Population genomic analysis using single-nucleotide polymorphisms revealed genomic regions highly differentiated between two cultivars and increased genetic uniformity within each cultivar. Gene ontologies associated with metabolic and biosynthetic processes and developmental processes were enriched in these genomic regions, indicating that these genes may determine the unique characteristics of each cultivar. Comprehensive genomic resources can provide valuable insights into genetic improvements in Egyptian clover and legume genomics.

A chromosome-level genome of the giant vinegaroon Mastigoproctus giganteus exhibits the signature of pre-Silurian whole genome duplication.

Within the arachnids, chromosome-level genome assemblies have greatly accelerated the understanding of gene family evolution and developmental genomics in key groups, such as spiders (Araneae), mites and ticks (Acariformes and Parasitiformes). Among other poorly studied arachnid orders that lack genome assemblies altogether are the clade Pedipalpi, which is comprised of three orders that form the sister group of spiders, which diverged over 400 Mya. We close this gap by generating the first chromosome-level assembly from a single specimen of the vinegaroon Mastigoproctus giganteus (Uropygi). We show that this highly complete genome retains plesiomorphic conditions for many gene families that have undergone lineage-specific derivations within the more diverse spiders. Consistent with the phylogenetic position of Uropygi, macrosynteny in the M. giganteus genome substantiates the signature of an ancient whole genome duplication.

Gene family rearrangements and transcriptional priming drive the evolution of vegetative desiccation tolerance in Selaginella.

Extreme dryness is lethal for nearly all plants, excluding the so-called resurrection plants, which evolved vegetative desiccation tolerance (VDT) by recruiting genes common in most plants. To better understand the evolution of VDT, we generated chromosome-level assemblies and improved genome annotations of two Selaginella species with contrasting abilities to survive desiccation. We identified genomic features and critical mechanisms associated with VDT through sister-group comparative genomics integrating multi-omics data. Our findings indicate that Selaginella evolved VDT through the expansion of some stress protection-related gene families and the contraction of senescence-related genes. Comparative analyses revealed that desiccation-tolerant Selaginella species employ a combination of constitutive and inducible protection mechanisms to survive desiccation. We show that transcriptional priming of stress tolerance-related genes and accumulation of flavonoids in unstressed plants are hallmarks of VDT in Selaginella. During water loss, the resurrection Selaginella induces phospholipids and glutathione metabolism, responses that are missing in the desiccation-sensitive species. Additionally, gene regulatory network analyses indicate the suppression of growth processes as a major component of VDT. This study presents novel perspectives on how gene dosage impacts crucial protective mechanisms and the regulation of central processes to survive extreme dehydration.

A high-quality chromosome-level genome assembly of the traditional Chinese medicinal herb Zanthoxylum nitidum

Dried roots of Zanthoxylum nitidum (2n=2x=70, family Rutaceae) was referred as “Liang-Mian-Zhen” in Chinese, acting as a valuable species due to its notable pharmacological activities. Herein, we combined PacBio HiFi data together with Hi-C mapping technology to construct a chromosome-scale reference genome assembly for Z. nitidum. The assembly reached a length of 2.24 Gb, successfully anchoring 99.31% of sequences onto 35 pseudo-chromosomes. Among these, 26 chromosomes achieved telomere-to-telomere assembly, and 11 chromosomes were gap-free. The contigs N50 and scaffolds N50 reached 57.61 Mb and 78.00 Mb, respectively. Transposable elements comprised 81.44% of the Z. nitidum genome, and over 78% of them were long-terminal repeat retrotransposon elements. Furthermore, 32,737 protein-coding genes were identified and 99.38% of all were functionally annotated. The completeness of the genome assembly and final gene sets reached 97.83% and 96.47% based on Benchmarking Universal Single-Copy Orthologs (BUSCO), respectively. Taken together, our results provided a high-quality chromosome-level assembly of Z. nitidum genome and will be a valuable resource that will facilitate breeding varieties with higher alkaloids content.