Benchmarking Universal Single-Copy Orthologs Research Articles

Lacewing‐specific Universal Single Copy Orthologs designed towards resolution of backbone phylogeny of Neuropterida

AbstractUniversal Single Copy Orthologs (USCOs), as a set of markers of nearly universal single‐copy genes, show a superiority in phylogenomic inference. Here, we developed a Benchmarking Universal Single Copy Orthologs (BUSCOs) dataset, neuropterida_odb10, tailored for Neuropterida, based on high‐quality genome assemblies and transcriptome data, comprising 5438 BUSCOs. A range of 1524–5328 complete and single‐copy USCOs could be captured from the genome assemblies and transcriptomes of 104 species of Neuropterida. The reconstruction of a higher‐level phylogeny of Neuropterida based on a comprehensive sampling and refined genomic data in reference to neuropterida_odb10 validates the efficiency of this BUSCO dataset for phylogenomic inference. We recovered Psychopsidae as the sister group to Ithonidae, and corroborated the sister group relationship between Sisyridae and Nevrorthidae within Osmyloidea and the sister group relationship between Chrysopidae and Mantispoidea. Furthermore, our findings highlight that focusing on alignments with a higher presence of parsimony‐informative sites, rather than on the total number of alignments, can diminish errors in gene tree estimation, a process notably vulnerable to error when using multispecies coalescent methods. The neuropterida_odb10 BUSCO reference dataset holds promise for phylogenetic studies at various hierarchical levels, as well as for comparative genomics and the exploration of species diversity within Neuropterida.

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.

A new high-quality genome assembly and annotation for the threatened Florida Scrub-Jay (Aphelocoma coerulescens).

The Florida Scrub-Jay (Aphelocoma coerulescens), a Federally Threatened, cooperatively-breeding bird, is an emerging model system in evolutionary biology and ecology. Extensive individual-based monitoring and genetic sampling for decades has yielded a wealth of data, allowing for the detailed study of social behavior, demography, and population genetics of this natural population. Here, we report a linkage map and a chromosome-level genome assembly and annotation for a female Florida Scrub-Jay made with long-read sequencing technology, chromatin conformation data, and the linkage map. We constructed a linkage map comprising 4,468 SNPs that had 34 linkage groups and a total sex-averaged autosomal genetic map length of 2446.78 cM. The new genome assembly is 1.33 Gb in length, consisting of 33 complete or near-complete autosomes and the sex chromosomes (ZW). This highly contiguous assembly has an NG50 of 68 Mb and a Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness score of 97.1% with respect to the Aves database. The annotated gene set has a BUSCO transcriptome completeness score of 95.5% and 17,964 identified protein-coding genes, 92.5% of which have associated functional annotations. This new, high-quality genome assembly and linkage map of the Florida Scrub-Jay provides valuable tools for future research into the evolutionary dynamics of small, natural populations of conservation concern.

Genome sequence of the sugarcane aphid, Melanaphis sacchari (Hemiptera: Aphididae).

The sugarcane aphid, Melanaphis sacchari (Zehntner, 1897), is an agricultural pest that causes damage to plants in the Poaceae (the grasses) family, such as sorghum and sugarcane. Here, we used Nanopore long reads and Hi-C interaction map to generate a chromosome-level assembly with a total length of 356.1 Mb, of which 85.5% (304.6 Mb) is contained within the three autosomes and the X chromosome. Repetitive sequences accounted for 16.29% of the chromosomes and a total of 12,530 protein-coding genes were annotated, achieving 95.8% benchmarking universal single-copy orthologs (BUSCO) gene completeness. This offers a substantial improvement compared to previous low-quality genomic resources. Phylogenomic analysis by comparing M. sacchari with twenty-four published aphid genomes representing three aphid tribes reveals that M. sacchari belongs to the tribe Aphidini and maintained a conserved chromosome structure with other Aphidini species. The high-quality genomic resources reported in this study will be useful for understanding the evolution of aphid genomes and studying pest management of M. sacchari.

A chromosome-level genome assembly of the gall maker pest inquiline, Diomorus aiolomorphi Kamijo (Hymenoptera: Torymidae)

Diomorus aiolomorphi Kamijo (Hymenoptera: Torymidae) is an inquiline of gall maker Aiolomorphus rhopaloides Walker (Hymenoptera: Eurytomidae). They are of significant economic significance and predominantly inhabit bamboo forest. So far, only four scaffold-level genomes have been published for the family Torymidae. In this study, we present a high-quality genome assembly of D. aiolomorphi at the chromosome level, achieved through the integration of Nanopore (ONT) long-read, Illumina pair-end DNA short-read, and High-through Chromosome Conformation Capture (Hi-C) sequencing methods. The final assembly was 1,084.56 Mb in genome size, with 1,083.41 Mb (99.89%) assigned to five pseudochromosomes. The scaffold N50 length reached 224.87 Mb, and the complete Benchmarking Universal Single-Copy Orthologs (BUSCO) score was 97.3%. The genome contained 762.12 Mb of repetitive elements, accounting for 70.27% of the total genome size. A total of 18,011 protein-coding genes were predicted, with 17,829 genes being functionally annotated. The high-quality genome assembly of D. aiolomorphi presented in this study will serve as a valuable genomic resource for future research on parasitoid wasps. The results of this study may also contribute to the development of biological control strategies for pest management in bamboo forests, enhancing ecological balance and economic sustainability.

A Chromosome-level genome assembly of giant river prawn (Macrobrachium rosenbergii)

The giant river prawn (Macrobrachium rosenbergii) is one of the most widely cultured crustacean species. In recent years, its aquaculture has faced challenges, including the degradation of germplasm resources and the emergence of viral diseases. Genomic information can be a valuable resource for developing molecular breeding programs for this important aquaculture species. Here we constructed a high-quality reference genome for M. rosenbergii by integrating Nanopore, Illumina, and high-throughput chromosome conformation capture (Hi-C) technologies. The final genome assembly is 3.18 Gb in size, with scaffold N50 and contig N50 of 62.73 Mb and 8.92 Mb, respectively. Approximately 98.6% of the assembled sequences were anchored into 59 pseudo-chromosomes. Benchmarking Universal Single-Copy Orthologs (BUSCO) benchmark of the genome assembly reached 94.5%. Repetitive sequences comprise 43.77% of the assembled genome, and 17,436 protein-coding genes were annotated. The high-quality genome of M. rosenbergii will empower molecular breeding efforts and provide invaluable resources for comparative genomic analysis of decapod species.

Refinement of the Antarctic fur seal (Arctocephalus gazella) reference genome increases continuity and completeness.

The Antarctic fur seal (Arctocephalus gazella) is an important top predator and indicator of the health of the Southern Ocean ecosystem. Although abundant, this species narrowly escaped extinction due to historical sealing and is currently declining as a consequence of climate change. Genomic tools are essential for understanding these anthropogenic impacts and for predicting long-term viability. However, the current reference genome ("arcGaz3") shows considerable room for improvement in terms of both completeness and contiguity. We therefore combined PacBio sequencing, haplotype-aware HiRise assembly and scaffolding based on Hi-C information to generate a refined assembly of the Antarctic fur seal reference genome ("arcGaz4_h1"). The new assembly is 2.53Gb long, has a scaffold N50 of 55.6Mb and includes 18 chromosome-sized scaffolds, which correspond to the 18 chromosomes expected in otariids. Genome completeness is greatly improved, with 23,408 annotated genes and a Benchmarking Universal Single-Copy Orthologs (BUSCO) score raised from 84.7% to 95.2%. We furthermore included the new genome in a reference-free alignment of the genomes of eleven pinniped species to characterize evolutionary conservation across the Pinnipedia using genome-wide Genomic Evolutionary Rate Profiling (GERP). We then implemented Gene Ontology (GO) enrichment analyses to identify biological processes associated with those genes showing the highest levels of either conservation or differentiation between the two major pinniped families, the Otariidae and Phocidae. We show that processes linked to neuronal development, the circulatory system and osmoregulation are overrepresented both in conserved as well as in differentiated regions of the genome.

Chromosome-scale reference genome of an ancient landrace: unveiling the genetic basis of seed weight in the food legume crop pigeonpea (Cajanus cajan).

Pigeonpea (Cajanus cajan) is a nutrient-rich and versatile food legume crop of tropical and subtropical regions. In this study, we describe the de novo assembly of a high-quality genome for the ancient pigeonpea landrace 'D30', achieved through a combination of Pacific Biosciences high-fidelity (PacBio HiFi) and high-throughput chromatin conformation capture (Hi-C) sequencing technologies. The assembled 'D30' genome has a size of 813.54Mb, with a contig N50 of 10.74Mb, a scaffold N50 of 73.07Mb, and a GC content of 35.67%. Genomic evaluation revealed that the 'D30' genome contains 99.2% of Benchmarking Universal Single-Copy Orthologs (BUSCO) and achieves a 29.06 long terminal repeat (LTR) assembly index (LAI). Genome annotation indicated that 'D30' encompasses 431.37Mb of repeat elements (53.02% of the genome) and 37 977 protein-coding genes. Identification of single-nucleotide polymorphisms (SNPs), insertions/deletions (indels), and structural variations between 'D30' and the published genome of pigeonpea cultivar 'Asha' suggests that genes affected by these variations may play important roles in biotic and abiotic stress responses. Further investigation of genomic regions under selection highlights genes enriched in starch and sucrose metabolism, with 42.11% of these genes highly expressed in seeds. Finally, we conducted genome-wide association studies (GWAS) to facilitate the identification of 28 marker-trait associations for six agronomic traits of pigeonpea. Notably, we discovered a calmodulin-like protein (CcCML) that harbors a dominant haplotype associated with the 100-seed weight of pigeonpea. Our study provides a foundational resource for developing genomics-assisted breeding programs in pigeonpea.

Long-Read-Based Hybrid Genome Assembly and Annotation of Snow Algal Strain CCCryo 101-99 (cf. Sphaerocystis sp., Chlamydomonadales).

Polar regions harbor a diversity of cold-adapted (cryophilic) algae, which can be categorized into psychrophilic (obligate cryophilic) and cryotrophic (nonobligate cryophilic) snow algae. Both can accumulate significant biomasses on glacier and snow habitats and play major roles in global climate dynamics. Despite their significance, genomic studies on these organisms remain scarce, hindering our understanding of their evolutionary history and adaptive mechanisms in the face of climate change. Here, we present the draft genome assembly and annotation of the psychrophilic snow algal strain CCCryo 101-99 (cf. Sphaerocystis sp.). The draft haploid genome assembly is 122.5 Mb in length and is represented by 664 contigs with an N50 of 0.86 Mb, a Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness of 92.9% (n = 1,519), a maximum contig length of 5.3 Mb, and a guanine-cystosine (GC) content of 53.1%. In total, 28.98% of the genome (35.5 Mb) contains repetitive elements. We identified 417 noncoding RNAs and annotated the chloroplast genome. The predicted proteome comprises 14,805 genes with a BUSCO completeness of 97.8%. Our preliminary analyses reveal a genome with a higher repeat content compared with mesophilic chlorophyte relatives, alongside enrichment in gene families associated with photosynthesis and flagella functions. Our current data will facilitate future comparative studies, improving our understanding of the likely response of polar algae to a warming climate as well as their evolutionary trajectories in permanently cold environments.

A multi-tissue de novo transcriptome assembly and relative gene expression of the vulnerable freshwater salmonid Thymallus ligericus

Freshwater ecosystems are among the most endangered ecosystems worldwide. While numerous taxa are on the verge of extinction as a result of global changes and direct or indirect anthropogenic activity, genomic and transcriptomic resources represent a key tool for comprehending species' adaptability and serve as the foundation for conservation initiatives. The Loire grayling, Thymallus ligericus, is a freshwater European salmonid endemic to the upper Loire River basin. The species is comprised of fragmented populations that are dispersed over a small area and it has been identified as a vulnerable species. Here, we provide a multi-tissue de novo transcriptome assembly of T. ligericus. The completeness and integrity of the transcriptome were assessed before and after redundancy removal with lineage-specific libraries from Eukaryota, Metazoa, Vertebrata, and Actinopterygii. Relative gene expression was assessed for each of the analyzed tissues, using the de novo assembled transcriptome and a genome-based analysis using the available T. thymallus genome as a reference. The final assembly, with a contig N50 of 1221 and Benchmarking Universal Single-Copy Orthologs (BUSCO) scores above 94%, is made accessible along with structural and functional annotations and relative gene expression of the five tissues (NCBI SRA and FigShare databases). This is the first transcriptomic resource for this species, which provides a foundation for future research on this and other salmonid species that are increasingly exposed to environmental stressors.

Chromosome-level genome assembly and annotation of the cold-water species Ophiura sarsii

The cold-water species Ophiura sarsii, a brittle star, is a key echinoderm in the Arctic continental shelf region, highly sensitive to climate change. However, the absence of a high-quality genome has hindered a thorough understanding of its adaptive evolution. In this study, we reported the first chromosome-level genome assembly of O. sarsii. The genome assembly totalled 1.57 Gb, encompassing 19 chromosomes with a GC content of 37.11% and a scaffold N50 length of 78.03 Mb. The Benchmarking Universal Single-Copy Orthologs (BUSCO) assessment yielded a completeness estimate of 93.5% for this assembly. We predicted a total of 27,099 protein-coding genes, with 25,079 functionally annotated. The genome was comprised of 58.09% transposable elements. This chromosome-level genome of O. sarsii contributes to our understanding of the origin and evolution of marine organisms.

The first high-quality genome assembly and annotation of Lantana camara, an important ornamental plant and a major invasive species

This study presents the first annotated, haplotype-resolved, chromosome-scale genome of Lantana camara, a flowering shrub native to Central America and known for its dual role as an ornamental plant and an invasive species. Despite its widespread cultivation and ecological impact, the lack of a high-quality genome has hindered the investigation of traits of both ornamental and invasive. This research bridges the gap in genomic resources for L. camara, which is crucial for both ornamental breeding programs and invasive species management. Whole-genome and transcriptome sequencing were utilized to elucidate the genetic complexity of a diploid L. camara breeding line UF-T48. The genome was assembled de novo using HiFi and Hi-C reads, resulting in two phased genome assemblies with high Benchmarking Universal Single-Copy Orthologs (BUSCO) scores of 97.7%, indicating their quality. All 22 chromosomes were assembled with pseudochromosomes averaging 117 Mb. The assemblies revealed 29 telomeres and an extensive presence of repetitive sequences, primarily long terminal repeat transposable elements. The genome annotation identified 83,775 protein-coding genes, with 83% functionally annotated. In particular, the study mapped 42 anthocyanin and carotenoid candidate gene clusters and 12 herbicide target genes to the assembly, identifying 38 genes spread across the genome that are integral to flower color development and 53 genes for herbicide targeting in L. camara. This comprehensive genomic study not only enhances the understanding of L. camara’s genetic makeup but also sets a precedent for genomic research in the Verbenaceae family, offering a foundation for future studies in plant genetics, conservation, and breeding.

A chromosome-level genome assembly of an avivorous bat species (Nyctalus aviator)

Currently, three carnivorous bat species, namely Ia io, Nyctalus lasiopterus, and Nyctalus aviator, are known to actively prey on seasonal migratory birds (hereinafter referred to as “avivorous bats”). However, the absence of reference genomes impedes a thorough comprehension of the molecular adaptations of avivorous bat species. Herein, we present the high-quality chromosome-scale reference genome of N. aviator based on PacBio subreads, DNBSEQ short-reads and Hi-C sequencing data. The genome assembly size of N. aviator is 1.77 Gb, with a scaffold N50 of 102 Mb, of which 99.8% assembly was anchored into 21 pseudo-chromosomes. After masking 635.1 Mb repetitive sequences, a total of 19,412 protein-coding genes were identified, of which 99.3% were functionally annotated. The genome assembly and gene prediction reached 96.1% and 96.1% completeness of Benchmarking Universal Single-Copy Orthologs (BUSCO), respectively. This chromosome-level reference genome of N. aviator fills a gap in the existing information on the genomes of carnivorous bats, especially avivorous ones, and will be valuable for mechanism of adaptations to dietary niche expansion in bat species.

Whole-genome sequencing of Ganoderma boninense, the causal agent of basal stem rot disease in oil palm, via combined short- and long-read sequencing

The hemibiotrophic Basidiomycete pathogen Ganoderma boninense (Gb) is the dominant causal agent of oil palm basal stem rot disease. Here, we report a complete chromosomal genome map of Gb using a combination of short-read Illumina and long-read Pacific Biosciences (PacBio) sequencing platforms combined with chromatin conformation capture data from the Chicago and Hi-C platforms. The genome was 55.87 Mb in length and assembled to a high contiguity (N50: 304.34 kb) of 12 chromosomes built from 112 scaffolds, with a total of only 4.34 Mb (~ 7.77%) remaining unplaced. The final assemblies were evaluated for completeness of the genome by using Benchmarking Universal Single Copy Orthologs (BUSCO) v4.1.4, and based on 4464 total BUSCO polyporales group searches, the assemblies yielded 4264 (95.52%) of the conserved orthologs as complete and only a few fragmented BUSCO of 42 (0.94%) as well as a missing BUSCO of 158 (3.53%). Genome annotation predicted a total of 21,074 coding genes, with a GC content ratio of 59.2%. The genome features were analyzed with different databases, which revealed 2471 Gene Ontology/GO (11.72%), 5418 KEGG (Kyoto Encyclopedia of Genes and Genomes) Orthologous/KO (25.71%), 13,913 Cluster of Orthologous Groups of proteins/COG (66.02%), 60 ABC transporter (0.28%), 1049 Carbohydrate-Active Enzymes/CAZy (4.98%), 4005 pathogen–host interactions/PHI (19%), and 515 fungal transcription factor/FTFD (2.44%) genes. The results obtained in this study provide deep insight for further studies in the future.

The genome of the Arctic snow alga Limnomonas spitsbergensis (Chlamydomonadales).

Snow algae are a diverse group of extremophilic microeukaryotes found on melting polar and alpine snowfields. They play an important role in the microbial ecology of the cryosphere, and their propagation on snow and ice surfaces may in part accelerate climate-induced melting of these systems. High-quality snow algae genomes are needed for studies on their unique physiology, adaptive mechanisms, and genome evolution under multiple forms of stress, including cold temperatures and intense sunlight. Here, we assembled and annotated the genome of Limnomonas spitsbergensis, a cryophilic biciliate green alga originally isolated from melting snow on Svalbard, in the Arctic. The L. spitsbergensis genome assembly is based primarily on the use of PacBio long reads and secondly Illumina short reads, with an assembly size of 260.248 Mb in 124 contigs. A combination of 3 alternative annotation strategies was used including protein homology, RNA-seq evidence, and PacBio full-length transcript isoforms. The best merged set of annotations identified 18,277 protein-coding genes, which were 95.2% complete based on Benchmarking Universal Single-Copy Orthologs analysis. We also provide the annotated mitogenome, which is a relatively large 77.942 kb circular mapping sequence containing extensive repeats. The L. spitsbergensis genome will provide a new resource for research on snow algae adaptation, behavior, and natural selection in unique, low-temperature terrestrial environments that are under threat from climate change.

A Chromosomal-Level Genome of Dermatophagoides farinae, a Common Allergenic Mite Species.

Genome data have been used to find novel allergen from house dust mites. Here, we aim to construct a chromosome-level genome assembly of Dermatophagoides farinae, a common allergenic mite species. We achieved a chromosome-level assembly of D. farinae's genome by integrating PacBio single-molecule real-time sequencing, Illumina paired-end sequencing, and Hi-C technology, followed by annotating allergens and mapping them to specific chromosomes. A 62.43 Mb genome was assembled with a 0.52% heterozygosity rate and a 36.11 Merqury-estimated quality value. The assembled genome represents 92.1% completeness benchmarking universal single-copy orthologs with a scaffold N50 value of 7.11 Mb. Hi-C scaffolding of the genome resulted in construction of 10 pseudochromosomes. The genome comprises 13.01% (7.66 Mb) repetitive sequences and predicts 10,709 protein-coding genes, 96.57% of which are functionally annotated. Moreover, we identified and located 36 allergen groups on specific chromosomes, including allergens Der f 1, Der f 2, Der f 23, Der f 4, Der f 5, Der f 7, and Der f 21 located on chromosomes 2, 1, 7, 3, 4, 6, and 4, respectively. This comprehensive genomic data provides valuable insights into mite biology and evolutionary adaptations, potentially advancing D. farinae allergy research and treatment strategies.

Genome assembly of Melilotus officinalis provides a new reference genome for functional genomics

BackgroundSweet yellow clover (Melilotus officinalis) is a diploid plant (2n = 16) that is native to Europe. It is an excellent legume forage. It can both fix nitrogen and serve as a medicine. A genome assembly of Melilotus officinalis that was collected from Best corporation in Beijing is available based on Nanopore sequencing. The genome of Melilotus officinalis was sequenced, assembled, and annotated.ResultsThe latest PacBio third generation HiFi assembly and sequencing strategies were used to produce a Melilotus officinalis genome assembly size of 1,066 Mbp, contig N50 = 5 Mbp, scaffold N50 = 130 Mbp, and complete benchmarking universal single-copy orthologs (BUSCOs) = 96.4%. This annotation produced 47,873 high-confidence gene models, which will substantially aid in our research on molecular breeding. A collinear analysis showed that Melilotus officinalis and Medicago truncatula shared conserved synteny. The expansion and contraction of gene families showed that Melilotus officinalis expanded by 565 gene families and shrank by 56 gene families. The contacted gene families were associated with response to stimulus, nucleotide binding, and small molecule binding. Thus, it is related to a family of genes associated with peptidase activity, which could lead to better stress tolerance in plants.ConclusionsIn this study, the latest PacBio technology was used to assemble and sequence the genome of the Melilotus officinalis and annotate its protein-coding genes. These results will expand the genomic resources available for Melilotus officinalis and should assist in subsequent research on sweet yellow clover plants.

The chromosome-level genome assembly of the giant dobsonfly Acanthacorydalis orientalis (McLachlan, 1899)

Acanthacorydalis orientalis (McLachlan, 1899) (Megaloptera: Corydalidae) is an important freshwater-benthic invertebrate species that serves as an indicator for water-quality biomonitoring and is valuable for conservation from East Asia. Here, a high-quality reference genome for A. orientalis was constructed using Oxford Nanopore sequencing and High throughput Chromosome Conformation Capture (Hi-C) technology. The final genome size is 547.98 Mb, with the N50 values of contig and scaffold being 7.77 Mb and 50.53 Mb, respectively. The longest contig and scaffold are 20.57 Mb and 62.26 Mb in length, respectively. There are 99.75% contigs anchored onto 13 pseudo-chromosomes. Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis showed that the completeness of the genome assembly is 99.01%. There are 10,977 protein-coding genes identified, of which 84.00% are functionally annotated. The genome contains 44.86% repeat sequences. This high-quality genome provides substantial data for future studies on population genetics, aquatic adaptation, and evolution of Megaloptera and other related insect groups.

A high-quality chromosome-level genome assembly of the Chinese medaka Oryzias sinensis

Oryzias sinensis, also known as Chinese medaka or Chinese ricefish, is a commonly used animal model for aquatic environmental assessment in the wild as well as gene function validation or toxicology research in the lab. Here, a high-quality chromosome-level genome assembly of O. sinensis was generated using single-tube long fragment read (stLFR) reads, Nanopore long-reads, and Hi-C sequencing data. The genome is 796.58 Mb, and a total of 712.17 Mb of the assembled sequences were anchored to 23 pseudo-chromosomes. A final set of 22,461 genes were annotated, with 98.67% being functionally annotated. The Benchmarking Universal Single-Copy Orthologs (BUSCO) benchmark of genome assembly and gene annotation reached 95.1% (93.3% single-copy) and 94.6% (91.7% single-copy), respectively. Furthermore, we also use ATAC-seq to uncover chromosome transposase-accessibility as well as related genome area function enrichment for Oryzias sinensis. This study offers a new improved foundation for future genomics research in Chinese medaka.

Whole genome assembly and annotation of the King Angelfish (Holacanthus passer) gives insight into the evolution of marine fishes of the Tropical Eastern Pacific.

Holacanthus angelfishes are some of the most iconic marine fishes of the Tropical Eastern Pacific (TEP). However, very limited genomic resources currently exist for the genus. In this study we: (i) assembled and annotated the nuclear genome of the King Angelfish (Holacanthus passer), and (ii) examined the demographic history of H. passer in the TEP. We generated 43.8 Gb of ONT and 97.3 Gb Illumina reads representing 75× and 167× coverage, respectively. The final genome assembly size was 583 Mb with a contig N50 of 5.7 Mb, which captured 97.5% of the complete Actinoterygii Benchmarking Universal Single-Copy Orthologs (BUSCOs). Repetitive elements accounted for 5.09% of the genome, and 33,889 protein-coding genes were predicted, of which 22,984 were functionally annotated. Our demographic analysis suggests that population expansions of H. passer occurred prior to the last glacial maximum (LGM) and were more likely shaped by events associated with the closure of the Isthmus of Panama. This result is surprising, given that most rapid population expansions in both freshwater and marine organisms have been reported to occur globally after the LGM. Overall, this annotated genome assembly provides a novel molecular resource to study the evolution of Holacanthus angelfishes, while facilitating research into local adaptation, speciation, and introgression in marine fishes.