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Abstract The common bed bug, Cimex lectularius, is a globally distributed pest insect of medical, veterinary, and economic importance. Previous reference genome assemblies for this species were generated from short read sequencing data, resulting in a ~650 Mb composed of thousands of contigs. Here, we present a haplotype-resolved, chromosome-level reference genome, generated from an adult Harlen strain female specimen. Using PacBio long read and Omni-C proximity sequencing, we generated a 540 Mb genome with 15 chromosomes (13 autosomes and 2 sex chromosomes - X1X2) with an N50 > 30 Mb and BUSCO > 90%. Previous karyotyping efforts indicate an XY sex chromosome system, with 2n=26 and X1X1X2X2 females and X1X2Y males; however significant fragmentation of the X chromosome has also been reported. We further use whole genome resequencing data from males and females to identify the X1 and X2 chromosomes based on sex biases in coverage. This highly contiguous reference genome assembly provides a much-improved resource for identifying chromosomal genome architecture, and for interpreting patterns of urban outbreaks and signatures of selection linked to insecticide resistance.
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A haplotype-resolved chromosomal reference genome for the porcini mushroom Boletus edulis
Abstract Haplotype-resolved chromosomal reference genomes are increasingly available for many fungi, offering insights into the evolution of pathogenic and symbiotic lifestyles. However, these resources remain scarce for ectomycorrhizal fungi, which play crucial roles in forest ecosystems. Here, we used a combination of chromatin conformation capture and PacBio sequencing to construct a haplotype-resolved chromosomal genome assembly for Boletus edulis, a prized edible fungus and emerging model for ectomycorrhizal fungal research. Our new reference assembly, “BolEdBiel_h2,” derives from a B. edulis sporocarp sampled in Bielefeld, Germany. The genome assembly spans 41.8 Mb, with a scaffold N50 of 4.1 Mb, and includes 11 chromosome-level scaffolds, achieving near telomere-to-telomere coverage across multiple chromosomes. We annotated a total of 15,406 genes, with a Benchmarking Universal Single-Copy Orthologs score of 96.2%. Key genomic features such as mating loci, carbohydrate-active enzymes, and effector proteins, were identified. As a first application of this new genomic resource, we mapped whole-genome resequencing data from 53 genets to investigate the population structure and genetic diversity of the European lineage of B. edulis. We identified 2 distinct genetic clusters and found that high-latitude populations from Iceland and Fennoscandia exhibited greater nucleotide diversity than populations from the United Kingdom and Central Europe. Additionally, we discovered a 0.4-Mb inversion on chromosome 3 and identified several regions of locally elevated nucleotide diversity, which may represent candidates for ecological adaptation. This genomic resource will facilitate a deeper understanding of this ecologically and commercially important wild fungus.
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- Award ID(s):
- 2114785
- PAR ID:
- 10666570
- Editor(s):
- Sachs, M
- Publisher / Repository:
- G3 Genes|Genomes|Genetics
- Date Published:
- Journal Name:
- G3: Genes, Genomes, Genetics
- Volume:
- 15
- Issue:
- 6
- ISSN:
- 2160-1836
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Summary In the hyperdiverse fungi, the process of speciation is virtually unknown, including for the > 20 000 species of ectomycorrhizal mutualists. To understand this process, we investigated patterns of genome‐wide differentiation in the ectomycorrhizal porcini mushroom, Boletus edulis , a globally distributed species complex with broad ecological amplitude. By whole‐genome sequencing 160 individuals from across the Northern Hemisphere, we genotyped 792 923 single nucleotide polymorphisms to characterize patterns of genome‐wide differentiation and to identify the adaptive processes shaping global population structure. We show that B. edulis exhibits contrasting patterns of genomic divergence between continents, with multiple lineages present across North America, while a single lineage dominates Europe. These geographical lineages are inferred to have diverged 1.62–2.66 million years ago, during a period of climatic upheaval and the onset of glaciation in the Pliocene–Pleistocene boundary. High levels of genomic differentiation were observed among lineages despite evidence of substantial and ongoing introgression. Genome scans, demographic inference, and ecological niche models suggest that genomic differentiation is maintained by environmental adaptation, not physical isolation. Our study uncovers striking patterns of genome‐wide differentiation on a global scale and emphasizes the importance of local adaptation and ecologically mediated divergence, rather than prezygotic barriers such as allopatry or genomic incompatibility, in fungal population differentiation.more » « less
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CitationSnead, A.A., Meng, F., Largotta, N. et al. Diploid chromosome-level genome assembly and annotation for Lycorma delicatula. Sci Data 12, 579 (2025). https://doi.org/10.1038/s41597-025-04854-8AbstractThe spotted lanternfly (Lycorma delicatula) is a planthopper species (Hemiptera: Fulgoridae) native to China but invasive in South Korea, Japan, and the United States where it is a significant threat to agriculture. Hence, genomic resources are critical to both management and understand the genomic characteristics of successful invaders. Here, we report a haplotype-phased genome assembly and annotation using PacBio long-read sequencing, Hi-C technology, and RNA-seq data. The 2.2 Gbp genome comprises 13 chromosomes, and our whole genome sequencing of eighty-two adults indicated chromosome four as the sex chromosome and anXO sex-determination system.We identified over 12,000 protein coding genes and performed functional annotation, facilitating identification of several candidate genes which may hold importance for spotted lanternfly control. Both the assemblies and annotations were highly complete with over 96% of BUSCO genes complete regardless of the database employed (i.e., Eukaryota, Arthropoda, Insecta). This reference-quality genome will serve as an important resource for both development and optimization of management practices for the spotted lanternfly and invasive genomics as a whole.Description of the data and file structureThis dataset contains the haplotype-phased chromosome-level genome assembly of the spotted lanternfly (Lycorma delicatula) described and published in Snead & Meng et al. (in review). The genome combined long-read data and HiC data (SRA31402152-SRA31402153) to assembly and scaffold each haplotype. The annotation uses RNAseq data from 12 adults (SRA31411873-SRA31411894) to structurally annotate both haplotypes. Finally, whole-genome sequencing of 82 adult spotted lanternfly (bioproject PRJNA1136004) described in the metadata csv provided was used to identify punitive sex chromosomes. The dataset also include GO results for each chromosome not explicitly described in the results of the manuscript.Files and variablesFile: SLF_Hap1.fastaDescription: A fasta file of the assembled genome for the cleaned 13 chromosome haplotype 1 assembly.File: SLF_Hap2.fastaDescription: A fasta file of the assembled genome for the cleaned 13 chromosome haplotype 2 assembly.File: SLF_Hap1_Repeats.gffDescription: A gff file of the repeats annotated in the cleaned 13 chromosome haplotype 1 assembly.File: SLF_Hap2_Repeats.gffDescription: A gff file of the repeats annotated in the cleaned 13 chromosome haplotype 2 assembly.File: SLF_Hap1.gffDescription: A structural annotation of the 13 chromosome haplotype 1 assembly with functional annotations.File: SLF_Hap2.gffDescription: A structural annotation of the 13 chromosome haplotype 2 assembly with functional annotations.File: GO_plot_chr_1.pngDescription: An image of the top 20 GO term results for chromosome 1.File: GO_plot_chr_2.pngDescription: An image of the top 20 GO term results for chromosome 2.File: GO_plot_chr_3.pngDescription: An image of the top 20 GO term results for chromosome 3.File: GO_plot_chr_8.pngDescription: An image of the top 20 GO term results for chromosome 8.File: GO_plot_chr_5.pngDescription: An image of the top 20 GO term results for chromosome 5.File: GO_plot_chr_4.pngDescription: An image of the top 20 GO term results for chromosome 4.File: GO_plot_chr_6.pngDescription: An image of the top 20 GO term results for chromosome 6.File: GO_plot_chr_7.pngDescription: An image of the top 20 GO term results for chromosome 7.File: GO_plot_chr_11.pngDescription: An image of the top 20 GO term results for chromosome 11.File: GO_plot_chr_9.pngDescription: An image of the top 20 GO term results for chromosome 9.File: GO_plot_chr_10.pngDescription: An image of the top 20 GO term results for chromosome 10.File: GO_plot_chr_12.pngDescription: An image of the top 20 GO term results for chromosome 12.File: GO_plot_chr_13.pngDescription: An image of the top 20 GO term results for chromosome 13.File: SLF_Samples_SRA.csvDescription: A csv with the sequencing information, SRA numbers, and sexes of the adults used in to identify the putative sex chromosome.File: SLF_RNAseq_Metadata.csvDescription: A csv with the sequencing information, SRA numbers, and other metadata for the RNAseq used to annotation the genomes.Variablesaccession: The SRA accession numberstudy: The studyobject_status: If the NCBI submission was new or not.bioproject_accession: The bioproject accession numberbiosample_accession: The Biosample accession numberlibrary_ID: The ID used to identify that genomic library.title: The title of the study (the bioproject)library_strategy: Specific sequencing technique used to prepare the library.library_source: The biological material used to create the sequencing library.library_selection: The library preparation method.library_layout: The arrangement of reads within the sequencing library.platform: The sequencing platform.instrument_model: The model of the sequences.design_description: Description of the study design.filetype: Type of filefilename: First filefilename2: Second filesex: The biological sex of the adult.Code/softwareThe initial haplotype-phased scaffolded genome was assembled by Dovetail Genomics (Cantata Bio) with standard software outlined in the methods with default settings. Scripts for the remaining work including annotation, gene ontology enrichment, and other analyses are located in the Github repository (https://github.com/anthonysnead/SLF-Genome-Assembly(opens in new window)).Access informationOther publicly accessible locations of the data:The raw sequencing data and the annotated haplotype-phased genome assembly of Lycorma delicatula have been deposited at the National Center for Biotechnology Information (NCBI). The Hi-C and HiFi data can be found under SRA31402152 and SRA31402153. The RNA-seq data can be found under SRA31411873-SRA31411894, while the DNA-seq data can be found under bioproject PRJNA1136004.more » « less
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Pyhäjärvi, T (Ed.)Abstract Blackberries (Rubus spp.) are the fourth most economically important berry crop worldwide. Genome assemblies and annotations have been developed for Rubus species in subgenus Idaeobatus, including black raspberry (R. occidentalis), red raspberry (R. idaeus), and R. chingii, but very few genomic resources exist for blackberries and their relatives in subgenus Rubus. Here we present a chromosome-length assembly and annotation of the diploid blackberry germplasm accession “Hillquist” (R. argutus). “Hillquist” is the only known source of primocane-fruiting (annual-fruiting) in tetraploid fresh-market blackberry breeding programs and is represented in the pedigree of many important cultivars worldwide. The “Hillquist” assembly, generated using Pacific Biosciences long reads scaffolded with high-throughput chromosome conformation capture sequencing, consisted of 298 Mb, of which 270 Mb (90%) was placed on 7 chromosome-length scaffolds with an average length of 38.6 Mb. Approximately 52.8% of the genome was composed of repetitive elements. The genome sequence was highly collinear with a novel maternal haplotype-resolved linkage map of the tetraploid blackberry selection A-2551TN and genome assemblies of R. chingii and red raspberry. A total of 38,503 protein-coding genes were predicted, of which 72% were functionally annotated. Eighteen flowering gene homologs within a previously mapped locus aligning to an 11.2 Mb region on chromosome Ra02 were identified as potential candidate genes for primocane-fruiting. The utility of the “Hillquist” genome has been demonstrated here by the development of the first genotyping-by-sequencing-based linkage map of tetraploid blackberry and the identification of possible candidate genes for primocane-fruiting. This chromosome-length assembly will facilitate future studies in Rubus biology, genetics, and genomics and strengthen applied breeding programs.more » « less
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Summary White oak (Quercus alba) is an abundant forest tree species across eastern North America that is ecologically, culturally, and economically important.We report the first haplotype‐resolved chromosome‐scale genome assembly ofQ. albaand conduct comparative analyses of genome structure and gene content against other published Fagaceae genomes. We investigate the genetic diversity of this widespread species and the phylogenetic relationships among oaks using whole genome data.Despite strongly conserved chromosome synteny and genome size acrossQuercus, certain gene families have undergone rapid changes in size, including defense genes. Unbiased annotation of resistance (R) genes across oaks revealed that the overall number of R genes is similar across species – as are the chromosomal locations of R gene clusters – but, gene number within clusters is more labile. We found thatQ. albahas high genetic diversity, much of which predates its divergence from other oaks and likely impacts divergence time estimations. Our phylogenetic results highlight widespread phylogenetic discordance across the genus.The white oak genome represents a major new resource for studying genome diversity and evolution inQuercus. Additionally, we show that unbiased gene annotation is key to accurately assessing R gene evolution inQuercus.more » « less
- Free Publicly Accessible Full Text
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Accepted Manuscript
- Journal Article:
- https://doi.org/10.1093/g3journal/jkaf069
