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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.
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Two independent origins of XY sex chromosomes in Asparagus
File Contents Ahor_pb32m_HAP1_v1.0.chrY_regions.bed.gz Y chromosome nonrecombining region coordinatesAhor_pb32m_HAP1_v1.0.EDTA.TEanno.gff3.gz All TE annotations by EDTAAhor_pb32m_HAP1_v1.0.EDTA.TEintact.fa.gz Intact TE sequences by EDTAAhor_pb32m_HAP1_v1.0.EDTA.TEintact.gff3.gz Intact TE annotations by EDTAAhor_pb32m_HAP1_v1.0.entap_results.tsv Reciprocal functional gene annotations by EnTAPAhor_pb32m_HAP1_v1.0.fa.gz Haplotype assembly fasta fileAhor_pb32m_HAP1_v1.0.ISOFORMS.bed.gz Filtered gene annotations - all isoformsAhor_pb32m_HAP1_v1.0.ISOFORMS.CDS.fa.gz Filtered gene annotations (protein coding nucleotides) - all isoformsAhor_pb32m_HAP1_v1.0.ISOFORMS.gff3.gz Filtered gene annotations - all isoformsAhor_pb32m_HAP1_v1.0.ISOFORMS.peptides.fa.gz Filtered gene annotations (protein sequences) - all isoformsAhor_pb32m_HAP1_v1.0.PRIMARY.bed.gz Filtered gene annotations - longest isoforms onlyAhor_pb32m_HAP1_v1.0.PRIMARY.CDS.fa.gz Filtered gene annotations (protein coding nucleotides) - longest isoforms onlyAhor_pb32m_HAP1_v1.0.PRIMARY.gff3.gz Filtered gene annotations - longest isoforms onlyAhor_pb32m_HAP1_v1.0.PRIMARY.peptides.fa.gz Filtered gene annotations (protein sequences) - longest isoforms onlyAhor_pb32m_HAP1_v1.0.RM.TE.gff.gz All TE annotations by RepeatMaskerAhor_pb32m_HAP2_v1.0.chrX_regions.bed.gz X chromosome nonrecombining region coordinatesAhor_pb32m_HAP2_v1.0.EDTA.TEanno.gff3.gz All TE annotations by EDTAAhor_pb32m_HAP2_v1.0.EDTA.TEintact.fa.gz Intact TE sequences by EDTAAhor_pb32m_HAP2_v1.0.EDTA.TEintact.gff3.gz Intact TE annotations by EDTAAhor_pb32m_HAP2_v1.0.entap_results.tsv Reciprocal functional gene annotations by EnTAPAhor_pb32m_HAP2_v1.0.fa.gz Haplotype assembly fasta fileAhor_pb32m_HAP2_v1.0.ISOFORMS.bed.gz Filtered gene annotations - all isoformsAhor_pb32m_HAP2_v1.0.ISOFORMS.CDS.fa.gz Filtered gene annotations (protein coding nucleotides) - all isoformsAhor_pb32m_HAP2_v1.0.ISOFORMS.gff3.gz Filtered gene annotations - all isoformsAhor_pb32m_HAP2_v1.0.ISOFORMS.peptides.fa.gz Filtered gene annotations (protein sequences) - all isoformsAhor_pb32m_HAP2_v1.0.PRIMARY.bed.gz Filtered gene annotations - longest isoforms onlyAhor_pb32m_HAP2_v1.0.PRIMARY.CDS.fa.gz Filtered gene annotations (protein coding nucleotides) - longest isoforms onlyAhor_pb32m_HAP2_v1.0.PRIMARY.gff3.gz Filtered gene annotations - longest isoforms onlyAhor_pb32m_HAP2_v1.0.PRIMARY.peptides.fa.gz Filtered gene annotations (protein sequences) - longest isoforms onlyAhor_pb32m_HAP2_v1.0.RM.TE.gff.gz All TE annotations by RepeatMaskerAoff_pb81m_HAP1_v1.0.chrX_regions.bed.gz X chromosome nonrecombining region coordinatesAoff_pb81m_HAP1_v1.0.EDTA.TEanno.gff3.gz All TE annotations by EDTAAoff_pb81m_HAP1_v1.0.EDTA.TEintact.fa.gz Intact TE sequences by EDTAAoff_pb81m_HAP1_v1.0.EDTA.TEintact.gff3.gz Intact TE annotations by EDTAAoff_pb81m_HAP1_v1.0.entap_results.tsv Reciprocal functional gene annotations by EnTAPAoff_pb81m_HAP1_v1.0.fa.gz Haplotype assembly fasta fileAoff_pb81m_HAP1_v1.0.ISOFORMS.bed.gz Filtered gene annotations - all isoformsAoff_pb81m_HAP1_v1.0.ISOFORMS.CDS.fa.gz Filtered gene annotations (protein coding nucleotides) - all isoformsAoff_pb81m_HAP1_v1.0.ISOFORMS.gff3.gz Filtered gene annotations - all isoformsAoff_pb81m_HAP1_v1.0.ISOFORMS.peptides.fa.gz Filtered gene annotations (protein sequences) - all isoformsAoff_pb81m_HAP1_v1.0.PRIMARY.bed.gz Filtered gene annotations - longest isoforms onlyAoff_pb81m_HAP1_v1.0.PRIMARY.CDS.fa.gz Filtered gene annotations (protein coding nucleotides) - longest isoforms onlyAoff_pb81m_HAP1_v1.0.PRIMARY.gff3.gz Filtered gene annotations - longest isoforms onlyAoff_pb81m_HAP1_v1.0.PRIMARY.peptides.fa.gz Filtered gene annotations (protein sequences) - longest isoforms onlyAoff_pb81m_HAP1_v1.0.RM.TE.gff.gz All TE annotations by RepeatMaskerAoff_pb81m_HAP2_v1.0.chrY_regions.bed.gz Y chromosome nonrecombining region coordinatesAoff_pb81m_HAP2_v1.0.EDTA.TEanno.gff3.gz All TE annotations by EDTAAoff_pb81m_HAP2_v1.0.EDTA.TEintact.fa.gz Intact TE sequences by EDTAAoff_pb81m_HAP2_v1.0.EDTA.TEintact.gff3.gz Intact TE annotations by EDTAAoff_pb81m_HAP2_v1.0.entap_results.tsv Reciprocal functional gene annotations by EnTAPAoff_pb81m_HAP2_v1.0.fa.gz Haplotype assembly fasta fileAoff_pb81m_HAP2_v1.0.ISOFORMS.bed.gz Filtered gene annotations - all isoformsAoff_pb81m_HAP2_v1.0.ISOFORMS.CDS.fa.gz Filtered gene annotations (protein coding nucleotides) - all isoformsAoff_pb81m_HAP2_v1.0.ISOFORMS.gff3.gz Filtered gene annotations - all isoformsAoff_pb81m_HAP2_v1.0.ISOFORMS.peptides.fa.gz Filtered gene annotations (protein sequences) - all isoformsAoff_pb81m_HAP2_v1.0.PRIMARY.bed.gz Filtered gene annotations - longest isoforms onlyAoff_pb81m_HAP2_v1.0.PRIMARY.CDS.fa.gz Filtered gene annotations (protein coding nucleotides) - longest isoforms onlyAoff_pb81m_HAP2_v1.0.PRIMARY.gff3.gz Filtered gene annotations - longest isoforms onlyAoff_pb81m_HAP2_v1.0.PRIMARY.peptides.fa.gz Filtered gene annotations (protein sequences) - longest isoforms onlyAoff_pb81m_HAP2_v1.0.RM.TE.gff.gz All TE annotations by RepeatMaskerAhorridus_MSY_CODEML.zip CODEML M2a output for 11 MSY genes with evidence of positive selection in Asparagus horridus
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- PAR ID:
- 10661269
- Publisher / Repository:
- Zenodo
- Date Published:
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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