Haplotype Phased Chromosome-level <i>Lycorma delicatula </i>Genome and Annotation

CitationSnead, A.A., Meng, F., Largotta, N. <i>et al.</i> Diploid chromosome-level genome assembly and annotation for <i>Lycorma delicatula</i>. <i>Sci Data</i> <b>12</b>, 579 (2025). https://doi.org/10.1038/s41597-025-04854-8AbstractThe spotted lanternfly (<i>Lycorma delicatula</i>) 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 (<i>Lycorma delicatula</i>) described and published in Snead &amp; 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.fasta<b>Description:</b> A fasta file of the assembled genome for the cleaned 13 chromosome haplotype 1 assembly.File: SLF_Hap2.fasta<b>Description:</b> A fasta file of the assembled genome for the cleaned 13 chromosome haplotype 2 assembly.<b>File: SLF_Hap1_Repeats.gff</b><b>Description:</b> A gff file of the repeats annotated in the cleaned 13 chromosome haplotype 1 assembly.<b>File: SLF_Hap2_Repeats.gff</b><b>Description:</b> A gff file of the repeats annotated in the cleaned 13 chromosome haplotype 2 assembly.File: SLF_Hap1.gff<b>Description:</b> A structural annotation of the 13 chromosome haplotype 1 assembly with functional annotations.File: SLF_Hap2.gff<b>Description:</b> A structural annotation of the 13 chromosome haplotype 2 assembly with functional annotations.File: GO_plot_chr_1.png<b>Description:</b> An image of the top 20 GO term results for chromosome 1.File: GO_plot_chr_2.png<b>Description:</b> An image of the top 20 GO term results for chromosome 2.File: GO_plot_chr_3.png<b>Description:</b> An image of the top 20 GO term results for chromosome 3.File: GO_plot_chr_8.png<b>Description:</b> An image of the top 20 GO term results for chromosome 8.File: GO_plot_chr_5.png<b>Description:</b> An image of the top 20 GO term results for chromosome 5.File: GO_plot_chr_4.png<b>Description:</b> An image of the top 20 GO term results for chromosome 4.File: GO_plot_chr_6.png<b>Description:</b> An image of the top 20 GO term results for chromosome 6.File: GO_plot_chr_7.png<b>Description:</b> An image of the top 20 GO term results for chromosome 7.File: GO_plot_chr_11.png<b>Description:</b> An image of the top 20 GO term results for chromosome 11.File: GO_plot_chr_9.png<b>Description:</b> An image of the top 20 GO term results for chromosome 9.File: GO_plot_chr_10.png<b>Description:</b> An image of the top 20 GO term results for chromosome 10.File: GO_plot_chr_12.png<b>Description:</b> An image of the top 20 GO term results for chromosome 12.File: GO_plot_chr_13.png<b>Description:</b> An image of the top 20 GO term results for chromosome 13.File: SLF_Samples_SRA.csv<b>Description:</b> 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.csv<b>Description:</b> 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 <i>Lycorma delicatula</i> 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.<br>

搜集汇总

背景与挑战

背景概述

该数据集提供了斑点灯笼蝇（Lycorma delicatula）的单倍型定相染色体水平基因组和注释，旨在支持这种入侵性害虫的管理和基因组学研究。数据集包含两个单倍型的完整基因组组装（各13条染色体，总大小约2.2 Gbp）、重复序列和结构注释（识别超过12,000个蛋白质编码基因），以及基因本体（GO）分析结果和样本元数据，所有数据均基于PacBio、Hi-C和RNA-seq技术生成，具有高完整性（BUSCO完整度超过96%）。