Long read genome assembly of Automeris io (Lepidoptera: Saturniidae) an emerging model for the evolution of deimatic displays

Automeris moths are a morphologically diverse group with 145 described species that have a geographic range that spans from the New World temperate zone to the Neotropics. Many Automeris have hindwing eyespots that are thought to deter or disrupt the attack of potential predators, allowing the moth time to escape. Some species in the genus have vestigial eyespots or lack them completely, suggesting that this trait may provide a selective benefit. The Io moth (Automeris io), known for its striking eyespots, is the most widely studied species within the genus and is an emerging model system to study the evolution of deimatism, a predatory defense that combines visual stimuli and movement. Here we present a high-quality, PacBio HiFi genome assembly for Io moth to aid existing research on the molecular development of eyespots. Genomic research is needed to address questions involving antipredatory defenses and eyespot pattern development. BUSCO analysis for this genome shows a completeness ..., PacBio consensus reads were used to estimate genome size and heterozygosity using the program K-Mer counter (KMC) v.3.2.1 (RRID: SCR_001245). A k-mer length of 23 (-m 23) was used to create a histogram of k-mer frequencies and visualized using GenomeScope 2.0 (RRID:SCR_017014). PacBio consensus reads were assembled using the de novo assembler, HiFiasm v.0.16.1 r307 (RRID:SCR_021069), resulting in a 500 Mbp primary assembly. The assembly_stat.py script was used to assess assembly contiguity. BUSCO v.5.2.0 was used to assess completeness with 5,286 putative single copy genes from the lepidoptera_odb10.2019-11-20 database (RRID:SCR_015008; ). Therefore, we attempted to further collapse allelic variation using the Purge Haplotigs pipeline was used to purge additional duplicates. (purge_haplotigs v.1.1.2 ). A coverage histogram was used to choose a minimum, median, and maximum read depth cut off value for purging. This was produced by mapping raw reads to the primary assembly using minimap v..., Files can be opened in a text editor or a spreadsheet software. , # Data and supporting information for \"Genome assembly for Automeris io (Lepidoptera: Saturniidae)\" This readme file contains the list supporting files. Authors: Chelsea Skojec, R. Keating Godfrey, Akito Y. Kawahara --- ## **FILES** **readme.md** This file describes the files included in this supplemental material ### ***Files related to genome assembly*** * **full_table.tsv** BUSCO results from curated assembly using lepidoptera_odb10 database. Column headings Busco ID: orthologous group ID Status: missing or complete Sequence: sequence id Gene Start: beginning location of the gene Gene End: end location of the gene Strand: forward or reverse Score: scores are dereived from comparison of input sequences against a database of known orthologs Length: length of sequence OrthoDB url Description: url link to OrthoDB corresponding orthologous group * **short_summary.txt** Summary table of BUSCO results in txt format * **missing_busco_list.tsv** List of BUSCOs IDs n...透翅蛾属（Automeris）蛾类是一类形态多样的类群，目前已描述物种达145种，地理分布范围覆盖新温带区至新热带界。该属多数物种的后翅具眼斑，这类结构被认为可威慑或干扰潜在捕食者的攻击，为蛾类争取逃逸时间。本属部分物种的眼斑已退化为痕迹结构，或是完全缺失这一性状，这表明眼斑可能具有选择优势。以醒目眼斑闻名的伊奥透翅蛾（Automeris io）是该属中研究最为广泛的物种，同时也是研究恐吓行为（deimatism）演化的新兴模式系统——恐吓行为是一类结合视觉刺激与肢体动作的捕食防御策略。本研究报道了伊奥透翅蛾的高质量PacBio HiFi基因组组装结果，以助力现有关于眼斑分子发育机制的研究。当前亟需开展基因组学研究，以解答关于反捕食防御及眼斑图案发育的相关科学问题。该基因组的BUSCO（Benchmarking Universal Single-Copy Orthologs）分析显示其完整度……（原文此处未完成）。研究使用K-mer计数工具K-Mer Counter (KMC) v3.2.1（RRID: SCR_001245），基于PacBio共识序列估算基因组大小与杂合度。本次分析采用长度为23的k-mer（参数-m 23）构建k-mer频率直方图，并通过GenomeScope 2.0（RRID: SCR_017014）完成可视化。使用从头组装工具HiFiasm v0.16.1 r307（RRID: SCR_021069）对PacBio共识序列进行组装，最终得到500 Mbp的初级组装结果。通过assembly_stat.py脚本评估基因组组装的连续性。使用BUSCO v5.2.0，基于lepidoptera_odb10.2019-11-20数据库中的5286个推定单拷贝基因，评估基因组组装的完整度（RRID: SCR_015008）。因此，本研究尝试使用Purge Haplotigs流程（purge_haplotigs v1.1.2）进一步合并等位基因变异，以去除额外的重复序列。通过覆盖度直方图选取过滤所需的最低、中位及最高测序深度阈值，该直方图由minimap v[版本未完整给出]将原始测序序列比对至初级组装基因组得到。所有文件可通过文本编辑器或电子表格软件打开。# 《伊奥透翅蛾基因组组装（鳞翅目：天蚕蛾科）》相关数据与支撑材料 本README文件将列出本次补充材料包含的全部文件。 作者：Chelsea Skojec、R. Keating Godfrey、Akito Y. Kawahara --- ## **文件列表** **readme.md** 本文件用于说明本次补充材料包含的各类文件。 ### ***基因组组装相关文件*** * **"full_table.tsv"** 基于lepidoptera_odb10数据库对组装结果进行注释后得到的BUSCO分析结果文件。 列标题说明： Busco ID：直系同源群ID Status：缺失或完整 Sequence：序列ID Gene Start：基因起始位置 Gene End：基因终止位置 Strand：正链或负链 Score：通过输入序列与已知直系同源数据库比对得到的评分 Length：序列长度 OrthoDB url/Description：指向OrthoDB对应直系同源群的链接与说明 * **"short_summary.txt"** 以TXT格式存储的BUSCO分析结果汇总表 * **"missing_busco_list.tsv"** 缺失BUSCO条目ID列表（内容未完整展示）