Data Repository for Béchade et al. (2025). Species-specific bacterial associations emerge from stochastically assembled microbiomes in Northeastern American fireflies.

SHARING/ACCESS INFORMATIONRecommended citation for this repository: cite directly the published scientific article when available (Béchade et al. (2025), Species-specific bacterial associations emerge from stochastically assembled microbiomes in Northeastern American fireflies. Journal.).DATA & FILE OVERVIEW (14 datasets)REPOSITORY. Script for Bechade et al. firefly microbiome article.R: Complete R script used to process and analyze qPCR and sequencing data.REPOSITORY. Input data for R.rar: Input and intermediate files for data analysis in R.REPOSITORY. firefly_non-rarefied_otutable.csv: OTU table from phyloseq sequencing data analysis, including non-rarefied counts.REPOSITORY. firefly_rarefied_otutable.csv: OTU table from phyloseq sequencing data analysis, including rarefied counts at 30,000 reads.REPOSITORY. Rarefaction curves.pdf: Rarefaction curves.REPOSITORY. firefly16S_taxonomy_with_seqs.xlsx: Taxonomy table from phyloseq sequencing data analysis, including taxonomic classification of all sequenced variants and fasta sequences.REPOSITORY. contaminants.decontam.xlsx: Taxonomy table from phyloseq sequencing data analysis for variants classified as contaminant by our decontam run, including taxonomic classification of all sequenced reads and fasta sequences.REPOSITORY. Contaminant analysis 2.pdf: Examples of variants classified as contaminants or not based on the decontam frequency method.REPOSITORY. Percent reads retained, sequence length, and and distribution of sequencing depth 2.pdf: Information on the proportion of reads retained through quality filtering, length of sequences, and read depth.REPOSITORY. Multiple sequence alignments.rar: All 10 alignments used to build phylogenetic trees.REPOSITORY. Wolbachia multi-locus backbone tree.pdf: Full multi-locus, backbone Wolbachia phylogenetic tree.REPOSITORY. Serratia 6-locus and auto-MLST trees.pdf: Full 6-locus and auto-MLST Serratia phylogenetic tree.REPOSITORY. iNaturalist Pn. corruscus observations - 01-24-2025.xlsx: All observations of Photinus corruscus reported on iNaturalist, including tagged observations showing mating specimens in relevant states and years to our study.REPOSITORY. Specimen pictures.rar: Photos of insect specimens.共享与获取信息 本仓库的推荐引用格式：若可获取已发表的学术文章，请直接引用该文献（Béchade 等(2025)，《物种特异性细菌关联源自北美东北部萤火虫的随机组装菌群》，期刊）。 数据与文件概览（共14个数据集） 仓库：用于Béchade等人萤火虫菌群研究论文的R脚本。完整R脚本，用于处理和分析定量PCR（qPCR）及测序数据。 仓库：Input data for R.rar：用于R语言数据分析的输入及中间文件压缩包。 仓库：firefly_non-rarefied_otutable.csv：基于phyloseq测序数据分析得到的操作分类单元（OTU）表，包含未稀疏化的计数数据。 仓库：firefly_rarefied_otutable.csv：基于phyloseq测序数据分析得到的操作分类单元（OTU）表，包含以30000条读长进行稀疏化后的计数数据。 仓库：Rarefaction curves.pdf：稀疏化曲线图表。 仓库：firefly16S_taxonomy_with_seqs.xlsx：基于phyloseq测序数据分析得到的分类学表，包含所有测序变异体的分类学注释及FASTA序列。 仓库：contaminants.decontam.xlsx：基于phyloseq测序数据分析得到的分类学表，对应经decontam工具鉴定为污染物的变异体，包含所有测序读段的分类学注释及FASTA序列。 仓库：Contaminant analysis 2.pdf：基于decontam频率法鉴定污染物与非污染物变异体的示例分析图表。 仓库：Percent reads retained, sequence length, and distribution of sequencing depth 2.pdf：包含经质量过滤后保留的读段占比、序列长度及测序深度分布相关信息的图表。 仓库：Multiple sequence alignments.rar：用于构建系统发育树的全部10组多序列比对结果压缩包。 仓库：Wolbachia multi-locus backbone tree.pdf：完整的多位点沃尔巴克氏体（Wolbachia）系统发育主干树。 仓库：Serratia 6-locus and auto-MLST trees.pdf：完整的6位点及自动多位点序列分型（auto-MLST）沙雷氏菌（Serratia）系统发育树。 仓库：iNaturalist Pn. corruscus observations - 01-24-2025.xlsx：iNaturalist平台上报的所有Photinus corruscus（简写Pn. corruscus）观测数据，包含与本研究相关的、标注了对应状态与年份的交配标本的标记观测记录。 仓库：Specimen pictures.rar：昆虫标本照片压缩包。