Dataset for "Genome-resolved metagenomics of 171 leafhopper species reveals a modular microbiome architecture"

Genome-resolved global leafhopper microbiome resource This repository contains the datasets associated with the manuscript: "Genome-resolved metagenomics reveals conserved, flexible and emerging symbioses across global leafhoppers." The Genome-resolved global leafhopper microbiome resource comprises a genome-resolved collection of microbial genes and metagenome-assembled genomes (MAGs) reconstructed from 264 shotgun metagenomes representing 171 leafhopper species collected across 13 countries. Repository contents:ORFs_repfilt.fasta Non-redundant microbial gene catalog generated from all assembled metagenomes. Open reading frames (ORFs) were predicted using Prodigal and clustered at 95% sequence identity with MMseqs2, resulting in approximately 18.6 million non-redundant genes. This catalog was used as the reference for gene abundance estimation using Salmon. merged_MAGs.zip Compressed archive containing all non-redundant metagenome-assembled genomes (MAGs) recovered in this study after dereplication and manual curation. MAGs were evaluated using CheckM, CheckM2, and GUNC before inclusion in the Genome-resolved global leafhopper microbiome resource. metadata_mags.csv Metadata associated with every MAG included in the catalog. The table contains genome statistics and taxonomic information, including MAG identifiers, host species, taxonomic classification, completeness, contamination, genome size, GC content, N50, number of contigs, coding sequences, tRNAs, rRNAs, and other assembly metrics used throughout the study. metadata_catalog.zip Metadata associated with the non-redundant gene catalog. This archive contains the metadata table generated during catalog construction, including gene identifiers, host-taxonomic assignments, country. catalog_leafhopper_emapper.zip Functional annotation of the complete gene catalog generated using eggNOG-mapper. Annotations include functional information retrieved from multiple databases, including: eggNOG orthologous groupsKEGGGene Ontology (GO)Enzyme Commission (EC)COGCAZyPfam 16S_fixed.fasta Non-redundant 16S rRNA gene sequences recovered directly from the metagenomic assemblies. These sequences represent bacterial symbionts and other members of the leafhopper-associated microbial communities. They were extracted from assembled contigs, taxonomically classified, and used for phylogenetic reconstruction and microbial community analyses. Alignments_tree.zip Sequence alignments used for the phylogenetic reconstruction of bacterial symbiont communities recovered from leafhopper metagenomes.These alignments were used to generate the phylogenetic trees presented in the manuscript.Multiple sequence alignments used for the phylogenomic reconstruction of candidate novel bacterial species recovered in this study.These files correspond to the alignments used to infer the evolutionary placement of previously undescribed MAGs and candidate novel taxa presented in the manuscript. Annotation of MAGs Functional annotation of all metagenome-assembled genomes (MAGs) generated using Prokka. This archive contains the standard Prokka output files for each MAG, including annotated coding sequences (CDSs), rRNAs, tRNAs, proteins, and feature tables in GFF, GBK, FAA, FFN, FNA, and TSV formats, providing the complete structural and functional genome annotations used in this study. Data availability Raw sequencing datasets are publicly available through the NCBI Sequence Read Archive (SRA) under the BioProject accessions listed in Supplementary Table S1 of the manuscript. Metagenome-assembled genomes are also available through NCBI under BioProject PRJNA1450707. Citation If you use these datasets, please cite: Pellegrinetti TA, Molligan J, Santos AA, et al. Genome-resolved metagenomics reveals conserved, flexible and emerging symbioses across global leafhoppers. ISME host microbe, 2026 Contact For questions regarding these datasets, please contact: Prof. Edel Pérez-LópezUniversité LavalQuébec City, Canada