A complete-genome view of phylum Nanobdellota and recurrent Form III RuBisCO transfer between archaea and Patescibacteriota — analysis archive

This deposit accompanies the manuscript "A complete-genome view of phylum Nanobdellota and recurrent Form III RuBisCO transfer between archaea and Patescibacteriota" (Nielsen and Lui). We present 208 complete Nanobdellota genomes from Oxford Nanopore metagenomes of the Baltic Sea water column and Fennoscandian groundwater (69–201 m below sea level), rotated to the ORC1/Cdc6 replication origin — a 52-fold expansion of complete-genome representation for a phylum previously known from four closed assemblies. Combined with 238 high-quality NCBI MAGs spanning 12 named orders, the cohort supports a 446-genome phylum-level analysis. A Nanobdellota-tuned 71-marker phylogenomic instrument (ar71) was calibrated on 1,288 genomes and used to infer a 1,239-tip ML tree. A 4,262-tip rbcL gene-tree analysis identifies recurrent Form III RuBisCO transfer between archaea and Patescibacteriota, with archaea-to-CPR being the more frequently identified direction in our data. What this deposit contains - draft.md and draft.pdf — the manuscript text and rendered PDF. - AGENT_GUIDE.md — a 600+ line operating manual that describes every directory, file convention, and analysis step in enough detail for a future user (human or LLM) to reproduce, audit, or extend the work. - 256 Nanobdellota genomes — 208 complete (rotated to ORC1/Cdc6) plus 48 high-quality non-circular, with per-genome gene predictions (Pyrodigal v3.6.3) at genomes/, genes/, genomes_noncircular/, genes_noncircular/. - ar71 phylogenomic instrument — 71 Nanobdellota-tuned marker HMMs (custom_hmms/ar71/, including a pre-built concatenated ar71_combined.hmm with HMMER press files), supermatrix, IQ-TREE outputs (ar71_tree/), and the 1,239-tip ML tree. - 154 custom KO HMMs — custom_hmms/kofam/, with verdicts (94 ROBUST, 23 EXPANDED, 12 PARTIAL, 25 COLLAPSED) addressing systematic KofamScan under-detection of divergent archaeal orthologs in DPANN proteomes; the 94 ROBUST set is shipped pre-bundled as kofam_robust.hmm. - rbcL phylogeny v2 — rubisco_tree_v2/, including the 4,262-tip alignment, the 1,150-tip plant-rooted analysis tree, transfer-event annotations, and the IQ-TREE rbcl_v2.bestModel (LG+R10). - OrthoFinder outputs — orthofinder/, full results from the 1,288-genome run. - Per-step scripts — scripts/ (29 numbered scripts; see scripts/INDEX.md). - KofamScan tabular outputs, tRNAscan-SE results, cmsearch results, Foldseek validation outputs, and intermediate per-step artefacts under their respective directories. How to use this deposit Read AGENT_GUIDE.md first. It maps every directory, names the canonical inputs and outputs of each step, and points to the script in scripts/ that produced each artefact. It is written so that a reader unfamiliar with the project can re-run any single step against the supplied inputs. Citation Please cite the manuscript (DOI to be added once the preprint is posted) and this Zenodo record together. License This deposit is released under the Creative Commons Attribution 4.0 International (CC-BY-4.0) license. Integrity verification Nanobdellota_Zen.zip (8.4 GB, decompresses to 15 GB) SHA-256: 1257b93c8202a1f5c665081ed59283e20ec3f1248170ffa4643d6705f885a04c