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Integrated molecular, occurrence and environmental sequence data for the biogeography of Paramecium polycaryum

Version 1.0

Tarcz, Sebastian, 2026, "Integrated molecular, occurrence and environmental sequence data for the biogeography of Paramecium polycaryum", https://doi.org/10.18150/2ZXWKM, RepOD, V1

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Description

This dataset supports a reassessment of the documented molecular biogeography of Paramecium polycaryum. It integrates strain-derived mitochondrial cytochrome c oxidase subunit I (COI), nuclear ITS1–5.8S–ITS2 (ITS), and nuclear small-subunit rDNA V4 (18S V4) sequences with geographical metadata, historical and published occurrences, repository-derived taxonomic assignments, and environmental sequence evidence.

The dataset comprises an integrated catalogue of 43 records, a detailed evaluation of 11 environmental records, marker-specific sequence alignments, sequence-to-haplotype assignments, haplotype-diversity outputs, matrices of uncorrected pairwise nucleotide distances, and read-level documentation of a targeted PebbleScout feasibility pilot.

The PebbleScout analysis was designed to test whether taxonomically informative V4 reads could be recovered from selected public freshwater sequencing datasets and linked to sample-level metadata. It was not intended as an exhaustive survey of public sequence repositories and cannot be used to estimate the frequency, occupancy, or complete geographical distribution of P. polycaryum.

Original nucleotide sequences and environmental sequencing runs remain available from their source repositories under the accession numbers listed in Tables S1 and S2. The present dataset provides their integration, record-level provenance, haplotype assignments, verification categories, and derived analytical outputs.

(2026-11-03)
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Other
Keyword

Paramecium polycaryum, Ciliophora, Protista, microbial biogeography, haplotype diversity, environmental DNA, public sequence repositories, PebbleScout, legacy data, integration sampling bias, molecular records

CC BY - Creative Commons Attribution 4.0 CC BY - Creative Commons Attribution 4.0

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00_README.txt
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01_Table_S1_Supporting_Information_final.tab
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2 Variables, 12 Observations - UNF:6:+XPmF7MG+2JYA6ai7NWGsw==
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02_Table_S2_Supporting_Information_final.tab
Tabular Data - Original format: MS Excel (XLSX) - 2.6 KB - Nov 3, 2026 - 0 Downloads
License: CC BY - Creative Commons Attribution 4.0
2 Variables, 13 Observations - UNF:6:UP8BOTt2Xwo/QF9JO4leVQ==
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03_COI_alignment.fasta
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04_ITS_alignment.fasta
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05_V4_alignment.fasta
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06_PebbleScout_V4_queries.fasta
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07_V4_environmental_candidate_reads.fasta
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08_haplotype_assignments.tab
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12 Variables, 46 Observations - UNF:6:XcBiKtfOH7bwllnS4lNkpg==
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09_COI_haplotype_statistics.txt
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MD5: 42f761253c001995391066fa1d0eef1f
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