Data from: Long-lasting modification of soil fungal diversity associated with the introduction of rabbits to a remote sub-Antarctic archipelago

Pansu J, Winkworth RC, Hennion F, Gielly L, Taberlet P, Choler P

Date Published: July 28, 2015

DOI: http://dx.doi.org/10.5061/dryad.t8534

 

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Title Vegetation surveys data
Downloaded 6 times
Description This file contains data from vegetation surveys performed in study sites in Kerguelen Islands.The first row represent the percentage of vascular plant cover in each plot. Other rows contain the number of contacts of each plant species per plot (maximum 200 contacts per plot).
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Title Unfiltered sequencing data for fungal metabarcode (table format)
Downloaded 13 times
Description This table contains pre-filtered sequencing data (i.e. usable merged reads assigned to their original sample) for fungal metabarcode. Amplicons were amplified using the primers ITS5 : 5'-GGAAGTAAAAGTCGTAACAAGG-3' (White et al. 1990) and 5.8S_fungi : 5'- CAAGAGATCCGTTGTTGAAAGTT-3' primers (Epp et al. 2012). Sequences were produced by a 2 x 250 bp paired-end sequencing on Illumina MiSeq platform. First processing steps were performed using the OBITOOLS software (http://metabarcoding.org/obitools) as follows: (i) Direct and reverse reads corresponding to the same sequence were aligned and merged thanks to the IlluminaPairEnd program. Only merged sequences with a high alignment quality score were retained (>=40). (ii) Each merged sequence was assigned to its original sample using the tags information previously added to primers thanks to the ngsfilter program. For this step, only sequences containing both primers (with a maximum of 3 mismatches per primer) and exact tag sequences were selected. (iii) To reduce the file size, strictly identical sequences were merged together while keeping information about the origin of sequences. (iv) Sequences containing ambiguous nucleotides or shorter than 100 bp were discarded. (v) Pure singleton (sequences with 1 read among the whole dataset) were removed.
Download Pansu&al_BioLett_ITSfungi_unfiltered_data...xt.zip (8.170 Mb)
Download README.txt (3.065 Kb)
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Title Unfiltered sequencing data for fungal metabarcode (fasta format)
Downloaded 14 times
Description This fasta file contains unfiltered sequencing data (i.e. merged reads assigned to their original sample) for fungal metabarcode. Amplicons were amplified using the primers ITS5 : 5'-GGAAGTAAAAGTCGTAACAAGG-3' (White et al. 1990) and 5.8S_fungi : 5'- CAAGAGATCCGTTGTTGAAAGTT-3' primers (Epp et al. 2012). Sequences were produced by a 2 x 250 bp paired-end sequencing on Illumina MiSeq platform. First processing steps were performed using the OBITOOLS software (http://metabarcoding.org/obitools) as follows: (i) Direct and reverse reads corresponding to the same sequence were aligned and merged thanks to the IlluminaPairEnd program. Only merged sequences with a high alignment quality score were retained (>=40) (ii) Each merged sequence was assigned to its original sample using the tags information previously added to primers thanks to the ngsfilter program. For this step, only sequences containing both primers (with a maximum of 3 mismatches per primer) and exact tag sequences were selected. (iii) To reduce the file size, strictly identical sequences were merged together while keeping information about the origin of sequences.
Download Pansu&al_BioLett_ITSfungi_unfiltered_data...ta.zip (8.925 Mb)
Download README.txt (2.122 Kb)
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Title Filtered sequencing data (MOTUs) for fungal metabarcode
Downloaded 12 times
Description This table contains filtered MOTUs for the fungal metabarcode. Amplicons were amplified using ITS5 : 5'-GGAAGTAAAAGTCGTAACAAGG-3' (White et al. 1990) and 5.8S_fungi : 5'- CAAGAGATCCGTTGTTGAAAGTT-3' primers (Epp et al. 2012). Sequences were obtained by a 2 x 250 bp paired-end sequencing on Illumina MiSeq platform. Data filtering and MOTUs clustering were performed according to the procedure described in the supplementary materials of Pansu et al. (2015): 'Long-lasting modification of soil fungal diversity associated with the introduction of rabbits to a remote sub-Antarctic archipelago'.
Download Pansu&al_BioLett_ITSfungi_filtered_dataset.txt (412.5 Kb)
Download README.txt (3.213 Kb)
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Title Filtered sequencing data for plant metabarcode
Downloaded 8 times
Description This table contains the filtered sequences for the plant metabarcode. Amplicons were amplified using g (5'-GGGCAATCCTGAGCCAA-3') and h (5'-CCATTGAGTCTCTGCACCTATC-3') primers (Taberlet et al. 2007). The sequences have been produced by the Illumina technology (HiSeq 2500 platform, 2x100bp pair-end) and were filtered according to the filtering procedure describes in the supplementary materials of Pansu et al. (2015) ¬'Long-lasting modification of soil fungal diversity associated with the introduction of rabbit to a remote sub-Antarctic archipelago'.
Download Pansu&al_BioLett_gh_filtered_dataset.txt (11.88 Kb)
Download README.txt (3.166 Kb)
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Title Unfiltered sequencing data for plant metabarcode (fasta format)
Downloaded 5 times
Description This fasta file contains unfiltered sequencing data (i.e. merged reads assigned to their original sample) for plant metabarcode. Amplicons were amplified using the universal primers g (5'-GGGCAATCCTGAGCCAA-3') and h (5'-CCATTGAGTCTCTGCACCTATC-3') primers (Taberlet et al. 2007). Sequences were produced by a 2 x 100 bp paired-end sequencing on Illumina HiSeq 2500 platform. First processing steps were performed using the OBITOOLS software (http://metabarcoding.org/obitools) as follows: (i) Direct and reverse reads corresponding to the same sequence were aligned and merged thanks to the IlluminaPairEnd program. Only merged sequences with a high alignment quality score were retained (>=40) (ii) Each merged sequence was assigned to its original sample using the tags information previously added to primers thanks to the ngsfilter program. For this step, only sequences containing both primers (with a maximum of 3 mismatches per primer) and exact tag sequences were selected. (iii) To reduce the file size, strictly identical sequences were merged together while keeping information about the origin of sequences.
Download Pansu&al_BioLett_gh_unfiltered_dataset.fasta.zip (228.2 Kb)
Download README.txt (2.06 Kb)
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Title Pansu&al_BioLett_gh_unfiltered_dataset.txt
Downloaded 11 times
Description This table contains pre-filtered sequencing data (i.e. usable merged reads assigned to their original sample) for fungal metabarcode. Amplicons were amplified using the univerdal primers 'g' (5'-GGGCAATCCTGAGCCAA-3') and 'h' (5'-CCATTGAGTCTCTGCACCTATC-3') primers (Taberlet et al. 2007). Sequences were produced by a 2 x 100 bp paired-end sequencing on Illumina HiSeq 2500 platform. First processing steps were performed using the OBITOOLS software (http://metabarcoding.org/obitools) as follows: (i) Direct and reverse reads corresponding to the same sequence were aligned and merged thanks to the IlluminaPairEnd program. Only merged sequences with a high alignment quality score were retained (>=40). (ii) Each merged sequence was assigned to its original sample using the tags information previously added to primers thanks to the ngsfilter program. For this step, only sequences containing both primers (with a maximum of 3 mismatches per primer) and exact tag sequences were selected. (iii) To reduce the file size, strictly identical sequences were merged together while keeping information about the origin of sequences. (iv) Sequences containing ambiguous nucleotides or shorter than 7 bp were discarded. (v) Pure singleton (sequences with 1 read among the whole dataset) were removed.
Download Pansu&al_BioLett_gh_unfiltered_dataset.txt.zip (206.3 Kb)
Download README.txt (2.94 Kb)
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When using this data, please cite the original publication:

Pansu J, Winkworth RC, Hennion F, Gielly L, Taberlet P, Choler P (2015) Long-lasting modification of soil fungal diversity associated with the introduction of rabbits to a remote sub-Antarctic archipelago. Biology Letters 11(9): 20150408. http://dx.doi.org/10.1098/rsbl.2015.0408

Additionally, please cite the Dryad data package:

Pansu J, Winkworth RC, Hennion F, Gielly L, Taberlet P, Choler P (2015) Data from: Long-lasting modification of soil fungal diversity associated with the introduction of rabbits to a remote sub-Antarctic archipelago. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.t8534
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