Data from Species Distribution, Phylogenetic Structure, and Functional Roles of Detritius Inhabiting Fungi Across Contrasting Aquatic Environments.
Citation:
Miller, Andrew; Raudabaugh, Daniel (2020): Data from Species Distribution, Phylogenetic Structure, and Functional Roles of Detritius Inhabiting Fungi Across Contrasting Aquatic Environments.. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-6862941_V2
Persistent link for this dataset:
Related Thesis Raudabaugh, Daniel Bruce (2019). Species distribution, phylogenetic structure and functional roles of detritus inhabiting fungi across contrasting aquatic environments. Ph. D. Dissertation. University of Illinois at Urbana-Champaign.
Related Article Raudabaugh DB, Bach EM, Allen JM, Miller AN (2021) Fungal communities of submerged fine detritus from temperate peatland and stream habitats. Aquat Microb Ecol 86:191-207. https://doi.org/10.3354/ame01969
Dataset Description

This version 2 dataset contains 34 files in total with one (1) additional file, called "Culture-dependent Isolate table with taxonomic determination and sequence data.csv". The remaining files (33) are identical to version 1. The following is the information about the new file and its variables:

Culture-dependent Isolate table with taxonomic determination and sequence data.csv: Culture table with assigned taxonomy from NCBI. Single direction sequence for each isolate is include if one could be obtained. Sequence is derived from ITS1F-ITS4 PCR amplicons, with Sanger sequencing in one direction using ITS5. The files contains 20 variables with explanation as below:

IsolateNumber : unique number identify each isolate cultured
Time: season in which the sample was collected
Location: the specific name of the location
Habitat: type of habitat : either stream or peatland
State: state in the USA in which the specific location is located
Incubation_pH ID: pH of the medium during isolation of fungal cultures
Genus: phylogenetic genus of the fungal isolates (determined by sequence similarity)
Sequence_quality: base call quality of the entire sequence used for blast analysis, if known
%_coverage: sequence coverage reported from GenBank
%_ID: sequence similarity reported from GenBank
Life_style : ecological life style if known
Phylum: phylogenetic phylum as indicated by Index Fungorum
Subphylum: phylogenetic subphylum as indicated by Index Fungorum
Class: phylogenetic class as indicated by Index Fungorum
Subclass: phylogenetic subclass as indicated by Index Fungorum
Order: phylogenetic order as indicated by Index Fungorum
Family: phylogenetic Family as indicated by Index Fungorum
ITS5_Sequence: single direction sequence used for sequence similarity match using blastn. Primer ITS5
Fasta: sequence with nomenclature in a fasta format for easy cut and paste into phylogenetic software
Note: blank cells mean no data is available or unknown.

Subject Life Sciences
Keywords ITS1 forward reads; Illumina; peatlands; streams; bogs; fens
License CC0
Corresponding Creator Andrew Miller
Downloaded 531 times
Version DOI Comment Publication Date
2 10.13012/B2IDB-6862941_V2 "Culture-dependent Isolate table with taxonomic determination and sequence data.csv" file is added to this version 2020-11-05
1 10.13012/B2IDB-6862941_V1 2019-06-05
Alignment_file_ LSU_RDP_fungal_community.aln 5.28 MB File
Alignment_file_Agarcomycetes_trimmed_Phylip 2.33 MB File
Alignment_file_Dothidiomycetes_trimmed_Phylip 2.3 MB File
Alignment_file_Eurotiomycetes_trimmed_Phylip 1.51 MB File
Alignment_file_Leotiomycetes_Trimmed_Phylip 1.25 MB File
Alignment_file_Microbotryomycetes_trimmed_phylip 109 KB File
Alignment_file_Mortierellomycetes_Trimmed_phylip 299 KB File
Alignment_file_Saccharomycetes_Trimmed_Phylip 335 KB File
Alignment_file_Sordariomycetes_trimmed_Phylip 2.87 MB File
Alignment_file_Tremellomycetes_trimmed_phylip 823 KB File
Beta tubulin Index file.fastq 198 MB File
Beta tubulin OTU table with taxonomy and sequence data.csv 1.07 MB View File
Beta tubulin forward Illumina reads.fastq 1.38 GB File
Culture-dependent Isolate table with taxonomic determination and sequence data.csv 1.43 MB View File
ITS1 Index file.fastq 170 MB File
ITS1 OTU table with taxonomy and sequence data.csv 5.43 MB View File
ITS1 R1 forward Illumina reads.fastq 1.18 GB File
ITS2 Index file.fastq 138 MB File
ITS2 OTU table with taxonomy and sequence data.csv 3.43 MB View File
ITS2 R1 forward Illumina reads.fastq 979 MB File
LSU Index file.fastq 775 MB File
LSU OTU table with taxonomy and sequence data.csv 9.67 MB View File
LSU R1 forward Illumina reads.fastq 2.05 GB File
LSU_RDP_fungal_community_Tree.tree.txt 349 KB File
QIIME Map file.txt 6.16 KB File
RAxML_Agaricomycetes_ITS1_Tree.tre 21.4 KB File
RAxML_Dothideomycetes_ITS1_Tree.tre 34.9 KB File
RAxML_Eurotiomycetes_ITS1_Tree.tre 13 KB File
RAxML_Leotiomycetes_ITS1_Tree.tre 18.9 KB File
RAxML_Microbotryomycetes_ITS1_Tree.tre 3.24 KB File
RAxML_Mortierellomycetes_ITS1_Tree.tre 7.19 KB File
RAxML_Saccharomycetes_ITS1_Tree.tre 5.89 KB File
RAxML_Sordriomycetes_ITS1_Tree.tre 33.1 KB File
RAxML_Tremellomycetes_ITS1_Tree.tre 17.5 KB File

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