Data from Species Distribution, Phylogenetic Structure, and Functional Roles of Detritius Inhabiting Fungi Across Contrasting Aquatic Environments

This dataset contains the data files for the PhD thesis entitled: Species Distribution, Phylogenetic Structure and Functional Roles of Detritus Inhabiting Fungi Across Contrasting Aquatic Environments by Daniel Bruce Raudabaugh. More specifically, it contains the forward Illumina reads for ITS1, ITS2, Beta-tubulin and LSU in addition to the index files and map files needed to process the reads in QIIME 1.9.1. The sequences represent environmental sequencing from detrital samples from Black Moshannon State park (Pennsylvania), Pepper run (Pennsylvania), Nescopeck State park (Pennsylvania), Tannersville Cranberry bog (Pennsylvania), Beulah bog (Wisconsin) and Honey Creek Nature preserve (Wisconsin). The term Peatland includes both bogs and fens habitats. Peatland sites consisted of Black Moshannon State park, Tannersville Cranberry bog and Beulah bog. Stream sites consisted of Pepper Run, Nescopeck State park and Honey Creek Nature preserve. The data set also includes each OTU table with taxonomic determination and the OTU representative sequence, ITS1 alignment files for each fungal class and final RAxML phylogenetic tree

MiSeq v2 platform run number 1
QIIME Map file.txt: map file is needed to parse information in QIIME 1.9.1. This file is used in conjunction with ITS1, ITS2, beta-tubulin, and LSU R1 forward read and Index files.

ITS1 Index file.fastq: file is associated with ITS1 R1 forward Illumina reads.fastq.
ITS1 R1 forward Illumina reads.fastq: ITS1 forward reads from the Illumina MiSeq v2 250 bp run. Reads were generated using PCR product amplified using ITS1F (5'-CTTGGTCATTTAGAGGAAGTAA-'3) and ITS2 (5'-GCTGCGTTCTTCATCGATGC-'3) primers.

ITS2 Index file.fastq: file is associated with ITS2 R1 forward Illumina reads.fastq.
ITS2 R1 forward Illumina reads.fastq: ITS2 forward reads from the Illumina MiSeq v2 250 bp run. Reads were generated using PCR product amplified using fITS7 (5'-GTGARTCATCGAATCTTTG-'3) and ITS4 (5'-TCCTCCGCTTATTGATATGC-'3) primers.

Beta tubulin Index file.fastq: file is associated with Beta tubulin forward Illumina reads.fastq.
Beta tubulin forward Illumina reads.fastq: : Beta tubulin forward reads from the Illumina MiSeq v2 250 bp run. Reads were generated using PCR product amplified using BT2AF (5'-GGTAACCAAATCGGTGCTGCTTTC-'3) and BT2BR (5'-ACCCTCAGTGTAGTGACCCTTGGC-'3) primers.

MiSeq v2 platform run number 2
QIIME Map file is needed to parse information in QIIME 1.9.1. This file is used in conjunction with LSU R1forward read and Index files.

LSU Index file.fastq: file is associated with LSU R1 forward Illumina reads.fastq.
LSU R1 forward Illumina reads.fastq: : LSU forward reads from the Illumina MiSeq v2 250 bp run. Reads were generated using PCR product amplified using LROR (5'-CCGCTGAACTTAAGCATATCA-'3) and LR3 (5'-CCGTGTTTCAAGACGGG-'3) primers.

OTU tables
ITS1 OTU table with taxonomy and sequence data.csv: Standard OTU table with assigned taxonomy from Unite, NCBI, and CONSTAX. The representative sequence for each OTU is included.
ITS2 OTU table with taxonomy and sequence data.csv: Standard OTU table with assigned taxonomy from Unite, NCBI, and CONSTAX. The representative sequence for each OTU is included.
Beta tubulin OTU table with taxonomy and sequence data.csv: Standard OTU table with assigned taxonomy from NCBI. In addition, the representative. The representative sequence for each OTU is included.
LSU OTU table with taxonomy and sequence data.csv: Standard OTU table with assigned taxonomy from SILVA and NCBI. The representative sequence for each OTU is included.

Alignment files and resulting RAxML tree for Class level community phylogenetic analyses
Alignments were completed in PASTA using the MAFFT alignment option. All alignment files contain backbone sequences obtained from TBAS or NCBI in addition to OTU sequences. All phylogenetic trees were completed in PASTA using the RAxML post-processing option.

Alignment_file_Agarcomycetes_trimmed_Phylip
RAxML_Agaricomycetes_ITS1_Tree.tre

Alignment_file_Dothidiomycetes_trimmed_Phylip
RAxML_Dothideomycetes_ITS1_Tree.tre

Alignment_file_Eurotiomycetes_trimmed_Phylip:
RAxML_Eurotiomycetes_ITS1_Tree.tre

Alignment_file_Leotiomycetes_Trimmed_Phylip
RAxML_Leotiomycetes_ITS1_Tree.tre

Alignment_file_Microbotryomycetes_trimmed_phylip
RAxML_Microbotryomycetes_ITS1_Tree.tre

Alignment_file_Mortierellomycetes_Trimmed_phylip
RAxML_Mortierella_ITS1_Tree.tre

Alignment_file_Saccharomycetes_Trimmed_Phylip
RAxML_Saccharomycetes_ITS1_Tree.tre

Alignment_file_Sordariomycetes_trimmed_Phylip
RAxML_Sordriomycetes_ITS1_Tree.tre

Alignment_file_Tremellomycetes_trimmed_phylip
RAxML_Tremellomycetes_ITS1_Tree.tre

Alignment file and resulting RAxML tree for Community level phylogenetic analyses
Alignment was completed in PASTA using the MAFFT alignment option and resulting tree was completed using the RAxML post-processing option.

Alignment_file_ LSU_RDP_fungal_community.aln
LSU_RDP_fungal_community_Tree.tre