DOI: 10.5061/dryad.jr6r5
title: Data from: Lessons from genome skimming of arthropod-preserving ethanol

description: Field-collected specimens of invertebrates are regularly killed and
 preserved in ethanol, prior to DNA extraction from the specimens, while
 the ethanol fraction is usually discarded. However, DNA may be released
 from the specimens into the ethanol, which can potentially be exploited to
 study species diversity in the sample without the need for DNA extraction
 from tissue. We used shallow shotgun sequencing of the total DNA to
 characterize the preservative ethanol from two pools of insects (from a
 freshwater habitat and terrestrial habitat) to evaluate the efficiency of
 DNA transfer from the specimens to the ethanol. In parallel, the specimens
 themselves were subjected to bulk DNA extraction and shotgun sequencing,
 followed by assembly of mitochondrial genomes for 39 of 40 species in the
 two pools. Shotgun sequencing from the ethanol fraction and read-matching
 to the mitogenomes detected ~40% of the arthropod species in the ethanol,
 confirming the transfer of DNA whose quantity was correlated to the
 biomass of specimens. The comparison of diversity profiles of microbiota
 in specimen and ethanol samples showed that ‘closed association’ (internal
 tissue) bacterial species tend to be more abundant in DNA extracted from
 the specimens, while ‘open association’ symbionts were enriched in the
 preservative fluid. The vomiting reflex of many insects also ensures that
 gut content is released into the ethanol, which provides easy access to
 DNA from prey items. Shotgun sequencing of DNA from preservative ethanol
 provides novel opportunities for characterizing the functional or
 ecological components of an ecosystem and their trophic interactions.
description: Aquatic Ethanol (AE)
 Metagenome (Illumina reads)Illumina reads after
 quality control with Trimmomatic and Printseq (data generation and
 protocols described in the manuscript). Reads in fasta
 format.mod_3AWB.qc.fasta.gzTerrestrial Ethanol (TE) Metagenome (Illumina reads)Illumina reads after quality control with Trimmomatic and Printseq (data generation and protocols described in the manuscript). Reads in fasta format.mod_run3_4AGB.qc.fasta.gzTerrestrial Voucher (TV) Metagenome (Illumina reads)Illumina reads after quality control with Trimmomatic and Printseq (data generation and protocols described in the manuscript). Reads in fasta format.mod_2VGB.qc.fasta.gzAquatic Voucher PART 1 (AV) Metagenome (Illumina reads)Illumina reads after quality control with Trimmomatic and Printseq (data generation and protocols described in the manuscript). Reads in fasta format. # this archive was split in 2 files with the unix command $ gzip -c my_large_file | split -b 1024MiB - myfile_split.gz_ # to uncompress, use $ cat myfile_split.gz_* | gunzip -c &gt; my_large_file # to uncompress in windows (ensure file parts are in correct order) $ copy /b file_aa + file_ab + file_ac + file_ad filetogethermod_1VWB.qc.fasta.gz_aaAquatic Voucher PART 2 (AV) Metagenome (Illumina reads)Illumina reads after quality control with Trimmomatic and Printseq (data generation and protocols described in the manuscript). Reads in fasta format. # this archive was split in 2 files with the unix command $ gzip -c my_large_file | split -b 1024MiB - myfile_split.gz_ # to uncompress, use $ cat myfile_split.gz_* | gunzip -c &gt; my_large_file # to uncompress in windows (ensure file parts are in correct order) $ copy /b file_aa + file_ab + file_ac + file_ad filetogethermod_1VWB.qc.fasta.gz_ab