DOI: 10.5061/dryad.n6278
title: Data from: Detection and decay rates of prey and prey symbionts in the gut of a predator through metagenomics

description: DNA methods are useful to identify ingested prey items from the gut of
 predators, but reliable detection is hampered by low amounts of degraded
 DNA. PCR-based methods can retrieve minute amounts of starting material
 but suffer from amplification biases and cross-reactions with the predator
 and related species genomes. Here, we use PCR-free direct shotgun
 sequencing of total DNA isolated from the gut of the harlequin ladybird
 Harmonia axyridis at five time points after feeding on a single pea aphid
 Acyrthosiphon pisum. Sequence reads were matched to three reference
 databases: Insecta mitogenomes of 587 species, including H. axyridis
 sequenced here; A. pisum nuclear genome scaffolds; and scaffolds and
 complete genomes of 13 potential bacterial symbionts. Immediately after
 feeding, multicopy mtDNA of A. pisum was detected in tens of reads, while
 hundreds of matches to nuclear scaffolds were detected. Aphid nuclear DNA
 and mtDNA decayed at similar rates (0.281 and 0.11 h−1 respectively), and
 the detectability periods were 32.7 and 23.1 h. Metagenomic sequencing
 also revealed thousands of reads of the obligate Buchnera aphidicola and
 facultative Regiella insecticola aphid symbionts, which showed exponential
 decay rates significantly faster than aphid DNA (0.694 and 0.80 h−1,
 respectively). However, the facultative aphid symbionts Hamiltonella
 defensa, Arsenophonus spp. and Serratia symbiotica showed an unexpected
 temporary increase in population size by 1–2 orders of magnitude in the
 predator guts before declining. Metagenomics is a powerful tool that can
 reveal complex relationships and the dynamics of interactions among
 predators, prey and their symbionts.
description: DPP-T50-1_S1_L001_R1_001_QCZipped Fastq file (R1) of the sequenced TruSeq-Illumina library of the gut contents of Harmonia axyridis before feeding (negative control).DPP-T50-1_S1_L001_R2_001_QCZipped Fastq file (R2) of the sequenced TruSeq-Illumina library of the gut contents of Harmonia axyridis before feeding (negative control).DPP-T50-2_S2_L001_R1_001_QCZipped Fastq file (R1) of the sequenced TruSeq-Illumina library of the gut contents of Harmonia axyridis immediately after feeding.DPP-T50-2_S2_L001_R2_001_QCZipped Fastq file (R2) of the sequenced TruSeq-Illumina library of the gut contents of Harmonia axyridis immediately after feeding.DPP-T50-3_S3_L001_R1_001_QCZipped Fastq file (R1) of the sequenced TruSeq-Illumina library of the gut contents of Harmonia axyridis 3 hours after feeding.DPP-T50-3_S3_L001_R2_001_QCZipped Fastq file (R2) of the sequenced TruSeq-Illumina library of the gut contents of Harmonia axyridis 3 hours after feeding.DPP-T50-4_S4_L001_R1_001_QCZipped Fastq file (R1) of the sequenced TruSeq-Illumina library of the gut contents of Harmonia axyridis 24 hours after feeding.DPP-T50-4_S4_L001_R2_001_QCZipped Fastq file (R2) of the sequenced TruSeq-Illumina library of the gut contents of Harmonia axyridis 24 hours after feeding.DPP-T50-5_S5_L001_R1_001_QCZipped Fastq file (R1) of the sequenced TruSeq-Illumina library of the gut contents of Harmonia axyridis 48 hours after feeding (negative control).DPP-T50-5_S5_L001_R2_001_QCZipped Fastq file (R2) of the sequenced TruSeq-Illumina library of the gut contents of Harmonia axyridis 48 hours after feeding.DPP-T50-6_S6_L001_R1_001_QCZipped Fastq file (R1) of the sequenced TruSeq-Illumina library of the gut contents of Harmonia axyridis 96 hours after feeding.DPP-T50-6_S6_L001_R2_001_QCZipped Fastq file (R2) of the sequenced TruSeq-Illumina library of the gut contents of Harmonia axyridis 96 hours after feeding.