DOI: 10.5061/dryad.sj6mf40
title: Data from: Deciphering host-parasitoid interactions and parasitism rates of crop pests using DNA metabarcoding

description: An accurate estimation of parasitism rate and diversity in insect pests is
 a prerequisite to explore processes leading to efficient natural
 biocontrol. While traditional methods, such as rearing, is often limited
 to taxonomic identification, mortality and intensive work. The advent of
 high-throughput sequencing (HTS) techniques, such as DNA metabarcoding, is
 increasingly seen as a reliable and powerful alternative approach.
 However, benefits from such an approach to estimate parasitism rate and
 diversity in an agricultural context have been poorly explored. In this
 study, we compared the parasitoid species composition and parasitism rates
 between rearing and DNA metabarcoding of host eggs and larvae of the
 millet head miner, Heliocheilus albipunctella (de Joannis), collected from
 millet fields in Senegal. We first assessed the detection threshold of ten
 main endoparasitoids by sequencing PCR products of artificial dilution
 gradients of the DNA target in host DNA. We then assessed the potential of
 DNA metabarcoding, to diagnose parasitism rates from field-collected
 samples. Our results showed that, under controlled conditions, relative
 low quantities of parasitoid DNA were successfully detected within a
 eight-fold higher quantity of host DNA. Parasitoid diversity and
 parasitism rates were always higher through DNA metabarcoding than that
 obtained from host rearing. Furthermore, metabarcoding detected
 multi-parasitism, cryptic parasitoid species, and differences of
 parasitism rate between two contrasted sampling sites. Metabarcoding is a
 promising avenue to better understand the importance and complexity of
 host-parasitoid interactions in agroecosystems, to improve pest biocontrol
 strategies.
description: MiSeq raw sequences of
 the COI minibarcode from 1113 moth field samples (part 1)
 This ZIP file
 contains the FASTQ files of the paired-end reads (R1: reads 1; R2: reads
 2) produced for each moth field samples in triplicate using the MiSeq
 platform MiSeq reads COI moth samples
 (part 1).rar MiSeq raw sequences of
 the COI minibarcode from 1113 moth field samples (part 2)
 This ZIP file
 contains the FASTQ files of the paired-end reads (R1: reads 1; R2: reads
 2) produced for each moth field samples in triplicate using the MiSeq
 platform MiSeq reads COI moth samples
 (part 2).rar MiSeq raw sequences of
 the COI minibarcode from 114 DNA dilution test samples This ZIP file contains
 the FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2)
 produced for each DNA dilution in triplicate using the MiSeq
 platform MiSeq reads COI dilution
 test.zip   <strong>Preprocess_2steps_forFrogs.sh</strong>   Shell script for preprocessing of raw sequences (before running Frogs) : From demultiplexed fastq.gz files produced from an Illumina MiSeq amplicon library, this script merges read 1 and read 2 (with flash), then cuts reads from 3' primers (with cutadapt), and collects processed fastq.gz files with a sufficient number of sequences in an archive.   <strong>Preprocess_2steps_forFrogs_parameters_file_COI.txt</strong>   This text file contain parameters needed by the shell script "Preprocess_2steps_forFrogs.sh"