Deciphering host-parasitoid interactions and parasitism rates of crop pests using DNA metabarcoding

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 po...,
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
 
Preprocess_2steps_forFrogs.sh
 
Shell script for preprocessing of raw sequences (before running Frogs) : From demultiplexed fastq.gz files produ..., ,