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Monitoring agricultural arthropod diversity by eDNA metabarcoding from plant cleaning fluid
Xiaoxiao Song, Cong Dang, Ran Li, Fang Wang, Hongwei Yao, David W. Stanley, Gongyin Ye
2026, 25 (4): 1586-1596.   DOI: 10.1016/j.jia.2025.07.014
Abstract74)      PDF in ScienceDirect      

Arthropods serve essential roles in crop production as pollinators, predators, and pests.  Understanding arthropod biodiversity is crucial for assessing agroecosystem health, functions, and services.  Traditional survey methods are labor-intensive, costly, and rely on diminishing taxonomic expertise, limiting their agricultural applications.  Environmental DNA (eDNA) metabarcoding of diverse samples provides comprehensive species composition data through efficient and non-invasive sampling.  However, this method remains underutilized in rice field studies.  This research examined four sample substrates - rice plant cleaning fluid (RPCF), rice pollen, soil, and water - using various barcoding primers to identify optimal substrates for monitoring rice paddy arthropod diversity.  The method was implemented in Bt rice and non-Bt rice fields to evaluate its biomonitoring potential.  Results indicate that the COI primer (mlCOIintF/jgHCO2198R) identified the highest number of rice field arthropod species.  The eDNA collected from RPCF detected 15% more arthropod species compared to vacuum sampling of whole arthropods.  Rice pollen collection during the heading stage also revealed considerable arthropod diversity.  Alpha diversity and taxonomic composition remained consistent between Bt and non-Bt rice fields, aligning with traditional survey findings.  These results suggest that eDNA metabarcoding of plant cleaning fluid offers an effective approach for monitoring agricultural arthropod communities, contributing to agricultural production optimization.

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Genome-wide characterization of miRNA and siRNA pathways in the parasitoid wasp Pteromalus puparum
XIAO Shan, FANG Qi, LIU Ming-ming, ZHANG Jiao, WANG Bei-bei, YAN Zhi-chao, WANG Fang, David W. STANLEY, YE Gong-yin
2022, 21 (4): 1106-1115.   DOI: 10.1016/S2095-3119(20)63465-7
Abstract256)      PDF in ScienceDirect      
microRNAs (miRNAs) and small interfering RNAs (siRNAs) are small non-coding RNAs (ncRNAs) that trigger RNA interference (RNAi) in eukaryotic organisms.  The biogenesis pathways for these ncRNAs are well established in Drosophila melanogaster, Aedes aegypti, Bombyx mori and other insects, but lacking in hymenopteran species, particularly in parasitoid wasps.  Pteromalus puparum is a parasitoid of pupal butterflies.  This study identified and analyzed two pathways by interrogating the P. puparum genome.  All core genes of the two pathways are present in the genome as a single copy, except for two genes in the siRNA pathway, R2D2 (two copies) and Argonaute-2 (three).  Conserved domain analyses showed the protein structures in P. puparum were similar to cognate proteins in other insect species.  Phylogenetic analyses of hymenopteran Dicer and Argonaute genes suggested that the siRNA pathway-related genes evolved faster than those in the miRNA pathway.  The study found a decelerated evolution rate of P. puparum Dicer-2 with respect to Dicer-1, which was contrary to other hymenopterans.  Expression analyses revealed high mRNA levels for all miRNA pathway genes in P. puparum adults and the siRNA related genes were expressed in different patterns.  The findings add valuable new knowledge of the miRNA and siRNA pathways and their regulatory actions in parasitoid wasps.
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