Exploring S-RNase diversity in the Andean black cherry (Prunus serotina) using MinION sequencing: a cost-effective approach with increased genotyping resolution

Becerra-Wong, Mónica; Gordillo-Romero, Milton; Baus, Lisa C.; Terán-Velástegui, Martín; Torres, Maria de Lourdes; Torres, Andres F.

doi:10.1007/s10681-023-03227-9

Cited by 1 publication

(1 citation statement)

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“…To recover some additional reads, manual demultiplexing and trimming of unclassified and unused barcodes were performed using Porechop (v0.2.4, https://github.com/rrwick/Porechop) (Wick et al., 2017). To quantify the enhancement in recovered sequences per barcode, we calculated the percent increase by comparing the number of sequences before and after applying Porechop (Becerra‐Wong et al., 2023); notably, this resulted in a 55–82% increase in the number of reads per barcode in this dataset. The resultant demultiplexed and trimmed reads were consolidated into a single directory.…”

Section: Methodsmentioning

confidence: 99%

Environmental DNA–RNA dynamics provide insights for effective monitoring of marine invasive species

Scriver,

von Ammon,

Pochon

et al. 2024

Environmental DNA

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Environmental DNA and RNA (eDNA/eRNA) can serve as molecular tools for biodiversity monitoring and biosecurity surveillance. However, uncertainties still exist regarding the persistence and dynamics of marine nucleic acids in the environment and the effects of post‐sampling storage on species detectability. To bridge these gaps, an experiment was conducted in an Auckland marina, a known New Zealand entry point for marine non‐indigenous species (NIS). We targeted a prominent invader, the Mediterranean fanworm Sabella spallanzanii, for eDNA/eRNA‐based detection. Permeable dialysis bags filled with seawater collected near an S. spallanzanii colony were deployed in the marina to simulate environmental conditions, with a subset of bags stored on ice to mimic field storage conditions. Sabella spallanzanii eDNA/eRNA signal was quantified using droplet digital PCR on samples collected over 24 h of dialysis bag deployment. Results challenged traditional first‐order decay models, showing inconsistent eDNA/eRNA signal patterns and no significant concentration changes between 0 and 24 h. Consequently, total eDNA fragmentation was assessed using the Agilent 2100 Bioanalyzer® electrophoresis system, which revealed a rise in the number of total eDNA fragments and an unexpected increase in the median fragment size of total eDNA under field conditions over time, likely originating from the ambient microbiome. Additional analysis using long‐read sequencing (Oxford Nanopore Technologies, UK) revealed an increase in microbial eDNA reads within the in‐field samples, suggesting potential microbial growth within the dialysis bags. In contrast, the ice‐stored samples exhibited no significant changes in the number of reads assigned to microbial taxa, implying limited microbial growth in cold storage. These findings provide insights into total eDNA dynamics and its potential impact on targeted eDNA concentration and detection. Further comprehensive research on eDNA/eRNA dynamics, particularly focused on eRNA, is essential, as this understanding is crucial for refining survey interpretation and sampling design for effective environmental management.

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Section: Methodsmentioning

confidence: 99%