Environmental (e)RNA advances the reliability of eDNA by predicting its age

Abstract Environmental DNA (eDNA) analysis has advanced conservation biology and biodiversity management. However, accurate estimation of age and origin of eDNA is complicated by particle transport and the presence of legacy genetic material, which can obscure accurate interpretation of eDNA detecti...

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Autores principales:	Nathaniel T. Marshall, Henry A. Vanderploeg, Subba Rao Chaganti
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/1cd47bbe9eab4f8db68f8f166c58e44a
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spelling	oai:doaj.org-article:1cd47bbe9eab4f8db68f8f166c58e44a2021-12-02T14:06:56ZEnvironmental (e)RNA advances the reliability of eDNA by predicting its age10.1038/s41598-021-82205-42045-2322https://doaj.org/article/1cd47bbe9eab4f8db68f8f166c58e44a2021-02-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-82205-4https://doaj.org/toc/2045-2322Abstract Environmental DNA (eDNA) analysis has advanced conservation biology and biodiversity management. However, accurate estimation of age and origin of eDNA is complicated by particle transport and the presence of legacy genetic material, which can obscure accurate interpretation of eDNA detection and quantification. To understand the state of genomic material within the environment, we investigated the degradation relationships between (a) size of fragments (long vs short), (b) genomic origins (mitochondrial vs nuclear), (c) nucleic acids (eDNA vs eRNA), and (d) RNA types (messenger (m)RNA vs ribosomal (r)RNA) from non-indigenous Dreissena mussels. Initial concentrations of eRNA followed expected transcriptional trends, with rRNAs found at > 1000 × that of eDNA, and a mitosis-associated mRNA falling below detection limits within 24 h. Furthermore, the ratio of eRNA:eDNA significantly decreased throughout degradation, potentially providing an estimate for the age of genomic material. Thus, eRNA quantification can increase detection due to the high concentrations of rRNAs. Furthermore, it may improve interpretation of positive detections through the eRNA:eDNA ratio and/or by detecting low abundant mitosis-associated mRNAs that degrade within ~ 24 h.Nathaniel T. MarshallHenry A. VanderploegSubba Rao ChagantiNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-11 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Nathaniel T. Marshall Henry A. Vanderploeg Subba Rao Chaganti Environmental (e)RNA advances the reliability of eDNA by predicting its age
description	Abstract Environmental DNA (eDNA) analysis has advanced conservation biology and biodiversity management. However, accurate estimation of age and origin of eDNA is complicated by particle transport and the presence of legacy genetic material, which can obscure accurate interpretation of eDNA detection and quantification. To understand the state of genomic material within the environment, we investigated the degradation relationships between (a) size of fragments (long vs short), (b) genomic origins (mitochondrial vs nuclear), (c) nucleic acids (eDNA vs eRNA), and (d) RNA types (messenger (m)RNA vs ribosomal (r)RNA) from non-indigenous Dreissena mussels. Initial concentrations of eRNA followed expected transcriptional trends, with rRNAs found at > 1000 × that of eDNA, and a mitosis-associated mRNA falling below detection limits within 24 h. Furthermore, the ratio of eRNA:eDNA significantly decreased throughout degradation, potentially providing an estimate for the age of genomic material. Thus, eRNA quantification can increase detection due to the high concentrations of rRNAs. Furthermore, it may improve interpretation of positive detections through the eRNA:eDNA ratio and/or by detecting low abundant mitosis-associated mRNAs that degrade within ~ 24 h.
format	article
author	Nathaniel T. Marshall Henry A. Vanderploeg Subba Rao Chaganti
author_facet	Nathaniel T. Marshall Henry A. Vanderploeg Subba Rao Chaganti
author_sort	Nathaniel T. Marshall
title	Environmental (e)RNA advances the reliability of eDNA by predicting its age
title_short	Environmental (e)RNA advances the reliability of eDNA by predicting its age
title_full	Environmental (e)RNA advances the reliability of eDNA by predicting its age
title_fullStr	Environmental (e)RNA advances the reliability of eDNA by predicting its age
title_full_unstemmed	Environmental (e)RNA advances the reliability of eDNA by predicting its age
title_sort	environmental (e)rna advances the reliability of edna by predicting its age
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/1cd47bbe9eab4f8db68f8f166c58e44a
work_keys_str_mv	AT nathanieltmarshall environmentalernaadvancesthereliabilityofednabypredictingitsage AT henryavanderploeg environmentalernaadvancesthereliabilityofednabypredictingitsage AT subbaraochaganti environmentalernaadvancesthereliabilityofednabypredictingitsage
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Environmental (e)RNA advances the reliability of eDNA by predicting its age

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