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Genome skimming reveals novel plastid markers for the molecular identification of illegally logged African timber species

Tropical forests represent vast carbon stocks and continue to be key carbon sinks and buffer climate changes. The international policy constructed several mechanisms aiming at conservation and sustainable use of these forests. Illegal logging is an important threat of forests, especially in the trop...

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Autores principales: Mascarello, Maurizio, Amalfi, Mario, Asselman, Pieter, Smets, Erik, Hardy, Olivier J., Beeckman, Hans, Janssens, Steven B.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8195358/
https://www.ncbi.nlm.nih.gov/pubmed/34115787
http://dx.doi.org/10.1371/journal.pone.0251655
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author Mascarello, Maurizio
Amalfi, Mario
Asselman, Pieter
Smets, Erik
Hardy, Olivier J.
Beeckman, Hans
Janssens, Steven B.
author_facet Mascarello, Maurizio
Amalfi, Mario
Asselman, Pieter
Smets, Erik
Hardy, Olivier J.
Beeckman, Hans
Janssens, Steven B.
author_sort Mascarello, Maurizio
collection PubMed
description Tropical forests represent vast carbon stocks and continue to be key carbon sinks and buffer climate changes. The international policy constructed several mechanisms aiming at conservation and sustainable use of these forests. Illegal logging is an important threat of forests, especially in the tropics. Several laws and regulations have been set up to combat illegal timber trade. Despite significant enforcement efforts of these regulations, illegal logging continues to be a serious problem and impacts for the functioning of the forest ecosystem and global biodiversity in the tropics. Microscopic analysis of wood samples and the use of conventional plant DNA barcodes often do not allow to distinguish closely-related species. The use of novel molecular technologies could make an important contribution for the identification of tree species. In this study, we used high-throughput sequencing technologies and bioinformatics tools to obtain the complete de-novo chloroplast genome of 62 commercial African timber species using the genome skimming method. Then, we performed a comparative genomic analysis that revealed new candidate genetic regions for the discrimination of closely-related species. We concluded that genome skimming is a promising method for the development of plant genetic markers to combat illegal logging activities supporting CITES, FLEGT and the EU Timber Regulation.
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spelling pubmed-81953582021-06-21 Genome skimming reveals novel plastid markers for the molecular identification of illegally logged African timber species Mascarello, Maurizio Amalfi, Mario Asselman, Pieter Smets, Erik Hardy, Olivier J. Beeckman, Hans Janssens, Steven B. PLoS One Research Article Tropical forests represent vast carbon stocks and continue to be key carbon sinks and buffer climate changes. The international policy constructed several mechanisms aiming at conservation and sustainable use of these forests. Illegal logging is an important threat of forests, especially in the tropics. Several laws and regulations have been set up to combat illegal timber trade. Despite significant enforcement efforts of these regulations, illegal logging continues to be a serious problem and impacts for the functioning of the forest ecosystem and global biodiversity in the tropics. Microscopic analysis of wood samples and the use of conventional plant DNA barcodes often do not allow to distinguish closely-related species. The use of novel molecular technologies could make an important contribution for the identification of tree species. In this study, we used high-throughput sequencing technologies and bioinformatics tools to obtain the complete de-novo chloroplast genome of 62 commercial African timber species using the genome skimming method. Then, we performed a comparative genomic analysis that revealed new candidate genetic regions for the discrimination of closely-related species. We concluded that genome skimming is a promising method for the development of plant genetic markers to combat illegal logging activities supporting CITES, FLEGT and the EU Timber Regulation. Public Library of Science 2021-06-11 /pmc/articles/PMC8195358/ /pubmed/34115787 http://dx.doi.org/10.1371/journal.pone.0251655 Text en © 2021 Mascarello et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Mascarello, Maurizio
Amalfi, Mario
Asselman, Pieter
Smets, Erik
Hardy, Olivier J.
Beeckman, Hans
Janssens, Steven B.
Genome skimming reveals novel plastid markers for the molecular identification of illegally logged African timber species
title Genome skimming reveals novel plastid markers for the molecular identification of illegally logged African timber species
title_full Genome skimming reveals novel plastid markers for the molecular identification of illegally logged African timber species
title_fullStr Genome skimming reveals novel plastid markers for the molecular identification of illegally logged African timber species
title_full_unstemmed Genome skimming reveals novel plastid markers for the molecular identification of illegally logged African timber species
title_short Genome skimming reveals novel plastid markers for the molecular identification of illegally logged African timber species
title_sort genome skimming reveals novel plastid markers for the molecular identification of illegally logged african timber species
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8195358/
https://www.ncbi.nlm.nih.gov/pubmed/34115787
http://dx.doi.org/10.1371/journal.pone.0251655
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