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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...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2021
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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. |
format | Online Article Text |
id | pubmed-8195358 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
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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