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

• Published in: PloS one Vol. 16; no. 6; p. e0251655
• Main Authors: Mascarello, Maurizio, Amalfi, Mario, Asselman, Pieter, Smets, Erik, Hardy, Olivier J, Beeckman, Hans, Janssens, Steven B
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 11.06.2021; Public Library of Science (PLoS)
• Subjects: Africa; Analysis; Biodiversity; Biology; Biology and Life Sciences; Chloroplasts; Conservation of Natural Resources - methods; DNA Barcoding, Taxonomic - methods; Economic importance; Engineering and Technology; Forensic science; Forensic sciences; Forest management; Forestry laws; Forests; Genetic aspects; Genetic Markers; Genetic testing; Genome, Chloroplast; Genomes; High-Throughput Nucleotide Sequencing; Identification; Law enforcement; Logging; Molecular mechanics; Phylogeny; Plant species; Plastids - genetics; Research and Analysis Methods; Ribosomal DNA; Species; Timber; Trade; Trees - genetics; Wildlife conservation; Wood products; Africa; Belgium; United States > US
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0251655

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.