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

PloS One
Maurizio MascarelloSteven B Janssens

Abstract

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 ...Continue Reading

References

Jan 1, 1988·Proceedings of the National Academy of Sciences of the United States of America·M HildebrandD P Bourque
Jul 24, 2002·Nucleic Acids Research·Kazutaka KatohTakashi Miyata
Dec 16, 2006·Nucleic Acids Research·Pierre TaberletEske Willerslev
Aug 12, 2009·Proceedings of the National Academy of Sciences of the United States of America·UNKNOWN CBOL Plant Working Group
Dec 17, 2009·BMC Bioinformatics·Christiam CamachoThomas L Madden
Mar 23, 2011·Plant Molecular Biology·Susann WickeDietmar Quandt
Jan 1, 2009·Molecular Ecology Resources·Alice ValentiniPierre Taberlet
Nov 22, 2011·Proceedings of the National Academy of Sciences of the United States of America·UNKNOWN China Plant BOL GroupGuang-Wen Duan
Nov 24, 2011·Proceedings of the National Academy of Sciences of the United States of America·Peter M Hollingsworth
Mar 6, 2012·Nature Methods·Ben Langmead, Steven L Salzberg
Apr 18, 2012·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Anton BankevichPavel A Pevzner
Apr 9, 2013·PloS One·Ingrid ParmentierOlivier J Hardy
Jan 29, 2016·Molecular Ecology·Eric CoissacPierre Taberlet
May 15, 2016·Analytical and Bioanalytical Chemistry·Martijn StaatsEsther Kok
Aug 3, 2016·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Peter M HollingsworthAlex D Twyford
Oct 30, 2016·Molecular Ecology Resources·Alex D Twyford, Rob W Ness
Oct 14, 2017·Molecular Biology and Evolution·Julio RozasAlejandro Sánchez-Gracia
Mar 2, 2018·International Journal of Molecular Sciences·Malte MaderBirgit Kersten
May 9, 2019·Nucleic Acids Research·Linchun ShiChang Liu

❮ Previous
Next ❯

Software Mentioned

SPAdes
FLEGT
DnaSP
CpGAVAS2
Geneious Prime
Bowtie
Bowtie2
MAFFT
GetOrganelle

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.