DNA profiling of oaks (Quercus spp.)

Pencakowski, Bartosz; Tokarski, Miron; Jonkisz, Anna; Czosnykowska-Łukacka, Matylda; Lenard, Ewa; Małodobra-Mazur, Małgorzata

doi:10.5114/amsik.2018.75942

Cited by 3 publications

(2 citation statements)

References 13 publications

(26 reference statements)

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“…Different types of molecular markers for DNA profiling of Quercus spp. or Quercus species groups were developed in other studies, e.g., based on plastid SNPs and InDels [ 78 ], short tandem repeat loci [ 79 ], or inter-primer binding sites [ 80 ].…”

Section: Discussionmentioning

confidence: 99%

Mitochondrial Genome of Fagus sylvatica L. as a Source for Taxonomic Marker Development in the Fagales

Mäder¹,

Schroeder²,

Schott³

et al. 2020

Plants

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European beech, Fagus sylvatica L., is one of the most important and widespread deciduous tree species in Central Europe and is widely managed for its hard wood. The complete DNA sequence of the mitochondrial genome of Fagus sylvatica L. was assembled and annotated based on Illumina MiSeq reads and validated using long reads from nanopore MinION sequencing. The genome assembled into a single DNA sequence of 504,715 bp in length containing 58 genes with predicted function, including 35 protein-coding, 20 tRNA and three rRNA genes. Additionally, 23 putative protein-coding genes were predicted supported by RNA-Seq data. Aiming at the development of taxon-specific mitochondrial genetic markers, the tool SNPtax was developed and applied to select genic SNPs potentially specific for different taxa within the Fagales. Further validation of a small SNP set resulted in the development of four CAPS markers specific for Fagus, Fagaceae, or Fagales, respectively, when considering over 100 individuals from a total of 69 species of deciduous trees and conifers from up to 15 families included in the marker validation. The CAPS marker set is suitable to identify the genus Fagus in DNA samples from tree tissues or wood products, including wood composite products.

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Section: Discussionmentioning

confidence: 99%

Mitochondrial Genome of Fagus sylvatica L. as a Source for Taxonomic Marker Development in the Fagales

Mäder¹,

Schroeder²,

Schott³

et al. 2020

Plants

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“…Третьим и последним этапом экстракции является очистка нуклеиновых кислот, т. е. удаление ингибиторов полимеразной цепной реакции (ПЦР) [18].…”

Section: Biology and Biotechnologiesunclassified

Selection and optimization of DNA extraction methods from the leaves of Gleditsia triacanthos L.

Ryabuha,

Kuz'min

2024

Agrarian Bulletin of The

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Abstract. Currently, molecular genetic methods using DNA markers are increasingly used in studies of polymorphism of various populations of woody and shrubby plants. The purpose of this work was the evaluation and selection of protocols for the isolation and purification of DNA from the leaves of Gleditsia triacanthos L. for further studies using DNA labeling. Methods. Four protocols were used to isolate DNA from the leaf blade of Gleditsia triacanthos L. Anionic detergent sodium dodecyl sulfate was used in three isolation protocols for cell lysis, potassium acetate was used for purification from polysaccharides and proteins. In the fourth protocol, a cationic surfactant cetyltrimethyl ammonium bromide was used for cell lysis, the extract was purified with a mixture of chloroform-isoamyl alcohol (24 : 1). Precipitation of the isolated DNA was carried out with isopropanol. The quality of the isolated DNA was evaluated by spectrophotometry, horizontal electrophoresis and Real-time PCR with two types of primers. Results. Optimal conditions for DNA extraction from samples of Gleditsia triacanthos L. containing a large number of metabolites affecting the quality of the isolated extract were selected. By electrophoresis, it was found that both the isolation protocol with sodium dodecyl sulfate and the isolation protocol with cetyltrimethyl ammonium bromide make it possible to obtain a sufficient amount of DNA. The most purified DNA was obtained by the third protocol using sodium dodecyl sulfate and dithiotreitol and by the fourth protocol using cetyltrimethylammonium bromide. The results of PCR of the obtained samples with ITS and psbI-psbK primers indicate that a sufficient amount of product has been obtained and the reproducibility of ISSR markers. The scientific novelty of the work consists in choosing the optimal method of DNA extraction from the leaves of Gleditsia triacanthos L., which is a complex object containing a large number of potential PCR inhibitors. The protocol with sodium dodecyl sulfate and dithiotreitol made it possible to obtain DNA in the right amount and of acceptable quality.

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Forensic botany: time to embrace natural history collections, large scale environmental data and environmental DNA

Spencer

2021

Emerging Topics in Life Sciences

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Forensic botany is a diverse discipline that spans many aspects of plant sciences, particularly taxonomy, field botany, anatomy, and ecology. Internationally, there is a significant opportunity to expand the application of forensic botany in criminal investigations, especially war crimes, genocide, homicide, sexual violence, serious physical assault, illegal trade in endangered species and wildlife crime. In civil proceedings, forensic botany may, for example, be called upon in trade disputes such as accidental contamination of commodities. Despite the potential, there are barriers to the wider application of forensic botany in criminal cases; there is a widespread need to improve the efficiency of botanical trace evidence identification. This could partly be addressed by embracing innovations in image recognition and by accessing the huge quantity of specimens and images housed in natural history collections worldwide. Additionally, the recent advances in DNA sequencing technologies and the expansion of environmental DNA (eDNA) and forensic ecogenomics, offers opportunities to more rapidly provide species-level identifications. The impact of taphonomic processes upon vegetation, and vice versa, remains poorly understood; improved understanding of these interactions and their ecological impacts may be invaluable in improving clandestine burial search protocols.

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DNA profiling of oaks (Quercus spp.)

Cited by 3 publications

References 13 publications

Mitochondrial Genome of Fagus sylvatica L. as a Source for Taxonomic Marker Development in the Fagales

Mitochondrial Genome of Fagus sylvatica L. as a Source for Taxonomic Marker Development in the Fagales

Selection and optimization of DNA extraction methods from the leaves of Gleditsia triacanthos L.

Forensic botany: time to embrace natural history collections, large scale environmental data and environmental DNA

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