Molecular diagnostics and species identification

The relevance of species identification has increasing significantly over the last years. Correct biological identifications are important for the assessment of biodiversity, discovery of invasive species, detection of illegal trade of endangered species, fisheries management, food authentication, diagnosis and control of infectious diseases, etc. Advances in the field of molecular biology have revolutionized the way that we classify and identify species. The main advance has occurred with the development of DNA-based methods due to the ubiquity, molecular stability and higher information content provided by DNA. Among the available methods, DNA sequencing is currently the most used procedure, particularly of mitochondrial genes.

Despite the widespread use of DNA sequencing, some practical limitations still remain for those researchers analysing mixtures or small and degraded samples, where the available DNA is either fragmented or in small amounts. Moreover, most barcoding projects are designed for a single taxonomic group (e.g., fishes, birds, butterflies), requiring a priori knowledge of the taxonomic groups represented in the sample, which is not always possible.

Our aim is to develop reliable and cost-effective methods for broad spectrum species identification that are appropriate for use in suboptimal samples and are amenable to different high-throughput genotyping platforms. We also develop molecular kits to be used for characterization of domestic breeds and fraud detection in processed food products.

Related Publications


Monteiro J, Videira A., Pereira F
Quantification of Neurospora crassa mitochondrial DNA using quantitative real‐time PCR.
Letters in Applied Microbiology. 2020. DOI: 10.1111/lam.13294

Santos C, Pereira F
Identification of plant species using variable length chloroplast DNA sequences
Forensic Science International: Genetics. 2018. 36:1-12. DOI: 10.1016/j.fsigen.2018.05.009

Arenas M, Pereira F, Oliveira M, Pinto N, Lopes AM, Gomes V, Carracedo A, Amorim A
Forensic genetics and genomics: much more than just a human affair
PLoS Genetics. 2017. 13(9): e1006960. DOI:

Castro C, Amorim M, Moreira F, Pereira F
A method to assemble DNA fragments mimicking junctions of transgenic elements: application to the AquAdvantage salmon
Food Control. 2017. 82: 179-183. DOI:

Moreira F, Carneiro J, Pereira F
A proposal for standardization of transgenic reference sequences used in food forensics
Forensic Science International: Genetics. 2017. 29: e26-e28. DOI: 10.1016/j.fsigen.2017.04.022

Alves C, Pereira R, Prieto L, Aler M, Amaral C, Arévalo C, Berardi G, Di Rocco F, Caputo M, Carmona CH, Catelli L, Costal HA, Coufalova P, Furfuro S, García O, Gaviria A, Goios A, Gómez JJB, Hernández A, Hernández ECB, Miranda L, Parra D, Pedrosa S, Porto MJA, Rebelo ML, Spirito M, Torres MCV, Amorim A, Pereira F.
Species identification in forensic samples using the SPInDel approach: A GHEP-ISFG inter-laboratory collaborative exercise
Forensic Science International: Genetics. 2017. 28: 219–224. DOI:

Santos C, Pereira F.
Design and evaluation of PCR primers for amplification of four chloroplast DNA regions in plants
Conservation Genetics Resources. 2017. 9(1), 9-12. DOI: 10.1007/s12686-016-0605-0

Gonçalves J, Marks CA, Obendorf D, Amorim A, Pereira F.
A multiplex PCR assay for identification of the red fox (Vulpes vulpes) using the mitochondrial ribosomal RNA genes
Conservation Genetics Resources. 2015. 7(1): 45-48. DOI: 10.1007/s12686-014-0343-0

Gonçalves J, Marks CA, Obendorf D, Amorim A, Pereira F.
The risks of using “species-specific” PCR assays in wildlife research: The case of red fox (Vulpes vulpes) identification in Tasmania.
Forensic Science International: Genetics. 2014. 11:e9-11. doi: 10.1016/j.fsigen.2014.03.009

Pereira F, Carneiro J, Matthiesen R, van Asch B, Pinto N, Gusmão L, Amorim A.
Identification of species by multiplex analysis of variable-length sequences.
Nucleic Acids Research. 2010. 38 (22): e203.

Pereira F, Carneiro J, van Asch B.
A guide for mitochondrial DNA analysis in non-human forensic investigations.
The Open Forensic Science Journal. 2009.3:33-44.

Pereira F, Carneiro J, Amorim A.
Identification of species with DNA-based technology: current progress and challenges.
Recent Patents on DNA & Gene Sequences. 2008. 2:187-200.

van Asch B, Pereira L, Pereira F, Amorim A.
Mitochondrial DNA lineages of the Portuguese Podengo autochthonous dog breed.
The Portuguese Podengo, pp 264-274. Vítor Veiga, Coord.; Alan Hedges, UK Editor.



Pereira F, van Asch B, Gusmão L.
Process for animal species identification in samples with genetic material based on mitochondrial DNA size variation.
Portuguese patent application nº 103599. Priority Date: 06 November 2006.
WO PCT/IB2007/054509