Filipe Pereira

CIIMAR/CIMAR - University of Porto, Portugal

Research topics

Non-B DNA conformations, genomic rearrangements and disease

Genetic analysis of animal domestication

Molecular diagnostics and species identification

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.

Selected publications:
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.
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

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

Carneiro J, Pereira F, Amorim A.
SPInDel: a multi-functional workbench for species identification using insertion/deletion variants.
Molecular Ecology Resources. 2012. 12(6):1190-5.

Gonçalves J, Pereira F, Amorim A, van Asch B.
New method for the simultaneous identification of cow, sheep, goat, and water buffalo in dairy products by analysis of short species-specific mitochondrial DNA targets.
Journal of Agricultural and Food Chemistry. 2012. 60(42):10480-10485.

van Asch B, Silva Santos L, Carneiro J, Pereira F, Amorim A.
Identification of mtDNA lineages of Sus scrofa by multiplex single base extension for the authentication of processed food products.
Journal of Agricultural and Food Chemistry. 2011. 59(13): 6920-6926.

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.

van Asch B, Pereira F.
State-of-the-art and future prospects of canine STR-based genotyping.
The Open Forensic Science Journal. 2009. 3:45-52.

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.

Pereira F, Carneiro J, Soares P, Maciel S, Nejmeddine F, Lenstra JA, Gusmão L, Amorim A.
A multiplex primer extension assay for the rapid identification of paternal lineages in domestic goat (Capra hircus): laying the foundations for a detailed caprine Y chromosome phylogeny.
Molecular Phylogenetics and Evolution. 2008. 49:663-668.