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The study genetically characterized the remaining indigenous pigs of Angola, a population brought close to disappearance by decades of social upheaval and by crossbreeding with imported European breeds. Whole genomes from a remote population in Huambo province were compared with 78 publicly available genomes of European and Asian pig breeds and wild boars. The results showed that Angolan pigs fall within the European cluster and are clearly separated from Asian breeds, yet carry signatures of selection that are entirely their own. These point to selection for feed efficiency and metabolism, and consistently highlighted CDKAL1, a gene involved in insulin and cholesterol metabolism, as unique to the Angolan pigs — consistent with adaptation to an environment where food and water are scarce. This is the first assessment of how Angolan pigs relate to other pig populations worldwide, and identifies them as a genetic resource worth conserving.
The study genetically characterized the endangered Landim pig, an indigenous breed from Mozambique, using whole-genome sequencing. The results showed that Landim pigs are genetically distinct and closely related to Angolan pigs, although they have some recent genetic influence from European commercial breeds. The researchers also identified signs of natural selection in immune-related genes, suggesting adaptations that may improve disease resistance and survival. These findings highlight the importance of conserving the Landim pig as a valuable source of genetic diversity for future breeding and conservation programs.
The study investigated the genetic basis of resistance to coccidiosis, a parasitic gut infection that quietly reduces growth in young lambs, in Portuguese Merino sheep. Using a genome-wide association study of faecal oocyst counts in more than 400 genotyped animals drawn from a phenotyped population of 1,022 sheep, the researchers identified twelve genomic regions associated with resistance. Two groups of genes stood out: claudins, which form the barrier between gut cells that the parasite must cross, and Rab proteins, which control the internal cell traffic that parasites hijack to survive. These findings provide the first candidate markers for coccidiosis resistance in Portuguese Merino and could support marker-assisted selection, reducing dependence on antiparasitic drugs and strengthening the breed's conservation and management programme.
2026
Varela-Martínez E, Afonso A, Mainou D, Teixeira F, Nunes T, Vieira P, Sarraguça I, Martins C, Campbell N, da Silva RC, Perloiro T, de Carvalho LM, Ferreira AC, Telo da Gama L, Waap H, Amaral AJ. Claudin and Rab proteins are key molecular components involved in coccidiosis resistance in Portuguese Merino sheep. Genetics Selection Evolution 58:2. 10.1186/s12711-025-01020-x
Clark EL, Amaral A, Baranasic D, et al. Establishing the ELIXIR Domestic Animals Genome and Phenome Community [version 1; peer review: awaiting peer review]. F1000Research 2026, 15(ELIXIR):339. 10.12688/f1000research.177500.1
2025
Teixeira F, Sá P, Santos D, Garrine C, Zimba R, Augusto L, Varela-Martínez E, Chiaia H, Sebastino K, Cordeiro JM, Leitão A, Gama LT, Amaral AJ (2025). Genetic uniqueness and selection of endangered Landim pigs for survival and innate immune response. Frontiers in Veterinary Science — Livestock Genomics 12. 10.3389/fvets.2025.1633365
Langer BE, Amaral A, … Espinosa-Carrasco J, Notredame C, and the nf-core community. Empowering bioinformatics communities with Nextflow and nf-core. Genome Biology 26:228. 10.1186/s13059-025-03673-9
Moreira da Silva J, Menezes J, Fernandes L, Marques CF, Costa SS, Timofte D, Amaral AJ, Pomba C. Evaluation of multidrug-resistant bacteria and their molecular mechanisms found in small animal veterinary practices in Portugal. Frontiers in Cellular and Infection Microbiology 15. 10.3389/fcimb.2025.1582411
2024
Ruvinskiy D, Amaral A, Weldenegodguad M, et al. Adipose gene expression profiles in Northern Finncattle, Mirandesa cattle, Yakutian cattle and commercial Holstein cattle. Scientific Reports 14:22216. 10.1038/s41598-024-73023-5
Marques JP, Alves PC, Amorim, … Amaral AJ, et al. Building a Portuguese coalition for biodiversity genomics. npj Biodiversity 3:27. 10.1038/s44185-024-00061-7
Menezes J, Frosini SM, Weese S, Perreten V, Schwarz S, Amaral AJ, Loeffler A, Pomba C. Transmission dynamics of ESBL/AmpC and carbapenemase-producing Enterobacterales between companion animals and humans. Frontiers in Microbiology. 10.3389/fmicb.2024.1432240
Fanalli SL, Gomes JD, de Novais FJ, Gervásio IC, Fukumasu H, Moreira GCM, Coutinho LL, Koltes J, Amaral AJ, Cesar ASM. Key co-expressed genes correlated with blood serum parameters of pigs fed with different fatty acid profile diets. Frontiers in Genetics 15:1394971. 10.3389/fgene.2024.1394971
Moreira da Silva J, Menezes J, Fernandes L, Marques C, Costa SS, Timofte D, Amaral A, Pomba C. Dynamics of blaOXA-23 gene transmission in Acinetobacter spp. from contaminated veterinary environmental surfaces: an emerging One Health threat? Journal of Hospital Infection. 10.1016/j.jhin.2024.02.001
Moreira da Silva J, Menezes J, Fernandes L, Costa SS, Amaral A, Pomba C. Carbapenemase-producing Enterobacterales strains causing infections in companion animals — Portugal. Microbiology Spectrum. 10.1128/spectrum.03416-23
2023
Menezes J, Frosini SM, Belas A, Marques C, Silva JM, Amaral AJ, Loeffler A, Pomba C. Longitudinal study of ESBL/AmpC-producing Enterobacterales strains sharing between cohabiting healthy companion animals and humans in Portugal and in the United Kingdom. European Journal of Clinical Microbiology & Infectious Diseases. 10.1007/s10096-023-04629-2
2022
Menezes J, Silva JM, Frosini SM, Loeffler A, Weese S, Perreten V, Schwarz S, Gama LT, Amaral AJ, Pomba C. mcr-1sharing between co-habiting dogs and humans in the community, Lisbon, Portugal, 2018–2020. Eurosurveillance27(44):2101144. 10.2807/1560-7917.ES.2022.27.44.2101144
Moreira da Silva J, Menezes J, Mendes G, Santos Costa S, Caneiras C, Poirel L, Amaral AJ, Pomba C. KPC-3-producing Klebsiella pneumoniae sequence type 392 from a dog's clinical isolate in Portugal. Microbiology Spectrum. 10.1128/spectrum.00893-22
Sá P, Santos D, Leitão A, Moras-Cordeiro J, Gama LT, Amaral AJ. Lost pigs of Angola: whole genome sequencing reveals unique regions of selection with emphasis on metabolism and feed efficiency. Frontiers in Genetics 13:1003069. 10.3389/fgene.2022.1003069
Bressan MC, Belo AT, Amaral A, Cordeiro D, Boari CB, et al. The impact of genetic groups (Alentejano and F1 Landrace × Large White pigs) and body weight (90, 120, 160 kg) on blood metabolites. Livestock Science 255:104810. 10.1016/j.livsci.2021.104810
2021
Vasconcelos AM, Carmo MB, Ferreira B, Viegas I, Gama-Carvalho M, Ferreira A, Amaral AJ*. IsomiR_Window: a system for analyzing small-RNA-seq data in an integrative and user-friendly manner. BMC Bioinformatics 22:37. 10.1186/s12859-021-03955-6
2020
Amaral AJ, Pavão AL, Gama LT. Genomic tools for the conservation and genetic improvement of a highly fragmented breed — the Ramo Grande cattle from the Azores. Animals 10:1089. 10.3390/ani10061089
2019
Amaral AJ, Bressan MC, Almeida J, et al. Combining genome-wide association analyses and gene interaction networks to reveal new genes associated with carcass traits, meat quality and fatty acid profiles in pigs. Livestock Science 220:180–189. ?
Almeida JM, Bressan MC, Amaral AJ, Bettencourt C, Santos-Silva J, Moreira O, Gama LT. Body weight and ultrasound measurements over the finishing period in Iberian and F1 Large White × Landrace pigs raised intensively or in free-range conditions. Livestock Science 229:170–178. ?
2017
Amaral AJ, Andrade J, Foxall RB, Matoso P, Matos AM, Soares RS, Tendeiro R, Serra-Caetano A, Guerra-Assunção JA, Santa-Marta M, Gonçalves J, Gama-Carvalho M, Sousa AE. Deep sequencing of human naive CD4 T cells identifies miR-34c-5p as a novel regulator of T cell activation and HIV replication. The EMBO Journal 36(3):346–360. ?
Silva SL, Albuquerque A, Amaral AJ, Li Q, Mota C, Cheynier R, Victorino RMM, Pereira-Santos MC, Sousa AE. Autoimmunity and allergy control in adults submitted to complete thymectomy early in infancy. PLoS ONE. 10.1371/journal.pone.0180385
2015
Bruford M, Ginja C, Hoffmann I, Joost S, Orozco-terWengel P, Alberto FJ, Amaral AJ, et al. Prospects and challenges for the conservation of farm animal genomic resources, 2015–2025. Frontiers in Genetics 6:314. 10.3389/fgene.2015.00314
2014
Amaral AJ*, Brito FF, Chobanyan T, Yoshikawa S, Yokokura T, Van Vactor D, Gama-Carvalho M. Quality assessment and control of tissue specific RNA-seq libraries of Drosophila transgenic RNAi models. Frontiers in Genetics 5:43. 10.3389/fgene.2014.00043
2013
Brás-Rosário L, Matsuda A, Pinheiro AI, Gardner R, Lopes T, Amaral AJ, et al. Expression profile of microRNAs regulating proliferation and differentiation in mouse adult cardiac stem cells. PLoS ONE 8(5):e63041. 10.1371/journal.pone.0063041
Dodson MV, Boudina S, Albrecht E, Bucci L, Culver F, Wei S, Bergen WG, Amaral AJ, et al. Why have intensive explorations of fat cell biology not yet resulted in effective, long-term treatments for obesity? Experimental Biology and Medicine. 10.1177/1535370213477603
2011
Amaral AJ*, Ferretti L, Megens H-J, Crooijmans RPMA, Nie H, Ramos-Onsins SE, et al. Genome-wide footprints of pig domestication and selection revealed through massive parallel sequencing of pooled DNA. PLoS ONE 6(4):e14782. 10.1371/journal.pone.0014782
2009
Ramos AM, Crooijmans RPMA, Affara NA, Amaral AJ, Archibald AL, Beever JE, et al. Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology. PLoS ONE 4(8):e6524. 10.1371/journal.pone.0006524
Amaral AJ*, Megens H-J, Kerstens HD, Heuven HCM, Crooijmans RPMA, den Dunnen JT, Groenen MAM. Application of massive parallel sequencing to whole genome SNP discovery in the porcine genome. BMC Genomics10:374. ?
2008
Amaral AJ, Megens H-J*, Heuven HCM, Crooijmans RPMA, Groenen MAM. Linkage disequilibrium decay and haplotype block structure in the pig. Genetics 179:569–579. 10.1534/genetics.107.084277
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