Animal genomics

Institution: Centro de Investigación Agrigenómica (CRAG)

Members (researchers): Alexandre Clop i Ponte

Home page: https://www.cragenomica.es/research-groups/animal-genomics
Contact email: alex.clop@cragenomica.es

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Research topics:

Animal genomics, RNA Sequencing (RNA-seq), Single-cell (scRNA-seq), Single-cell omics

Publications

Sa, P., Gòdia, M., Lewis, N., Lian, Y., & Clop, A. (2024). Genomic, transcriptomic and epigenomic analysis towards the understanding of porcine semen quality traits. Past, current and future trends. Animal Reproduction Science, 269, 107543. https://doi.org/10.1016/j.anireprosci.2024.107543

Ureña, I., González, C., Ramón, M., Gòdia, M., Clop, A., Calvo, J. H., Carabaño, M. J., & Serrano, M. (2022). Exploring the ovine sperm transcriptome by RNAseq techniques. I Effect of seasonal conditions on transcripts abundance. PLOS ONE, 17(3), e0264978. https://doi.org/10.1371/journal.pone.0264978

Lian, Y., Gòdia, M., Castello, A., Rodriguez-Gil, J. E., Balasch, S., Sanchez, A., & Clop, A. (2021). Characterization of the Impact of Density Gradient Centrifugation on the Profile of the Pig Sperm Transcriptome by RNA-Seq. Frontiers in Veterinary Science, 8. https://doi.org/10.3389/fvets.2021.668158

Cardoso, T. F., Luigi‐Sierra, M. G., Castelló, A., Cabrera, B., Noce, A., Mármol‐Sánchez, E., García‐González, R., Fernández‐Arias, A., Alabart, J. L., López‐Olvera, J. R., Mentaberre, G., Granados‐Torres, J. E., Cardells‐Peris, J., Molina, A., Sànchez, A., Clop, A., & Amills, M. (2021). Assessing the levels of intraspecific admixture and interspecific hybridization in Iberian wild goats (Capra pyrenaica). Evolutionary Applications, 14(11), 2618–2634. Portico. https://doi.org/10.1111/eva.13299

Ablondi, M., Gòdia, M., Rodriguez-Gil, J. E., Sánchez, A., & Clop, A. (2020). Characterisation of sperm piRNAs and their correlation with semen quality traits in swine. https://doi.org/10.1101/2020.03.16.994178

Godia, M., Reverter, A., Gonzalez-Prendes, R., Ramayo-Caldas, Y., Castello, A., Rodriguez-Gil, J. E., Sanchez, A., & Clop, A. (2020). An integrative systems biology approach to identify the molecular basis of sperm quality in swine. https://doi.org/10.21203/rs.3.rs-19366/v1

Gòdia, M., Castelló, A., Rocco, M., Cabrera, B., Rodríguez-Gil, J. E., Balasch, S., Lewis, C., Sánchez, A., & Clop, A. (2020). Identification of circular RNAs in porcine sperm and evaluation of their relation to sperm motility. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-64711-z

Gòdia, M., Ramayo-Caldas, Y., Zingaretti, L. M., Darwich, L., López, S., Rodríguez-Gil, J. E., Yeste, M., Sánchez, A., & Clop, A. (2020). A pilot RNA-seq study in 40 pietrain ejaculates to characterize the porcine sperm microbiome. Theriogenology, 157, 525–533. https://doi.org/10.1016/j.theriogenology.2020.08.001

Gòdia, M., Casellas, J., Ruiz-Herrera, A., Rodríguez-Gil, J. E., Castelló, A., Sánchez, A., & Clop, A. (2020). Whole genome sequencing identifies allelic ratio distortion in sperm involving genes related to spermatogenesis in a swine model. DNA Research, 27(5). https://doi.org/10.1093/dnares/dsaa019

Gòdia, M., Reverter, A., González-Prendes, R., Ramayo-Caldas, Y., Castelló, A., Rodríguez-Gil, J.-E., Sánchez, A., & Clop, A. (2020). A systems biology framework integrating GWAS and RNA-seq to shed light on the molecular basis of sperm quality in swine. Genetics Selection Evolution, 52(1). https://doi.org/10.1186/s12711-020-00592-0

Gòdia, M., Estill, M., Castelló, A., Balasch, S., Rodríguez-Gil, J. E., Krawetz, S. A., Sánchez, A., & Clop, A. (2019). A RNA-Seq Analysis to Describe the Boar Sperm Transcriptome and Its Seasonal Changes. Frontiers in Genetics, 10. https://doi.org/10.3389/fgene.2019.00299

Cirera, S., Clop, A., Jacobsen, M. J., Guerin, M., Lesnik, P., Jørgensen, C. B., Fredholm, M., & Karlskov‐Mortensen, P. (2018). A targeted genotyping approach enhances identification of variants in taste receptor and appetite/reward genes of potential functional importance for obesity‐related porcine traits. Animal Genetics, 49(2), 110–118. Portico. https://doi.org/10.1111/age.12641

Gòdia, M., Mayer, F. Q., Nafissi, J., Castelló, A., Rodríguez-Gil, J. E., Sánchez, A., & Clop, A. (2018). A technical assessment of the porcine ejaculated spermatozoa for a sperm-specific RNA-seq analysis. Systems Biology in Reproductive Medicine, 64(4), 291–303. https://doi.org/10.1080/19396368.2018.1464610

Eusebi, P. G., González‐Prendes, R., Quintanilla, R., Tibau, J., Cardoso, T. F., Clop, A., & Amills, M. (2017). A genome‐wide association analysis for carcass traits in a commercial Duroc pig population. Animal Genetics, 48(4), 466–469. Portico. https://doi.org/10.1111/age.12545

Rodriguez-Cortes, A., Martori, C., Martinez-Florez, A., Clop, A., Amills, M., Kubejko, J., Llull, J., Nadal, J. M., & Alberola, J. (2017). Canine Leishmaniasis Progression is Associated with Vitamin D Deficiency. Scientific Reports, 7(1). https://doi.org/10.1038/s41598-017-03662-4

Clop, A., Huisman, A., van As, P., Sharaf, A., Derdak, S., & Sanchez, A. (2016). Identification of genetic variation in the swine toll-like receptors and development of a porcine TLR genotyping array. Genetics Selection Evolution, 48(1). https://doi.org/10.1186/s12711-016-0206-0

Clop, A., Bertoni, A., Spain, S. L., Simpson, M. A., Pullabhatla, V., Tonda, R., Hundhausen, C., Di Meglio, P., De Jong, P., Hayday, A. C., Nestle, F. O., Barker, J. N., Bell, R. J. A., Capon, F., & Trembath, R. C. (2013). An In-Depth Characterization of the Major Psoriasis Susceptibility Locus Identifies Candidate Susceptibility Alleles within an HLA-C Enhancer Element. PLoS ONE, 8(8), e71690. https://doi.org/10.1371/journal.pone.0071690

Clop, A., Vidal, O., & Amills, M. (2012). Copy number variation in the genomes of domestic animals. Animal Genetics, 43(5), 503–517. Portico. https://doi.org/10.1111/j.1365-2052.2012.02317.x

Knight, J., Spain, S. L., Capon, F., Hayday, A., Nestle, F. O., Clop, A., Barker, J. N., Weale, M. E., & Trembath, R. C. (2012). Conditional analysis identifies three novel major histocompatibility complex loci associated with psoriasis. Human Molecular Genetics, 21(23), 5185–5192. https://doi.org/10.1093/hmg/dds344

Hundhausen, C., Bertoni, A., Mak, R. K., Botti, E., Di Meglio, P., Clop, A., Laggner, U., Chimenti, S., Hayday, A. C., Barker, J. N., Trembath, R. C., Capon, F., & Nestle, F. O. (2012). Allele-Specific Cytokine Responses at the HLA-C Locus: Implications for Psoriasis. Journal of Investigative Dermatology, 132(3), 635–641. https://doi.org/10.1038/jid.2011.378

Burri, A., Hysi, P., Clop, A., Rahman, Q., & Spector, T. D. (2012). A Genome-Wide Association Study of Female Sexual Dysfunction. PLoS ONE, 7(4), e35041. https://doi.org/10.1371/journal.pone.0035041

Zidi, A., Amills, M., Tomás, A., Vidal, O., Ramírez, O., Carrizosa, J., Urrutia, B., Serradilla, J. M., & Clop, A. (2010). Short communication: Genetic variability in the predicted microRNA target sites of caprine casein genes. Journal of Dairy Science, 93(4), 1749–1753. https://doi.org/10.3168/jds.2009-2741

Clop, A., Zidi, A., & Amills, M. (2010). Identification of positively selected sites in the goat kappa casein (CSN3) gene. Animal Genetics, 41(3), 332–332. Portico. https://doi.org/10.1111/j.1365-2052.2009.02001.x

Valeyev, N. V., Hundhausen, C., Umezawa, Y., Kotov, N. V., Williams, G., Clop, A., Ainali, C., Ouzounis, C., Tsoka, S., & Nestle, F. O. (2010). A Systems Model for Immune Cell Interactions Unravels the Mechanism of Inflammation in Human Skin. PLoS Computational Biology, 6(12), e1001024. https://doi.org/10.1371/journal.pcbi.1001024

Matika, O., Sechi, S., Pong-Wong, R., Houston, R. D., Clop, A., Woolliams, J. A., & Bishop, S. C. (2010). Characterization of OAR1 and OAR18 QTL associated with muscle depth in British commercial terminal sire sheep. Animal Genetics, 42(2), 172–180. https://doi.org/10.1111/j.1365-2052.2010.02121.x

Ramirez, O., Ojeda, A., Tomas, A., Gallardo, D., Huang, L. S., Folch, J. M., Clop, A., Sanchez, A., Badaoui, B., Hanotte, O., Galman-Omitogun, O., Makuza, S. M., Soto, H., Cadillo, J., Kelly, L., Cho, I. C., Yeghoyan, S., Perez-Enciso, M., & Amills, M. (2009). Integrating Y-Chromosome, Mitochondrial, and Autosomal Data to Analyze the Origin of Pig Breeds. Molecular Biology and Evolution, 26(9), 2061–2072. https://doi.org/10.1093/molbev/msp118

Hadjipavlou, G., Matika, O., Clop, A., & Bishop, S. C. (2008). Two single nucleotide polymorphisms in the myostatin (GDF8) gene have significant association with muscle depth of commercial Charollais sheep. Animal Genetics, 39(4), 346–353. Portico. https://doi.org/10.1111/j.1365-2052.2008.01734.x

Hamelin, M., Sayd, T., Chambon, C., Bouix, J., Bibé, B., Milenkovic, D., Leveziel, H., Georges, M., Clop, A., Marinova, P., & Laville, E. (2007). Differential expression of sarcoplasmic proteins in four heterogeneous ovine skeletal muscles. PROTEOMICS, 7(2), 271–280. Portico. https://doi.org/10.1002/pmic.200600309

Hamelin, M., Sayd, T., Chambon, C., Bouix, J., Bibé, B., Milenkovic, D., Leveziel, H., Georges, M., Clop, A., Marinova, P., & Laville, E. (2006). Proteomic analysis of ovine muscle hypertrophy1. Journal of Animal Science, 84(12), 3266–3276. https://doi.org/10.2527/jas.2006-162

Clop, A., Marcq, F., Takeda, H., Pirottin, D., Tordoir, X., Bibé, B., Bouix, J., Caiment, F., Elsen, J.-M., Eychenne, F., Larzul, C., Laville, E., Meish, F., Milenkovic, D., Tobin, J., Charlier, C., & Georges, M. (2006). A mutation creating a potential illegitimate microRNA target site in the myostatin gene affects muscularity in sheep. Nature Genetics, 38(7), 813–818. https://doi.org/10.1038/ng1810

Clop, A., Amills, M., Noguera, J. L., Fernández, A., Capote, J., Ramón, M. M., Kelly, L., Kijas, J. M. H., Andersson, L., & Sànchez, A. (2004). Estimating the frequency of Asian cytochrome B haplotypes in standard European and local Spanish pig breeds. Genetics Selection Evolution, 36(1). https://doi.org/10.1186/1297-9686-36-1-97

Clop, A., Ovilo, C., Perez-Enciso, M., Cercos, A., Tomas, A., Fernandez, A., Coll, A., Folch, J. M., Barragan, C., Diaz, I., Oliver, M. A., Varona, L., Silio, L., Sanchez, A., & Noguera, J. L. (2003). Detection of QTL affecting fatty acid composition in the pig. Mammalian Genome, 14(9), 650–656. https://doi.org/10.1007/s00335-002-2210-7

Cristina, Ó., Oliver, A., Noguera, J. L., Clop, A., Barragán, C., Varona, L., Rodríguez, C., Toro, M., Sánchez, A., Pérez-Enciso, M., & Silió, L. (2002). Test for positional candidate genes for body composition on pig chromosome 6. Genetics Selection Evolution, 34(4). https://doi.org/10.1186/1297-9686-34-4-465

VARONA, L., OVILO, C., CLOP, A., NOGUERA, J. L., PÉREZ-ENCISO, M., COLL, A., FOLCH, J. M., BARRAGÁN, C., TORO, M. A., BABOT, D., & SÁNCHEZ, A. (2002). QTL mapping for growth and carcass traits in an Iberian by Landrace pig intercross: additive, dominant and epistatic effects. Genetical Research, 80(2), 145–154. https://doi.org/10.1017/s0016672302005803

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