Research lines

Evolution of lineage-specific genes

Lineage-specific genes are those exclusively found in one species or group of related species. Their study can shed light into the mechanisms of formation of new genes. Recent research in the group has shown that many lineage-specific genes are likely to have originated de novo from genomic non-coding regions. We are currently using RNA-Seq and Ribo-Seq data to further understand the mechanisms of formation of new genes.

Ruiz-Orera, J., Verdaguer-Grau, P., Villanueva-Cañas, J-l., Messeguer, X., Albà, M.M. (2018). Translation of neutrally evolving peptides provides a basis for de novo gene evolution. Nature Ecology and Evolution 2:890-896.

Villanueva-Cañas, J-L. Ruiz-Orera, J., M.I., Gallo, M., Andreu, D., Albà, M.M. (2017) New genes and functional innovation in mammals. Genome Biology and Evolution 9: 1886–1900.

Ruiz-Orera, J., Hernandez-Rodriguez, J., Chiva, C., Sabidó, E., Kondova, I., Bontrop, R., Marqués-Bonet, T., Albà, M.M (2015) Origins of de novo genes in human and chimpanzee. Plos Genetics, 11 (12), pp. e1005721.

Ruiz-Orera, J., Messeguer, X., Subirana J.A., Albà M.M. (2014) Long non-coding RNAs as a source of new peptides. eLife, 3:e03523.

Toll-Riera, M., Radó-Trilla, N., Martys, F., Albà, M.M. (2012) Role of low-complexity sequences in the formation of novel protein coding sequences. Molecular Biology and Evolution, 29: 883-886.

Toll-Riera, M., Bosch, N., Bellora, N., Castelo, R., Armengol,Ll., Estivill, X., Albà, M.M. (2009) Origin of primate orphan genes: a comparative genomics approach. Molecular Biology and Evolution, 26:603-612.

Hibernation

During hibernation, animals lower their metabolism to survive harsh environmental periods. We are studying gene expression changes associated with hibernation to better understand how animals have adapted to this condition. We have used RNA sequencing data to assemble the transcriptome of fat-tailed dwarf lemurs and subsequently performed differential gene expression analysis to identify major metabolic switches when entering or exiting from hibernation.

Faherty, S.L.*#, Villanueva-Cañas, J-L.#, Blanco, M.B., Albà, M.M.*, Yoder, A.D. (2018) Transcriptomics in the wild: hibernation physiology in free-ranging dwarf lemurs. Molecular Ecology , 273:709-722.

Faherty, S.L.#, Villanueva-Cañas, J-L.#,Klopfer, P.H., Albà, M.M., Yoder, A.D. (2016): Gene expression profiling in the hibernating primate, Cheirogaleus medius. Genome Biology and Evolution 8: 2413–2426.

5. Villanueva-Cañas, J-L., Faherty, S.L., Yoder, A.D., Albà, M.M. (2014). Comparative Genomics of Mammalian Hibernators Using Gene Networks. Integrative and comparative biology 54:452-462.

Role of indels and low-complexity regions (LCRs) in protein evolution

Low-complexity sequences, including homopolymeric tracts and other short amino acid tandem repeats, are extremely abundant in eukaryotic proteins. These sequences may expand or contract rapidly by the action of replication slippage and/or recombination. We have investigated the role of natural selection in shaping the LCR content in vertebrate genomes and the impact of short insertions and deletions in the evolution of mammalian proteins.

Radó-Trilla, N., Arató, K., Pegueroles, C., Raya, A., de la Luna, S.*, Albà, M.M.* (2015) Key role of amino acid repeat expansions in the functional diversification of duplicated transcription factors. Molecular Biology and Evolution, 32(9):2263-72.

Radó-Trilla, N., Albà, M.M. (2012) Dissecting the role of low-complexity regions in the evolution of vertebrate proteins. BMC Evol. Biol., 12: 155.

Laurie, S., Toll-Riera, M., Radó-Trilla, Albà, M.M. (2012) Sequence shortening in the rodent ancestor. Genome Research, 22: 478-485.

Mularoni, L., Ledda, A., Toll-Riera, M., Albà, M.M. (2010) Natural selection drives the accumulation of amino acid tandem repeats in human proteins. Genome Research, 20: 745-754.

Consequences of gene duplication in protein evolution

Gene duplication is an important motor of protein functional diversification. We have investigated the changes in expression patterns of recent duplicated mammalian genes and observed that loss of expression domains is more common than gain of novel expression patterns. We have also used large gene duplicate sets to investigate how the sequences of initially redundant gene copies progressively diverge and which are the implications for protein function.

Pegueroles, C., Laurie, S., Albà, M.M. (2013) Accelerated evolution after gene duplication: a time-dependent process affecting just one copy.Molecular Biology and Evolution, 30:1830-1842.

Farré, D., Albà, M.M. (2010) Heterogeneous patterns of gene expression diversification in mammalian gene duplicates. Molecular Biology and Evolution, 27:325-335.

Adaptive molecular evolution in mammals

We have developed methods to identify shifts in the evolutionary rate of genes and to measure adaptive evolution in individual genes or clusters of functionally-related genes. We have shown that selecting isoforms of similar length with our software PALO reduces the fraction of misaligned positions and false positives in tests of selection.

Abascal, F. et al. (including Villanueva-Cañas, J-L., Ruiz-Orera, J., Albà, M.M.) (2016). Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx. Genome Biology, 17: 251.

Gayà-Vidal, M., Albà, M.M. (2014) Uncovering adaptive evolution in the human lineage. BMC Genomics, 15:599.

Villanueva-Cañas, J.L., Laurie, S., Albà, M.M. (2013) Improving genome-wide scans of positive selection by using protein isoforms of similar length. Genome Biology and Evolution, 5: 457-67.

Toll-Riera, M., Laurie, S., Albà, M.M. (2011) Lineage-specific Variation in Intensity of Natural Selection in Mammals. Molecular Biology and Evolution, 28: 383-398.