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 novel gene formation and into lineage-specific adaptations. We have investigated the mechanisms of formation of primate-specific genes and have found that many of them are likely to have originated de novo from genomic non-coding regions. Recently evolved genes appear to be very plastic and typically display high evolutionary rates. Furthermore, they are enriched in low-complexity sequences. We are currently performing research to further unravel how the age of a gene relates with its mode of evolution. We are also using RNA deep sequencing data (RNA-Seq) to improve the definition of gene evolutionary age and discriminate between coding and non-coding RNAs.

Ruiz-Orera, J., Hernandezz-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.

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 are performing several analysis to learn about the role of natural selection in shaping the LCR content in several vertebrate genomes. We are also investigating the impact of other kinds 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 a method to identify genes that show accelerated or decelerated evolution in particular branches of the mammalian phylogeny indicating a shift in the selective regime. We are investigating the relative contribution of negative and positive selection in causing lineage-specific deviations in the evolutionary rates. We have examined the effect of protein isoform selection in genome-wide scans of positive selection and shown that selecting isoforms of similar length reduces the fraction of misaligned positions and false positives in tests of selection. The selection of isoforms with the minimum length difference can be performed using our software PALO.

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.