Amino Acid Animals Computational Biology Databases de novo gene Evolution Genetic Genome Humans lncRNA Mice Molecular Molecular Sequence Data Nucleic Acid Proteins Proteins: chemistry Proteins: genetics Repetitive Sequences ribosome profiling RNA-Seq Selection Sequence Analysis Sequence Homology transcriptomics yeast
2017 |
José Luis Villanueva-Cañas, Jorge Ruiz-Orera, M.Isabel Agea, Maria Gallo, David Andreu, M.Mar Albà New genes and functional innovation in mammals (Article) Genome Biology and Evolution, 9 pp. 1886–1900, 2017. (Abstract | Links | BibTeX | Tags: de novo gene, innovation, mammal, protein function) @article{Albà2017, title = {New genes and functional innovation in mammals}, author = { José Luis Villanueva-Cañas, Jorge Ruiz-Orera, M.Isabel Agea, Maria Gallo, David Andreu, M.Mar Albà}, url = {https://academic.oup.com/gbe/article/doi/10.1093/gbe/evx136/3983271/New-genes-and-functional-innovation-in-mammals}, year = {2017}, date = {2017-07-21}, journal = {Genome Biology and Evolution}, volume = {9}, pages = { 1886–1900}, abstract = {The birth of genes that encode new protein sequences is a major source of evolutionary innovation. However, we still understand relatively little about how these genes come into being and which functions they are selected for. To address these questions, we have obtained a large collection of mammalian-specific gene families that lack homologues in other eukaryotic groups. We have combined gene annotations and de novo transcript assemblies from 30 different mammalian species, obtaining ∼6,000 gene families. In general, the proteins in mammalian-specific gene families tend to be short and depleted in aromatic and negatively charged residues. Proteins which arose early in mammalian evolution include milk and skin polypeptides, immune response components, and proteins involved in reproduction. In contrast, the functions of proteins which have a more recent origin remain largely unknown, despite the fact that these proteins also have extensive proteomics support. We identify several previously described cases of genes originated de novo from noncoding genomic regions, supporting the idea that this mechanism frequently underlies the evolution of new protein-coding genes in mammals. Finally, we show that most young mammalian genes are preferentially expressed in testis, suggesting that sexual selection plays an important role in the emergence of new functional genes.}, keywords = {de novo gene, innovation, mammal, protein function} } The birth of genes that encode new protein sequences is a major source of evolutionary innovation. However, we still understand relatively little about how these genes come into being and which functions they are selected for. To address these questions, we have obtained a large collection of mammalian-specific gene families that lack homologues in other eukaryotic groups. We have combined gene annotations and de novo transcript assemblies from 30 different mammalian species, obtaining ∼6,000 gene families. In general, the proteins in mammalian-specific gene families tend to be short and depleted in aromatic and negatively charged residues. Proteins which arose early in mammalian evolution include milk and skin polypeptides, immune response components, and proteins involved in reproduction. In contrast, the functions of proteins which have a more recent origin remain largely unknown, despite the fact that these proteins also have extensive proteomics support. We identify several previously described cases of genes originated de novo from noncoding genomic regions, supporting the idea that this mechanism frequently underlies the evolution of new protein-coding genes in mammals. Finally, we show that most young mammalian genes are preferentially expressed in testis, suggesting that sexual selection plays an important role in the emergence of new functional genes. |
2016 |
José Luis Villanueva-Cañas Jorge Ruiz-Orera Isabel Agea Maria Gallo David Andreu M.Mar Albà New genes and functional innovation in mammals (Article) bioRxiv, 2016. (Abstract | Links | BibTeX | Tags: adaptation, de novo genes, Evolution, gene family, mammal) @article{Alba2016, title = {New genes and functional innovation in mammals}, author = {José Luis Villanueva-Cañas Jorge Ruiz-Orera Isabel Agea Maria Gallo David Andreu M.Mar Albà}, url = {http://dx.doi.org/10.1101/090860 }, year = {2016}, date = {2016-12-02}, journal = {bioRxiv}, abstract = {The birth of genes that encode new proteins is a major source of evolutionary innovation. However, we still understand relatively little about how these genes come into being and which functions they are selected for. Here we address this question by generating a comprehensive list of mammalian-specific gene families originated at different times during mammalian evolution. We combine gene annotations and de novo transcript assemblies from 30 mammalian species, obtaining about 6,000 families with different species composition. We show that the families which arose early in mammalian evolution (basal) are relatively well-characterized. They are enriched in secreted proteins and include milk and skin polypeptides, immune response components and, proteins involved in spermatogenesis. In contrast, there is a severe lack of knowledge about the functions of proteins which have a more recent origin in certain mammalian groups (young), despite the fact that they have extensive proteomics support. Interestingly, we find that both young and basal mammalian-specific gene families show similar gene expression biases, with a marked enrichment in testis. Proteins from both groups tend to be short and depleted in aromatic and negatively charged residues. This indicates shared mechanisms of formation and suggests that the youngest proteins may have been retained for similar kinds of functions as the oldest ones. We identify several previously described cases of genes originated de novo from non-coding genomic regions, supporting the idea that this mechanism frequently underlies the evolution of new protein-coding genes. The catalogue of gene families generated here provides a unique resource for studies on the role of new genes in mammalian-specific adaptations.}, keywords = {adaptation, de novo genes, Evolution, gene family, mammal} } The birth of genes that encode new proteins is a major source of evolutionary innovation. However, we still understand relatively little about how these genes come into being and which functions they are selected for. Here we address this question by generating a comprehensive list of mammalian-specific gene families originated at different times during mammalian evolution. We combine gene annotations and de novo transcript assemblies from 30 mammalian species, obtaining about 6,000 families with different species composition. We show that the families which arose early in mammalian evolution (basal) are relatively well-characterized. They are enriched in secreted proteins and include milk and skin polypeptides, immune response components and, proteins involved in spermatogenesis. In contrast, there is a severe lack of knowledge about the functions of proteins which have a more recent origin in certain mammalian groups (young), despite the fact that they have extensive proteomics support. Interestingly, we find that both young and basal mammalian-specific gene families show similar gene expression biases, with a marked enrichment in testis. Proteins from both groups tend to be short and depleted in aromatic and negatively charged residues. This indicates shared mechanisms of formation and suggests that the youngest proteins may have been retained for similar kinds of functions as the oldest ones. We identify several previously described cases of genes originated de novo from non-coding genomic regions, supporting the idea that this mechanism frequently underlies the evolution of new protein-coding genes. The catalogue of gene families generated here provides a unique resource for studies on the role of new genes in mammalian-specific adaptations. |
