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Detection of de novo evolved genes through synteny and sequence similarity.
The birth of new genes can facilitate major evolutionary innovations. Several studies suggest that novel genes are associated with the emergence of novel morphologies, immune defense mechanisms, and ecological specialization across the tree of life.
New genes can emerge through gene duplication, new combinations of preexisting protein domains, or de novo gene emergence (i.e., the emergence of a gene from non-coding DNA). However, the detection of novel genes is not trivial, particularly for genes that are taxonomically restricted (i.e., genes that are only present in certain groups of organisms), since there are important methodological caveats where genes appear as being novel due to an artifact of their limited detectability rather than their true evolutionary novelty. The accurate detection of novel genes is necessary to make robust inferences about the nature of their emergence, their evolutionary dynamics, and the role they play in shaping lineage-specific traits.
We recently established a novel pipeline called GenEra to do exactly that: establish the relative ages of all the genes in any genome of interest and test for homology detection failure to separate truly novel genes from methodological artifacts. Click here to give it a try!
New genes can emerge through gene duplication, new combinations of preexisting protein domains, or de novo gene emergence (i.e., the emergence of a gene from non-coding DNA). However, the detection of novel genes is not trivial, particularly for genes that are taxonomically restricted (i.e., genes that are only present in certain groups of organisms), since there are important methodological caveats where genes appear as being novel due to an artifact of their limited detectability rather than their true evolutionary novelty. The accurate detection of novel genes is necessary to make robust inferences about the nature of their emergence, their evolutionary dynamics, and the role they play in shaping lineage-specific traits.
We recently established a novel pipeline called GenEra to do exactly that: establish the relative ages of all the genes in any genome of interest and test for homology detection failure to separate truly novel genes from methodological artifacts. Click here to give it a try!
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GenEra is an easy-to-use and highly customizable command-line tool that estimates gene-family founder events (i.e., the age of the last common ancestor of protein-coding gene families). https://github.com/josuebarrera/GenEra
I have a keen interest in studying the emergence of de novo evolved genes. The case of de novo gene birth addresses some critical questions in evolutionary biology, such as the origin of adaptive proteins in previously unexplored spaces of the protein structural landscape, the birth of novel gene families, how new genomic elements integrate into pre-existing cellular networks, and even the concept of function in Biology!
Current Projects:
- Detection of de novo gene birth events in the model brown alga Ectocarpus through comparative genomics, population genomics and ribosome profiling (collaboration with the Max Planck Institute for Biology Tübingen).
- Understanding the effects of effective population sizes on the evolution of de novo genes across various taxonomic groups (tree-of-life scale analysis).
- Detection of taxonomically-restricted genes across protist taxa and their association with the emergence of evolutionary novelties.