Josué Barrera Redondo

Humboldt Research Fellow | Max Planck Institute for Biology

Detection and emergence of novel genes


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.

I'm currently working on the establishment of bioinformatic methods to detect taxonomically-restricted genes throughout the tree of life and assess their novelty through homology detection failure tests. 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!
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 also got funding from the Alexander von Humboldt Foundation to study the emergence of de novo evolved genes in the brown algae.  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! We're currently working on ways to detect de novo gene emergence in the model brown alga Ectocarus through synteny analyses and prove that these elements are translated into proteins through the establishment of a ribosome profiling protocol.

Publications


A highly contiguous genome assembly reveals sources of genomic novelty in the symbiotic fungus Rhizophagus irregularis


Bethan F Manley, Jaruwatana S Lotharukpong, Josué Barrera-Redondo, Gokalp Yildirir, Jana Sperschneider, Nicolas Corradi, Uta Paszkowski, Eric A Miska, Alexandra Dallaire

G3: Genes, Genomes, Genetics, vol. 13(6), Cold Spring Harbor Laboratory, 2023, pp. jkad077




Uncovering gene-family founder events during major evolutionary transitions in animals, plants and fungi using GenEra


Josué Barrera-Redondo, Jaruwatana Sodai Lotharukpong, Hajk-Georg Drost, Susana M Coelho

Genome Biology, vol. 24(1), Cold Spring Harbor Laboratory, 2023, p. 54




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