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Ancestral Genomes: a resource for reconstructed ancestral genes and genomes across the tree of life

Xiaosong Huang, Laurent-Philippe Albou, Tremayne Mushayahama, Anushya Muruganujan, Haiming Tang, Paul D Thomas
2018 Nucleic Acids Research  
A growing number of whole genome sequencing projects, in combination with development of phylogenetic methods for reconstructing gene evolution, have provided us with a window into genomes that existed millions, and even billions, of years ago. Ancestral Genomes (http://ancestralgenomes.org) is a resource for comprehensive reconstructions of these 'fossil genomes'. Comprehensive sets of protein-coding genes have been reconstructed for 78 genomes of now-extinct species that were the common
more » ... ors of extant species from across the tree of life. The reconstructed genes are based on the extensive library of over 15 000 gene family trees from the PANTHER database, and are updated on a yearly basis. For each ancestral gene, we assign a stable identifier, and provide additional information designed to facilitate analysis: an inferred name, a reconstructed protein sequence, a set of inferred Gene Ontology (GO) annotations, and a 'proxy gene' for each ancestral gene, defined as the least-diverged descendant of the ancestral gene in a given extant genome. On the Ancestral Genomes website, users can browse the Ancestral Genomes by selecting nodes in a species tree, and can compare an extant genome with any of its reconstructed ancestors to understand how the genome evolved.
doi:10.1093/nar/gky1009 pmid:30371900 pmcid:PMC6323951 fatcat:7fnve3dahjgt5gdxufdzfjbt4i

PEREGRINE: A genome-wide prediction of enhancer to gene relationships supported by experimental evidence

Caitlin Mills, Anushya Muruganujan, Dustin Ebert, Crystal N Marconett, Juan Pablo Lewinger, Paul D Thomas, Huaiyu Mi
2020 PLoS ONE  
We thank Tremayne Mushayahama and Laurent-Philippe Albou for the help on the PEREGRINE website.  ... 
doi:10.1371/journal.pone.0243791 pmid:33320871 pmcid:PMC7737992 fatcat:b47f767tsndzfkp7eparerw5oe