Functional and evolutionary implications of gene orthology

By Toni Gabaldón, Eugene V. Koonin. 2013

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In Molecular Biology

Citations in the corpus

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses (2018, background): “Therefore, differentiating between these two subtypes of homology relationships is crucial to produce accurate functional predictions (2,4,5).”
Computational principles and challenges in single-cell data integration (2021, background): “Yet, there is no guarantee that the function and transcriptional profiles of homolog genes are preserved when mapping across large evolutionary distances 97 .”
The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes (2014, background): “The task of whole-genome alignment is to create a catalog of relationships between the sequences of each genome (ortholog, paralog, xenolog, and so on [25]) to reveal their evolutionary history [26,27].”
Homoeologs: What Are They and How Do We Infer Them? (2016, background): “As a consequence, orthologous relationships are not necessarily one-to-one between species and may exist in one-to-many or many-to-many relationships, especially among highly duplicated plant genomes [37].”
eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences (2015, background): “However, due to the intricate evolution of most gene families, which often involves multiple nested duplications, genomic rearrangements and horizontal gene transfers, orthology prediction remains as a highly challenging task (4,5), both analytically and computationally.”
OMA standalone: orthology inference among public and custom genomes and transcriptomes (2018, background): “Elucidation of orthology and paralogy relationships is also essential to reconstruct species trees, to better understand the mechanics of gene/genome evolution, to study adaptation, or to pinpoint the emergence of new gene functions (Gabaldón and Koonin, 2013) .”
OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs (2018, background): “Such gene genealogies, pinned to particular ancestor genes, enable the most specific functional hypothesis for the descendant genes (3,4).”
Advances and Applications in the Quest for Orthologs (2019, background): “This is due to the independent functionality of the domains, and their ability to create new genes by exon shuffling or domain promiscuity, creating complex homology relationships (Gabald on and Koonin 2013).”
Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper (2016, background): “At present, eggNOG HMM collection comprises sequence profiles of 1,911,745 OGs, spanning 1,678 bacteria, 115 archaea, 238 eukaryotes, and 352 viruses.”
OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs (2016, background): “inheritance of genes by speciation from a common ancestor (1) and thus most likely being ‘equivalent’ genes among species (2).”
Gearing up to handle the mosaic nature of life in the quest for orthologs (2017, background): “Although these implicit corollaries are not part of the orthology definition itself, they seem to hold for a large fraction of orthologous genes in large-scale comparative genomics studies (discussed in Gabaldón and Koonin, 2013).”