16 papers · ranked by Valyu relevance
Yibo Si, Kshitiz Adhikari, Laura E. Herring, Daniel Isom + 6 more
Paralogs engage in biological processes through both redundant and non-redundant functions. In the yeast Saccharomyces cerevisiae, approximately one-fifth of the genome consists of paralogs, with their encoded proteins involved in multiple pathways. However, the unique contributions of individual paralogs have remained…
Rohan Dandage, Christian R Landry
The protective redundancy of paralogous genes partly relies on the fact that they carry their functions independently. However, a significant fraction of paralogous proteins may form functionally dependent pairs, for instance, through heteromerization. As a consequence, one could expect these heteromeric paralogs to be…
Marit S Bratlie, Jostein Johansen, Brad T Sherman, Da Wei Huang + 2 more
'Richard A Lempicki' 'Finn Drabløs'] Background Gene duplication is a normal evolutionary process. If there is no selective advantage in keeping the duplicated gene, it is usually reduced to a pseudogene and disappears from the genome. However, some paralogs are retained. These gene products are likely to be beneficial…
Shu-Ting Pan, Danfeng Xue, Zhi-Ling Li, Zhi-Wei Zhou + 6 more
'Yinxue Yang' 'Tianxin Yang' 'Jia-Xuan Qiu' 'Shu-Feng Zhou' 'Ge Zhang'] The human cytochrome P450 (CYP) superfamily consisting of 57 functional genes is the most important group of Phase I drug metabolizing enzymes that oxidize a large number of xenobiotics and endogenous compounds, including therapeutic drugs and…
Radek Szklarczyk, Martijn A Huynen, Berend Snel
Background Thanks to recent high coverage mass-spectrometry studies and reconstructed protein complexes, we are now in an unprecedented position to study the evolution of biological systems. Gene duplications, known to be a major source of innovation in evolution, can now be readily examined in the context of protein…
Praveen Nadukkalam Ravindran, Paul Bentzen, Ian R. Bradbury, Robert G. Beiko
'Robert G. Beiko'] Title: Abstract Restriction-site associated DNA sequencing (RAD-seq) can identify and score thousands of genetic markers from a group of samples for population-genetics studies. One challenge of de novo RAD-seq analysis is to distinguish paralogous sequence variants (PSVs) from true single-nucleotide…
Barbara De Kegel, Colm J Ryan
Genomic instability is a hallmark of cancer, resulting in tumor genomes having large numbers of genetic aberrations, including homozygous deletions of protein coding genes. That tumor cells remain viable in the presence of such gene loss suggests high robustness to genetic perturbation. In model organisms and cancer…
Domenico Di Fraia, Mihaela Anitei, Marie-Therese Mackmull, Luca Parca + 7 more
'Luca Parca' 'Laura Behrendt' 'Amparo Andres-Pons' 'Darren Gilmour' 'Manuela Helmer Citterich' 'Christoph Kaether' 'Martin Beck' 'Alessandro Ori\u202c\u202c'] Paralog proteins promote fine tuning of protein complexes. The author identified a specific paralog signature conserved across vertebrate neuronal…
Brittany M Greco, Gerardo Zapata, Rohan Dandage, Mikhail Papkov + 6 more
'Vanessa Pereira' 'François Lefebvre' 'Guillaume Bourque' 'Leopold Parts' 'Elena Kuzmin' 'G Brown'] Title: Abstract Whole-genome duplication (WGD) events are common across various organisms; however, the retention and evolution of WGD paralogs is not fully understood. Quantitative measure of protein redistribution in…
Hugo V. S. Rody, Gregory J. Baute, Loren H. Rieseberg, Luiz O. Oliveira
'Luiz O. Oliveira'] Background All extant seed plants are successful paleopolyploids, whose genomes carry duplicate genes that have survived repeated episodes of diploidization. However, the survival of gene duplicates is biased with respect to gene function and mechanism of duplication. Transcription factors, in…
Kris A Christensen, Joseph P Brunelli, Matthew J Lambert, Jenefer DeKoning + 2 more
'Jenefer DeKoning' 'Ruth B Phillips' 'Gary H Thorgaard'] Background The common ancestor of salmonid fishes, including rainbow trout (Oncorhynchus mykiss), experienced a whole genome duplication between 20 and 100 million years ago, and many of the duplicated genes have been retained in the trout genome. This retention…
Robert D. Hoffmann, Michael Palmgren
Background Whole-genome duplications in the ancestors of many diverse species provided the genetic material for evolutionary novelty. Several models explain the retention of paralogous genes. However, how these models are reflected in the evolution of coding and non-coding sequences of paralogous genes is unknown.…
Olivia Mendivil Ramos, David E. K. Ferrier
Duplication of genetic material is clearly a major route to genetic change, with consequences for both evolution and disease. A variety of forms and mechanisms of duplication are recognised, operating across the scales of a few base pairs upto entire genomes. With the ever-increasing amounts of gene and genome sequence…
Natasha M. Glover, Henning Redestig, Christophe Dessimoz
The evolutionary history of nearly all flowering plants includes a polyploidization event. Homologous genes resulting from allopolyploidy are commonly referred to as ‘homoeologs’, although this term has not always been used precisely or consistently in the literature. With several allopolyploid genome sequencing…
Vicente Arnau, Miguel Gallach, J Ignasi Lucas, Ignacio Marín
Background The imprint of natural selection on gene sequences is often difficult to detect. A plethora of methods have been devised to detect genetic changes due to selective processes. However, many of those methods depend heavily on underlying assumptions regarding the mode of change of DNA sequences and often…
David Sankoff, Chunfang Zheng, Qian Zhu
Background Genome amplification through duplication or proliferation of transposable elements has its counterpart in genome reduction, by elimination of DNA or by gene inactivation. Whether loss is primarily due to excision of random length DNA fragments or the inactivation of one gene at a time is controversial.…