scholarly journals Recurrent sequence evolution after independent gene duplication

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Samuel H. A. von der Dunk ◽  
Berend Snel
Keyword(s):  
Gene Duplication ◽  
Sequence Evolution ◽  
Recurrent Sequence ◽  
Independent Gene ◽  
Independent Gene Duplication

scholarly journals Recurrent Sequence Evolution After Independent Gene Duplication

2020 ◽  
Author(s):  
Samuel Hermann Alexander Von Der Dunk ◽  
Berend Snel
Keyword(s):  
Gene Duplication ◽  
Experimental Testing ◽  
Parallel Evolution ◽  
Gene Families ◽  
Functional Differentiation ◽  
Functional Change ◽  
Neutral Evolution ◽  
Sequence Evolution ◽  
Recurrent Sequence ◽  
Independent Gene

Abstract Background Convergent and parallel evolution provide unique insights into the mechanisms of natural selection. Some of the most striking convergent and parallel (collectively recurrent ) amino acid substitutions in proteins are adaptive, but there are also many that are selectively neutral. Accordingly, genome-wide assessment has shown that recurrent sequence evolution in orthologs is chiefly explained by nearly neutral evolution. For paralogs, more frequent functional change is expected because additional copies are generally not retained if they do not acquire their own niche. Yet, it is unknown to what extent recurrent sequence differentiation is discernible after independent gene duplications in different eukaryotic taxa. Results We develop a framework that detects patterns of recurrent sequence evolution in duplicated genes. This is used to analyze the genomes of 90 diverse eukaryotes. We find a remarkable number of families with a potentially predictable functional differentiation following gene duplication. In some protein families, more than ten independent duplications show a similar sequence-level differentiation between paralogs. Based on further analysis, the sequence divergence is found to be generally asymmetric. Moreover, about 6\% of the recurrent sequence evolution between paralog pairs can be attributed to recurrent differentiation of subcellular localization. Finally, we reveal the specific recurrent patterns for the gene families Hint1/Hint2, Sco1/Sco2 and vma11/vma3. Conclusions The presented methodology provides a means to study the biochemical underpinning of functional differentiation between paralogs. For instance, two abundantly repeated substitutions are identified between independently derived Sco1 and Sco2 paralogs. Such identified substitutions allow direct experimental testing of the biological role of these residues for the repeated functional differentiation. We also uncover a diverse set of families with recurrent sequence evolution and reveal trends in the functional and evolutionary trajectories of this hitherto understudied phenomenon.

scholarly journals Recurrent Sequence Evolution After Independent Gene Duplication

2020 ◽  
Author(s):  
Samuel Hermann Alexander Von Der Dunk ◽  
Berend Snel
Keyword(s):  
Gene Duplication ◽  
Experimental Testing ◽  
Parallel Evolution ◽  
Gene Families ◽  
Functional Differentiation ◽  
Functional Change ◽  
Neutral Evolution ◽  
Sequence Evolution ◽  
Recurrent Sequence ◽  
Independent Gene

Abstract Background Convergent and parallel evolution provide unique insights into the mechanisms of natural selection. Some of the most striking convergent and parallel (collectively recurrent ) amino acid substitutions in proteins are adaptive, but there are also many that are selectively neutral. Accordingly, genome-wide assessment has shown that recurrent sequence evolution in orthologs is chiefly explained by nearly neutral evolution. For paralogs, more frequent functional change is expected because additional copies are generally not retained if they do not acquire their own niche. Yet, it is unknown to what extent recurrent sequence differentiation is discernible after independent gene duplications in different eukaryotic taxa. Results We develop a framework that detects patterns of recurrent sequence evolution in duplicated genes. This is used to analyze the genomes of 90 diverse eukaryotes. We find a remarkable number of families with a potentially predictable functional differentiation following gene duplication. In some protein families, more than ten independent duplications show a similar sequence-level differentiation between paralogs. Based on further analysis, the sequence divergence is found to be generally asymmetric. Moreover, about 6\% of the recurrent sequence evolution between paralog pairs can be attributed to recurrent differentiation of subcellular localization. Finally, we reveal the specific recurrent patterns for the gene families Hint1/Hint2, Sco1/Sco2 and vma11/vma3. Conclusions The presented methodology provides a means to study the biochemical underpinning of functional differentiation between paralogs. For instance, two abundantly repeated substitutions are identified between independently derived Sco1 and Sco2 paralogs. Such identified substitutions allow direct experimental testing of the biological role of these residues for the repeated functional differentiation. We also uncover a diverse set of families with recurrent sequence evolution and reveal trends in the functional and evolutionary trajectories of this hitherto understudied phenomenon.

scholarly journals Recurrent Sequence Evolution After Independent Gene Duplication

2020 ◽  
Author(s):  
Samuel Hermann Alexander Von Der Dunk ◽  
Berend Snel
Keyword(s):  
Gene Duplication ◽  
Experimental Testing ◽  
Parallel Evolution ◽  
Gene Families ◽  
Functional Differentiation ◽  
Functional Change ◽  
Neutral Evolution ◽  
Sequence Evolution ◽  
Recurrent Sequence ◽  
Independent Gene

Abstract Background Convergent and parallel evolution provide unique insights into the mechanisms of natural selection. Some of the most striking convergent and parallel (collectively recurrent ) amino acid substitutions in proteins are adaptive, but there are also many that are selectively neutral. Accordingly, genome-wide assessment has shown that recurrent sequence evolution in orthologs is chiefly explained by nearly neutral evolution. For paralogs, more frequent functional change is expected because additional copies are generally not retained if they do not acquire their own niche. Yet, it is unknown to what extent recurrent sequence differentiation is discernible after independent gene duplications in different eukaryotic taxa. Results We develop a framework that detects patterns of recurrent sequence evolution in duplicated genes. This is used to analyze the genomes of 90 diverse eukaryotes. We find a remarkable number of families with a potentially predictable functional differentiation following gene duplication. In some protein families, more than ten independent duplications show a similar sequence-level differentiation between paralogs. Based on further analysis, the sequence divergence is found to be generally asymmetric. Moreover, about 6\% of the recurrent sequence evolution between paralog pairs can be attributed to recurrent differentiation of subcellular localization. Finally, we reveal the specific recurrent patterns for the gene families Hint1/Hint2, Sco1/Sco2 and vma11/vma3. Conclusions The presented methodology provides a means to study the biochemical underpinning of functional differentiation between paralogs. For instance, two abundantly repeated substitutions are identified between independently derived Sco1 and Sco2 paralogs. Such identified substitutions allow direct experimental testing of the biological role of these residues for the repeated functional differentiation. We also uncover a diverse set of families with recurrent sequence evolution and reveal trends in the functional and evolutionary trajectories of this hitherto understudied phenomenon.

scholarly journals Comprehensive analysis of Lon proteases in plants highlights independent gene duplication events

2018 ◽  
Vol 70 (7) ◽  
pp. 2185-2197 ◽  
Author(s):  
Dikran Tsitsekian ◽  
Gerasimos Daras ◽  
Anastasios Alatzas ◽  
Dimitris Templalexis ◽  
Polydefkis Hatzopoulos ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Comprehensive Analysis ◽  
Independent Gene ◽  
Duplication Events ◽  
Lon Proteases ◽  
Independent Gene Duplication

scholarly journals Identification of residue inversions in large phylogenies of duplicated proteins

2021 ◽  
Author(s):  
Stefano Pascarelli ◽  
Paola Laurino
Keyword(s):  
Gene Duplication ◽  
Protein Sequence ◽  
Protein Function ◽  
High Throughput Sequencing ◽  
Functional Divergence ◽  
Growth Factor Receptor ◽  
Sequence Evolution ◽  
Protein Database ◽  
Sequencing Studies ◽  
Homology Relationship

Connecting protein sequence to function is becoming increasingly relevant since high-throughput sequencing studies accumulate large amounts of genomic data. Protein database annotation helps to bridge this gap; however, it is fundamental to understand the mechanisms underlying functional inheritance and divergence. If the homology relationship between proteins is known, can we determine whether the function diverged? In this work, we analyze different possibilities of protein sequence evolution after gene duplication and identify "residue inversions", i.e., sites where the relationship between the ancestry and the functional signal is decoupled. Residues in these sites play a role in functional divergence and could indicate a shift in protein function. We develop a method to recognize residue inversions in a phylogeny and test it on real and simulated datasets. In a dataset built from the Epidermal Growth Factor Receptor (EGFR) sequences found in 88 fish species, we identify 19 positions that went through inversion after gene duplication, mostly located at the ligand-binding extracellular domain.

scholarly journals Gene duplication and rate variation in the evolution of non-photosynthetic pathways in plastids

2021 ◽  
Author(s):  
Alissa M Williams ◽  
Olivia G Carter ◽  
Evan S Forsythe ◽  
Hannah K Mendoza ◽  
Daniel B Sloan
Keyword(s):  
Gene Duplication ◽  
Fatty Acid Biosynthesis ◽  
Single Copy ◽  
Rate Variation ◽  
Sequence Evolution ◽  
Catalytic Core ◽  
Multiple Species ◽  
Insight Into ◽  
Paralogous Proteins

While the chloroplast (plastid) is known for its role in photosynthesis, it is also involved in many other biosynthetic pathways essential for plant survival. As such, plastids contain an extensive suite of enzymes required for non-photosynthetic processes. The evolution of the associated genes has been especially dynamic in flowering plants (angiosperms), including examples of gene duplication and extensive rate variation. We examined the role of ongoing gene duplication in two key plastid enzymes, the acetyl-CoA carboxylase (ACCase) and the caseinolytic protease (Clp), responsible for fatty acid biosynthesis and protein turnover, respectively. In plants, there are two ACCase complexes: a homomeric version present in the cytosol and a heteromeric version present in the plastid. Duplications of the nuclear-encoded homomeric ACCase gene and retargeting to the plastid have been previously reported in multiple species. We find that these retargeted copies of the homomeric ACCase gene exhibit elevated rates of sequence evolution, consistent with neofunctionalization and/or relaxation of selection. The plastid Clp complex catalytic core is composed of nine paralogous proteins that arose via ancient gene duplication in the cyanobacterial/plastid lineage. We show that further gene duplication occurred more recently in the nuclear-encoded core subunits of this complex, yielding additional paralogs in many species of angiosperms. Moreover, in six of eight cases, subunits that have undergone recent duplication display increased rates of sequence evolution relative to those that have remained single copy. We also compared rate patterns between pairs of Clp core paralogs to gain insight into post-duplication evolutionary routes. These results show that gene duplication and rate variation continue to shape the plastid proteome.

scholarly journals Gene Duplication Accelerates the Pace of Protein Gain and Loss from Plant Organelles

2019 ◽  
Vol 37 (4) ◽  
pp. 969-981 ◽  
Author(s):  
Rona Costello ◽  
David M Emms ◽  
Steven Kelly
Keyword(s):  
Gene Duplication ◽  
Protein Targeting ◽  
Sequence Evolution ◽  
Ancestral State ◽  
Organelle Biogenesis ◽  
Molecular Sequence ◽  
Metabolic Functions ◽  
Encoded Proteins ◽  
Gain And Loss ◽  
And Function

Abstract Organelle biogenesis and function is dependent on the concerted action of both organellar-encoded (if present) and nuclear-encoded proteins. Differences between homologous organelles across the Plant Kingdom arise, in part, as a result of differences in the cohort of nuclear-encoded proteins that are targeted to them. However, neither the rate at which differences in protein targeting accumulate nor the evolutionary consequences of these changes are known. Using phylogenomic approaches coupled to ancestral state estimation, we show that the plant organellar proteome has diversified in proportion with molecular sequence evolution such that the proteomes of plant chloroplasts and mitochondria lose or gain on average 3.6 proteins per million years. We further demonstrate that changes in organellar protein targeting are associated with an increase in the rate of molecular sequence evolution and that such changes predominantly occur in genes with regulatory rather than metabolic functions. Finally, we show that gain and loss of protein target signals occurs at a higher rate following gene duplication, revealing that gene and genome duplication are a key facilitator of plant organelle evolution.

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