The distance and median problems in the single-cut-or-join model with single-gene duplications

We explore how whole-genome duplications (WGDs) may have given rise to complex innovations in cellular networks, innovations that could not have evolved through sequential single-gene duplications. We focus on two classical WGD events, one in bakers’ yeast and the other at the base of vertebrates (i.e., two rounds of whole-genome duplication: 2R-WGD). Two complex adaptations are discussed in detail: aerobic ethanol fermentation in yeast and the rewiring of the vertebrate developmental regulatory network through the 2R-WGD. These two examples, derived from diverged branches on the eukaryotic tree, boldly underline the evolutionary potential of WGD in facilitating major evolutionary transitions. We close by arguing that the evolutionary importance of WGD may require updating certain aspects of modern evolutionary theory, perhaps helping to synthesize a new evolutionary systems biology.

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Convergent evolution of gene networks by single‐gene duplications in higher eukaryotes

EMBO Reports ◽

10.1038/sj.embor.7400096 ◽

2004 ◽

Vol 5 (3) ◽

pp. 274-279 ◽

Cited By ~ 50

Author(s):

Gregory D Amoutzias ◽

David L Robertson ◽

Stephen G Oliver ◽

Erich Bornberg‐Bauer

Keyword(s):

Convergent Evolution ◽

Gene Networks ◽

Single Gene ◽

Gene Duplications ◽

Higher Eukaryotes

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Phylogenomic Analyses Of 2,786 Genes In 158 Lineages Support a Root of The Eukaryotic Tree of Life Between Opisthokonts (Animals, Fungi and Their Microbial Relatives) and All Other Lineages

10.1101/2021.02.26.433005 ◽

2021 ◽

Author(s):

Mario A Ceron Romero ◽

Miguel M Fonseca ◽

Leonardo de Oliveira Martins ◽

David Posada ◽

Laura A Katz

Keyword(s):

Tree Species ◽

High Throughput Sequencing ◽

Single Gene ◽

Gene Tree ◽

Gene Families ◽

Species Tree ◽

Tree Of Life ◽

Gene Duplications ◽

Tree Reconciliation ◽

Phylogenomic Analyses

Advances in phylogenetics and high throughput sequencing have allowed the reconstruction of deep phylogenetic relationships in the evolution of eukaryotes. Yet, the root of the eukaryotic tree of life remains elusive. The most popular hypothesis in textbooks and reviews is a root between Unikonta (Opisthokonta + Amoebozoa) and Bikonta (all other eukaryotes), which emerged from analyses of a single gene fusion. Subsequent highly cited studies based on concatenation of genes supported this hypothesis with some variations or proposed a root within Excavata. However, concatenation of genes neither considers phylogenetically informative events (i.e. gene duplications and losses), nor provides an estimate of the root. A more recent study using gene tree / species tree reconciliation methods suggested the root lies between Opisthokonta and all other eukaryotes, but only including 59 taxa and 20 genes. Here we apply a gene tree / species tree reconciliation approach to a gene-rich and taxon rich dataset (i.e. 2,786 gene families from two sets of 158 diverse eukaryotic lineages) to assess the root, and we iterate each analysis 100 times to quantify tree space uncertainty. We estimate a root between Fungi and all other eukaryotes, or between Opisthokonta and all other eukaryotes, and reject alternative roots from the literature. Based on further analysis of genome size we propose Opisthokonta + others as the most likely root.

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The Rooted SCJ Median with Single Gene Duplications

Comparative Genomics - Lecture Notes in Computer Science ◽

10.1007/978-3-030-00834-5_2 ◽

2018 ◽

pp. 28-48 ◽

Cited By ~ 1

Author(s):

Aniket C. Mane ◽

Manuel Lafond ◽

Pedro Feijão ◽

Cedric Chauve

Keyword(s):

Single Gene ◽

Gene Duplications

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Genetic Analysis of Wild-Isolated Neurospora crassa Strains Identified as Dominant Suppressors of Repeat-Induced Point Mutation

Genetics ◽

10.1093/genetics/164.3.947 ◽

2003 ◽

Vol 164 (3) ◽

pp. 947-961 ◽

Cited By ~ 1

Author(s):

Ashwin Bhat ◽

Felicite K Noubissi ◽

Meenal Vyas ◽

Durgadas P Kasbekar

Keyword(s):

Genetic Analysis ◽

Gene Silencing ◽

Neurospora Crassa ◽

Point Mutation ◽

Dna Sequences ◽

Single Gene ◽

Test System ◽

Gene Duplications ◽

Repeat Induced Point Mutation

Abstract Repeat-induced point mutation (RIP) in Neurospora results in inactivation of duplicated DNA sequences. RIP is thought to provide protection against foreign elements such as retrotransposons, only one of which has been found in N. crassa. To examine the role of RIP in nature, we have examined seven N. crassa strains, identified among 446 wild isolates scored for dominant suppression of RIP. The test system involved a small duplication that targets RIP to the easily scorable gene erg-3. We previously showed that RIP in a small duplication is suppressed if another, larger duplication is present in the cross, as expected if the large duplication competes for the RIP machinery. In two of the strains, RIP suppression was associated with a barren phenotype—a characteristic of Neurospora duplications that is thought to result in part from a gene-silencing process called meiotic silencing by unpaired DNA (MSUD). A suppressor of MSUD (Sad-1) was shown not to prevent known large duplications from impairing RIP. Single-gene duplications also can be barren but are too short to suppress RIP. RIP suppression in strains that were not barren showed inheritance that was either simple Mendelian or complex. Adding copies of the LINE-like retrotransposon Tad did not affect RIP efficiency.

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The Distance and Median Problems in the Single-Cut-or-Join model with Single-Gene Duplications

10.21203/rs.2.23403/v1 ◽

2020 ◽

Author(s):

Aniket Mane ◽

Manuel Lafond ◽

Pedro Feijao ◽

Cedric Chauve

Keyword(s):

Gene Duplication ◽

Genome Rearrangement ◽

Single Gene ◽

Linear Program ◽

Integer Linear Program ◽

Gene Duplications ◽

Duplicated Genes ◽

Median Problem ◽

Np Complete ◽

Directed Distance

Abstract Background: In the field of genome rearrangement algorithms, models accounting for gene duplication lead often to hard problems. For example, while computing the pairwise distance is tractable in most duplication-free models, it is NP-complete for most extensions of these models accounting for duplicated genes. Moreover, problems involving more than two genomes, such as the genome median and the Small Parsimony problem, are intractable for most duplication-free models, with some exceptions, for example the Single-Cut-or-Join (SCJ) model. Result: We introduce a variant of the SCJ distance that accounts for duplicated genes, in the context of directed evolution from an ancestral genome to a descendant genome where orthology relations between ancestral genes and their descendant are known. Our model includes two duplication mechanisms: single-gene tandem duplication and the creation of single-gene circular chromosomes. We prove that in this model, computing the directed distance and a parsimonious evolutionary scenario in terms of SCJ and single-gene duplication events can be done in linear time. We also show that the directed median problem is tractable for this distance, while the rooted median problem, where we assume that one of the given genomes is ancestral to the median, is NP-complete. We also describe an Integer Linear Program for solving this problem. We evaluate the directed distance and rooted median algorithms on simulated data. Conclusion: Our results provide a simple genome rearrangement model, extending the SCJ model to account for single-gene duplications, for which we prove a mix of tractability and hardness results. For the NP-complete rooted median problem, we design a simple Integer Linear Program. Our publicly available implementation of these algorithms for the directed distance and median problems allow to solve efficiently these problems on large instances. Availability: https://github.com/cchauve/SCJ-with-SGD

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Duodenases are a small subfamily of ruminant intestinal serine proteases that have undergone a remarkable diversification in cleavage specificity

PLoS ONE ◽

10.1371/journal.pone.0252624 ◽

2021 ◽

Vol 16 (5) ◽

pp. e0252624

Author(s):

Zhirong Fu ◽

Srinivas Akula ◽

Chang Qiao ◽

Jinhye Ryu ◽

Gurdeep Chahal ◽

...

Keyword(s):

Chemokine Receptors ◽

Serine Proteases ◽

Digestive System ◽

Intestinal Inflammation ◽

Single Gene ◽

Gene Duplications ◽

Cleavage Sites ◽

Chromosomal Locus ◽

Cleavage Specificity ◽

Lysozyme C

Ruminants have a very complex digestive system adapted for the digestion of cellulose rich food. Gene duplications have been central in the process of adapting their digestive system for this complex food source. One of the new loci involved in food digestion is the lysozyme c locus where cows have ten active such genes compared to a single gene in humans and where four of the bovine copies are expressed in the abomasum, the real stomach. The second locus that has become part of the ruminant digestive system is the chymase locus. The chymase locus encodes several of the major hematopoietic granule proteases. In ruminants, genes within the chymase locus have duplicated and some of them are expressed in the duodenum and are therefore called duodenases. To obtain information on their specificities and functions we produced six recombinant proteolytically active duodenases (three from cows, two from sheep and one from pigs). Two of the sheep duodenases were found to be highly specific tryptases and one of the bovine duodenases was a highly specific asp-ase. The remaining two bovine duodenases were dual enzymes with potent tryptase and chymase activities. In contrast, the pig enzyme was a chymase with no tryptase or asp-ase activity. These results point to a remarkable flexibility in both the primary and extended specificities within a single chromosomal locus that most likely has originated from one or a few genes by several rounds of local gene duplications. Interestingly, using the consensus cleavage site for the bovine asp-ase to screen the entire bovine proteome, it revealed Mucin-5B as one of the potential targets. Using the same strategy for one of the sheep tryptases, this enzyme was found to have potential cleavage sites in two chemokine receptors, CCR3 and 7, suggesting a role for this enzyme to suppress intestinal inflammation.

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Factors influencing the accuracy in dating single gene trees

10.1101/2020.08.24.264671 ◽

2020 ◽

Author(s):

Guillaume Louvel ◽

Hugues Roest Crollius

Keyword(s):

Gene Family ◽

Average Rate ◽

Single Gene ◽

Gene Families ◽

Molecular Dating ◽

Exact Science ◽

Gene Duplications ◽

Gene Sequences ◽

Unknown Parameters ◽

A Genome

AbstractMolecular dating is a cornerstone of evolutionary biology, yet it is by far not an exact science. The inference of precise dates using gene sequences is difficult, in part because of the stochastic process of DNA mutation, selective forces that alter substitution rates and many unknown parameters linked to population genetics in ancestral lineages. Dating species divergence is one important challenge in this field, which is usually performed by concatenating extant sequences sampled within a genome as representative of a lineage, and computing distances between these lineages. However, concatenates precludes the dating of events specific to a gene family, such as gene duplication. During evolutionary time, individual gene sequences record different signatures of base substitutions and at rates that may deviate substantially from the average rate. No formal study exists that quantifies which parameters influence this deviation. Here we designed a strategy to date events within a gene family, and we test the influence of more than 30 parameters on dating accuracy. We developed this approach on approximately 5,000 primate gene families comprising 12 genomes that display no gene loss nor gene duplications. We then test its relevance in the complete set of primate gene families to date gene duplications. Our result are compared to previous fossil and molecular dating approaches, and provide a practical set of guidelines for accurate molecular dating at the single gene family level.

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Integrative modeling of gene and genome evolution roots the archaeal tree of life

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1618463114 ◽

2017 ◽

Vol 114 (23) ◽

pp. E4602-E4611 ◽

Cited By ~ 104

Author(s):

Tom A. Williams ◽

Gergely J. Szöllősi ◽

Anja Spang ◽

Peter G. Foster ◽

Sarah E. Heaps ◽

...

Keyword(s):

Genome Evolution ◽

Single Gene ◽

Rooted Tree ◽

Gene Families ◽

Sister Group ◽

Work Place ◽

Gene Duplications ◽

Gene Trees ◽

Supertree Method ◽

Horizontal Transfers

A root for the archaeal tree is essential for reconstructing the metabolism and ecology of early cells and for testing hypotheses that propose that the eukaryotic nuclear lineage originated from within the Archaea; however, published studies based on outgroup rooting disagree regarding the position of the archaeal root. Here we constructed a consensus unrooted archaeal topology using protein concatenation and a multigene supertree method based on 3,242 single gene trees, and then rooted this tree using a recently developed model of genome evolution. This model uses evidence from gene duplications, horizontal transfers, and gene losses contained in 31,236 archaeal gene families to identify the most likely root for the tree. Our analyses support the monophyly of DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, Nanohaloarchaea), a recently discovered cosmopolitan and genetically diverse lineage, and, in contrast to previous work, place the tree root between DPANN and all other Archaea. The sister group to DPANN comprises the Euryarchaeota and the TACK Archaea, including Lokiarchaeum, which our analyses suggest are monophyletic sister lineages. Metabolic reconstructions on the rooted tree suggest that early Archaea were anaerobes that may have had the ability to reduce CO2 to acetate via the Wood–Ljungdahl pathway. In contrast to proposals suggesting that genome reduction has been the predominant mode of archaeal evolution, our analyses infer a relatively small-genomed archaeal ancestor that subsequently increased in complexity via gene duplication and horizontal gene transfer.

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Evolution of selenophosphate synthetases: emergence and relocation of function through independent duplications and recurrent subfunctionalization

10.1101/014928 ◽

2015 ◽

Author(s):

Marco Mariotti ◽

Didac Santesmasses ◽

Salvador Capella-Gutierrez ◽

Andrea Mateo ◽

Carme Arnan ◽

...

Keyword(s):

Amino Acid ◽

Protein Function ◽

Evolutionary History ◽

Single Gene ◽

Gene Duplications ◽

Rna Structures ◽

Independent Gene ◽

Uga Codon ◽

Molecular Origin ◽

Evolutionary Fate

SPS catalyzes the synthesis of selenophosphate, the selenium donor for the synthesis of the amino acid selenocysteine (Sec), incorporated in selenoproteins in response to the UGA codon. SPS is unique among proteins of the selenoprotein biosynthesis machinery in that it is, in many species, a selenoprotein itself, although, as in all selenoproteins, Sec is often replaced by cysteine (Cys). In metazoan genomes we found, however, SPS genes with lineage specific substitutions other than Sec or Cys. Our results show that these non-Sec, non-Cys SPS genes originated through a number of independent gene duplications of diverse molecular origin from an ancestral selenoprotein SPS gene. Although of independent origin, complementation assays in fly mutants show that these genes share a common function, which most likely emerged in the ancestral metazoan gene. This function appears to be unrelated to selenophosphate synthesis, since all genomes encoding selenoproteins contain Sec or Cys SPS genes (SPS2), but those containing only non-Sec, non-Cys SPS genes (SPS1) do not encode selenoproteins. Thus, in SPS genes, through parallel duplications and subsequent convergent subfunctionalization, two functions initially carried by a single gene are recurrently segregated at two different loci. RNA structures enhancing the readthrough of the Sec-UGA codon in SPS genes, which may be traced back to prokaryotes, played a key role in this process. The SPS evolutionary history in metazoans constitute a remarkable example of the emergence and evolution of gene function. We have been able to trace this history with unusual detail thanks to the singular feature of SPS genes, wherein the amino acid at a single site determines protein function, and, ultimately, the evolutionary fate of an entire class of genes.

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