Ancestral gene duplications in mosses characterized by integrated phylogenomic analyses

Loop 1 of APOBEC3C regulates its antiviral activity against HIV-1

10.1101/2020.02.05.936021 ◽

2020 ◽

Author(s):

Ananda Ayyappan Jaguva Vasudevan ◽

Kannan Balakrishnan ◽

Christoph G. W. Gertzen ◽

Fanni Borvető ◽

Zeli Zhang ◽

...

Keyword(s):

Antiviral Activity ◽

Consensus Sequence ◽

Antiviral Effect ◽

Last Common Ancestor ◽

Evolutionary Analysis ◽

Gene Duplications ◽

Ancestral Gene ◽

Catalytic Function ◽

And Function ◽

Hiv 1

ABSTRACTAPOBEC3 deaminases (A3s) provide mammals with an anti-retroviral barrier by catalyzing dC-to-dU deamination on viral ssDNA. Within primates, A3s have evolved diversely via gene duplications and fusions. Human APOBEC3C (hA3C) efficiently restricts the replication of viral infectivity factor (vif)-deficient Simian immunodeficiency virus (SIVΔvif), but for unknown reasons, it inhibits HIV-1Δvif weakly. In catarrhines (Old World monkeys and apes), the A3C loop 1 displays the conserved amino acid pair WE, while the corresponding consensus sequence in A3F and A3D is the largely divergent pair RK, which is also the inferred ancestral sequence for the last common ancestor of A3C|D|F in primates. Here, we report that modifying the WE residues in hA3C loop 1 to RK leads to stronger interactions with ssDNA substrate, facilitating catalytic function, which resulted in a drastic increase in both deamination activity and the ability to restrict HIV-1 and LINE-1 replication. Conversely, the modification hA3F_WE resulted only in a marginal decrease in HIV-1Δvif inhibition. The two series of ancestral gene duplications that generated A3C, A3D-CTD and A3F-CTD allowed neo/subfunctionalization: A3F-CTD maintained the ancestral RK residues in loop 1, while strong evolutionary pressure selected for the RK→WE modification in catarrhines A3C, possibly allowing for novel substrate specificity and function.AUTHOR SUMMARYThe restriction factors of the APOBEC3 (A3) family of cytidine deaminases inhibit the replication of Vif-deficient retroviruses mainly by mutating their viral genomes. While there are seven A3 proteins (A3A-A3H) found in humans only A3G and A3F potently inhibit HIV-1 replication. A3C in general and its retroviral restriction capacity have not been widely studied probably due to its weak anti-HIV-1 activity, however, it displays a strong antiviral effect against SIV. Understanding the role of A3C is important because it is highly expressed in CD4+ T cells, is upregulated upon HIV-1 infection, and is distributed cell-wide. In this study, we report that replacing two residues in loop 1 of A3C protein with conserved positively-charged amino acids enhance the substrate DNA binding, which markedly facilitates its deamination-dependent antiviral activity against HIV-1 as well as increasing the restriction of LINE-1 retroelements. Furthermore, our evolutionary analysis demonstrates that the pressure that caused the loss of potential loop 1 residues occurred only in A3C but not in primate homologues. Overall, our study highlights the possibility of A3C acting as a super restriction factor, however, this was likely evolutionarily selected against to achieve a balance between anti-viral/anti-LINE-1 activity and genotoxicity.

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A Burst of Genetic Innovation in Drosophila Actin-Related Proteins for Testis-Specific Function

Molecular Biology and Evolution ◽

10.1093/molbev/msz262 ◽

2019 ◽

Vol 37 (3) ◽

pp. 757-772

Author(s):

Courtney M Schroeder ◽

John R Valenzuela ◽

Isabel Mejia Natividad ◽

Glen M Hocky ◽

Harmit S Malik

Keyword(s):

Positive Selection ◽

Male Meiosis ◽

Cytoskeletal Proteins ◽

Gene Duplications ◽

Actin Networks ◽

Male Germline ◽

Phylogenomic Analyses ◽

Sperm Heteromorphism ◽

Related Proteins ◽

Obscura Group

Abstract Many cytoskeletal proteins perform fundamental biological processes and are evolutionarily ancient. For example, the superfamily of actin-related proteins (Arps) specialized early in eukaryotic evolution for diverse cellular roles in the cytoplasm and the nucleus. Despite its strict conservation across eukaryotes, we find that the Arp superfamily has undergone dramatic lineage-specific diversification in Drosophila. Our phylogenomic analyses reveal four independent Arp gene duplications that occurred in the common ancestor of the obscura group of Drosophila and have been mostly preserved in this lineage. All four obscura-specific Arp paralogs are predominantly expressed in the male germline and have evolved under positive selection. We focus our analyses on the divergent Arp2D paralog, which arose via a retroduplication event from Arp2, a component of the Arp2/3 complex that polymerizes branched actin networks. Computational modeling analyses suggest that Arp2D can replace Arp2 in the Arp2/3 complex and bind actin monomers. Together with the signature of positive selection, our findings suggest that Arp2D may augment Arp2’s functions in the male germline. Indeed, we find that Arp2D is expressed during and following male meiosis, where it localizes to distinct locations such as actin cones—specialized cytoskeletal structures that separate bundled spermatids into individual mature sperm. We hypothesize that this unprecedented burst of genetic innovation in cytoskeletal proteins may have been driven by the evolution of sperm heteromorphism in the obscura group of Drosophila.

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Selection following Gene Duplication Shapes Recent Genome Evolution in the Pea Aphid Acyrthosiphon pisum

Molecular Biology and Evolution ◽

10.1093/molbev/msaa110 ◽

2020 ◽

Vol 37 (9) ◽

pp. 2601-2615 ◽

Cited By ~ 3

Author(s):

Rosa Fernández ◽

Marina Marcet-Houben ◽

Fabrice Legeai ◽

Gautier Richard ◽

Stéphanie Robin ◽

...

Keyword(s):

Gene Duplication ◽

Acyrthosiphon Pisum ◽

High Capacity ◽

Chromatin Accessibility ◽

Pea Aphid ◽

Specific Gene ◽

Gene Duplications ◽

Evolutionary Mechanisms ◽

Ancestral Gene ◽

Species Specific

Abstract Ecology of insects is as wide as their diversity, which reflects their high capacity of adaptation in most of the environments of our planet. Aphids, with over 4,000 species, have developed a series of adaptations including a high phenotypic plasticity and the ability to feed on the phloem sap of plants, which is enriched in sugars derived from photosynthesis. Recent analyses of aphid genomes have indicated a high level of shared ancestral gene duplications that might represent a basis for genetic innovation and broad adaptations. In addition, there are a large number of recent, species-specific gene duplications whose role in adaptation remains poorly understood. Here, we tested whether duplicates specific to the pea aphid Acyrthosiphon pisum are related to genomic innovation by combining comparative genomics, transcriptomics, and chromatin accessibility analyses. Consistent with large levels of neofunctionalization, we found that most of the recent pairs of gene duplicates evolved asymmetrically, showing divergent patterns of positive selection and gene expression. Genes under selection involved a plethora of biological functions, suggesting that neofunctionalization and tissue specificity, among other evolutionary mechanisms, have orchestrated the evolution of recent paralogs in the pea aphid and may have facilitated host–symbiont cooperation. Our comprehensive phylogenomics analysis allowed us to tackle the history of duplicated genes to pave the road toward understanding the role of gene duplication in ecological adaptation.

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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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A burst of genetic innovation in actin-related proteins (Arps) for testis-specific function in a Drosophila lineage

10.1101/665299 ◽

2019 ◽

Cited By ~ 1

Author(s):

Courtney M. Schroeder ◽

John Valenzuela ◽

Glen M. Hocky ◽

Harmit S. Malik

Keyword(s):

Common Ancestor ◽

Cytoskeletal Proteins ◽

Biological Processes ◽

Gene Duplications ◽

Actin Networks ◽

Male Germline ◽

The Common ◽

Phylogenomic Analyses ◽

Sperm Heteromorphism ◽

Related Proteins

AbstractMany cytoskeletal proteins form the core of fundamental biological processes and are evolutionarily ancient. For example, the superfamily of actin-related proteins (Arps) specialized early in eukaryotic evolution for diverse cellular roles in the cytoplasm and the nucleus. Despite its strict conservation across eukaryotes, we find that the Arp superfamily has undergone dramatic lineage-specific diversification in Drosophila. Our phylogenomic analyses reveal four independent Arp gene duplications that originated in the common ancestor of the obscura group of Drosophila species and have been mostly preserved in this lineage. All four Arp paralogs have evolved under positive selection and are predominantly expressed in the male germline. We focus our analyses on the divergent Arp2D paralog, which arose via a retroduplication event from Arp2, a component of the 7-membered Arp2/3 complex that polymerizes branched actin networks. Computational modeling analyses suggest that Arp2D should be able to replace Arp2 in the Arp2/3 complex and bind daughter actin monomers, suggesting that Arp2D may augment Arp2’s functions in the male germline. We find that Arp2D is expressed during and following meiosis in the male germline, where it localizes to distinct locations such as actin cones–pecialized cytoskeletal structures that separate bundled spermatids into individual mature sperm. We hypothesize that this unprecedented burst of genetic innovation in cytoskeletal proteins may have been driven by the evolution of sperm heteromorphism in the obscura group of Drosophila.

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Selection following gene duplication shapes recent genome evolution in the pea aphid Acyrthosiphon pisum

10.1101/643544 ◽

2019 ◽

Cited By ~ 1

Author(s):

Rosa Fernández ◽

Marina Marcet-Houben ◽

Fabrice Legeai ◽

Gautier Richard ◽

Stéphanie Robin ◽

...

Keyword(s):

Gene Duplication ◽

Acyrthosiphon Pisum ◽

High Capacity ◽

Chromatin Accessibility ◽

Pea Aphid ◽

Specific Gene ◽

Gene Duplications ◽

Evolutionary Mechanisms ◽

Ancestral Gene ◽

Species Specific

AbstractEcology of insects is as wide as their diversity, which reflects their high capacity of adaptation in most of the environments of our planet. Aphids, with over 4,000 species, have developed a series of adaptations including a high phenotypic plasticity and the ability to feed on the phloem-sap of plants, which is enriched in sugars derived from photosynthesis. Recent analyses of aphid genomes have indicated a high level of shared ancestral gene duplications that might represent a basis for genetic innovation and broad adaptations. In addition, there is a large number of recent, species-specific gene duplications whose role in adaptation remains poorly understood. Here, we tested whether duplicates specific to the pea aphid Acyrthosiphon pisum are related to genomic innovation by combining comparative genomics, transcriptomics, and chromatin accessibility analyses. Consistent with large levels of neofunctionalization, we found that most of the recent pairs of gene duplicates evolved asymmetrically, showing divergent patterns of positive selection and gene expression. Genes under selection involved a plethora of biological functions, suggesting that neofunctionalization and tissue specificity, among other evolutionary mechanisms, have orchestrated the evolution of recent paralogs in the pea aphid and may have facilitated host-symbiont cooperation. Our comprehensive phylogenomics analysis allowed to tackle the history of duplicated genes to pave the road towards understanding the role of gene duplication in ecological adaptation.

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Improved transcriptome sampling pinpoints 26 paleopolyploidy events in Caryophyllales, including two paleo-allopolyploidy events

10.1101/143529 ◽

2017 ◽

Cited By ~ 1

Author(s):

Ya Yang ◽

Michael J. Moore ◽

Samuel F. Brockington ◽

Jessica Mikenas ◽

Julia Olivieri ◽

...

Keyword(s):

Tree Of Life ◽

List Type ◽

Gene Duplications ◽

Transcriptome Data ◽

Phylogenetic Distribution ◽

Homology Inference ◽

Genomic Scale ◽

Phylogenomic Analyses ◽

Inference Methods ◽

Incomplete Sampling

SummaryStudies of the macroevolutionary legacy of paleopolyploidy are limited by an incomplete sampling of these events across the tree of life. To better locate and understand these events, we need comprehensive taxonomic sampling as well as homology inference methods that accurately reconstruct the frequency and location of gene duplications.We assembled a dataset of transcriptomes and genomes from 169 species in Caryophyllales, of which 43 were newly generated for this study, representing one of the densest sampled genomic-scale datasets yet available. We carried out phylogenomic analyses using a modified phylome strategy to reconstruct the species tree. We mapped phylogenetic distribution of paleopolyploidy events by both tree-based and distance-based methods, and explicitly tested scenarios for paleo-allopolyploidy.We identified twenty-six paleopolyploidy events distributed throughout Caryophyllales, and using novel techniques inferred two to be paleo-allopolyploidy.Through dense phylogenomic sampling, we show the propensity of paleo-polyploidy in the clade Caryophyllales. We also provide the first method for utilizing transcriptome data to detect paleo-allopolyploidy, which is important as it may have different macro-evolutionary implications compared to paleo-autopolyploidy.

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The Genomic Tree as Revealed from Whole Proteome Comparisons

Genome Research ◽

10.1101/gr.9.6.550 ◽

1999 ◽

Vol 9 (6) ◽

pp. 550-557 ◽

Cited By ~ 10

Author(s):

Fredj Tekaia ◽

Antonio Lazcano ◽

Bernard Dujon

Keyword(s):

Partial Information ◽

Homo Sapiens ◽

Hierarchical Classification ◽

Gene Duplications ◽

Evolutionary Time ◽

Ancestral Gene ◽

Extant Species ◽

Genome Content ◽

Additional Approach

The availability of a number of complete cellular genome sequences allows the development of organisms’ classification, taking into account their genome content, the loss or acquisition of genes, and overall gene similarities as signatures of common ancestry. On the basis of correspondence analysis and hierarchical classification methods, a methodological framework is introduced here for the classification of the available 20 completely sequenced genomes and partial information for Schizosaccharomyces pombe, Homo sapiens, and Mus musculus. The outcome of such an analysis leads to a classification of genomes that we call a genomic tree. Although these trees are phenograms, they carry with them strong phylogenetic signatures and are remarkably similar to 16S-like rRNA-based phylogenies. Our results suggest that duplication and deletion events that took place through evolutionary time were globally similar in related organisms. The genomic trees presented here place the Archaea in the proximity of the Bacteria when the whole gene content of each organism is considered, and when ancestral gene duplications are eliminated. Genomic trees represent an additional approach for the understanding of evolution at the genomic level and may contribute to the proper assessment of the evolutionary relationships between extant species.

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