Global patterns of subgenome evolution in organelle-targeted genes of six allotetraploid angiosperms

Whole-genome duplications (WGDs), in which the number of nuclear genome copies is elevated as a result of autopolyploidy or allopolyploidy, are a prominent process of diversification in eukaryotes. The genetic and evolutionary forces that WGD imposes upon cytoplasmic genomes are not well understood, despite the central role that cytonuclear interactions play in eukaryotic function and fitness. Cellular respiration and photosynthesis depend upon successful interaction between the 3000+ nuclear-encoded proteins destined for the mitochondria or plastids and the gene products of cytoplasmic genomes in multi-subunit complexes such as OXPHOS, organellar ribosomes, Photosystems I and II, and Rubisco. Allopolyploids are thus faced with the critical task of coordinating interactions between nuclear and cytoplasmic genes that were inherited from different species. Because cytoplasmic genomes share a more recent history of common descent with the maternal nuclear subgenome than the paternal subgenome, evolutionary "mismatches" between the paternal subgenome and the cytoplasmic genomes in allopolyploids might lead to accelerated rates of evolution in the paternal homoeologs of allopolyploids, either through relaxed purifying selection or strong directional selection to rectify these mismatches. We tested this hypothesis in maternal vs. paternal copies of organelle-targeted genes in six allotetraploids: Brachypodium hybridum, Chenopodium quinoa, Coffea arabica, Gossypium hirsutum, Nicotiana tabacum, and Triticum dicoccoides. We report evidence that allopolyploid subgenomes exhibit unequal rates of protein-sequence evolution, but we did not observe global effects of cytonuclear incompatibilities on paternal homoeologs of organelle-targeted genes. Analyses of gene content revealed mixed evidence for whether organelle-targeted genes re-diploidize more rapidly than non-organelle-targeted genes. Together, these global analyses provide insights into the complex evolutionary dynamics of allopolyploids, showing that allopolyploid subgenomes have separate evolutionary trajectories despite sharing the same nucleus, generation time, and ecological context.

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Diversity and evolution of surface polysaccharide synthesis loci in Enterobacteriales

10.1101/709832 ◽

2019 ◽

Author(s):

Kathryn E. Holt ◽

Florent Lassalle ◽

Kelly L. Wyres ◽

Ryan Wick ◽

Rafal J. Mostowy

Keyword(s):

Evolutionary Dynamics ◽

Bacterial Species ◽

Purifying Selection ◽

Evolutionary Forces ◽

Polysaccharide Synthesis ◽

Surface Polysaccharides ◽

Surface Polysaccharide ◽

Selective Preservation ◽

Multiple Species

Bacterial capsules and lipopolysaccharides are diverse surface polysaccharides (SPs) that serve as the frontline for interactions with the outside world. While SPs can evolve rapidly, their diversity and evolutionary dynamics across different taxonomic scales has not been investigated in detail. Here, we focused on the bacterial order Enterobacteriales (including the medically-relevant Enterobacteriaceae), to carry out comparative genomics of two SP locus synthesis regions, cps and kps, using 27,334 genomes from 45 genera. We identified high-quality cps loci in 22 genera and kps in 11 genera, around 4% of which were detected in multiple species. We found SP loci to be highly dynamic genetic entities: their evolution was driven by high rates of horizontal gene transfer (HGT), both of whole loci and component genes, and relaxed purifying selection, yielding large repertoires of SP diversity. In spite of that, we found the presence of (near-)identical locus structures in distant taxonomic backgrounds that could not be explained by recent exchange, pointing to long-term selective preservation of locus structures in some populations. Our results reveal differences in evolutionary dynamics driving SP diversity within different bacterial species, with lineages of Escherichia coli, Enterobacter hormachei and Klebsiella aerogenes most likely to share SP loci via recent exchange; and lineages of Salmonella enterica, Citrobacter sakazakii and Serratia marcescens most likely to share SP loci via other mechanisms such as long-term preservation. Overall, the evolution of SP loci in Enterobacteriales is driven by a range of evolutionary forces and their dynamics and relative importance varies between different species.

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Evolutionary dynamics of bacteria in the gut microbiome within and across hosts

10.1101/210955 ◽

2017 ◽

Cited By ~ 10

Author(s):

Nandita R. Garud ◽

Benjamin H. Good ◽

Oskar Hallatschek ◽

Katherine S. Pollard

Keyword(s):

Evolutionary Dynamics ◽

Purifying Selection ◽

Gut Bacteria ◽

Fundamental Limits ◽

Evolutionary Forces ◽

Standard Population ◽

Evolutionary Changes ◽

Or Gene ◽

Adult Twins ◽

Long Timescales

AbstractGut microbiota are shaped by a combination of ecological and evolutionary forces. While the ecological dynamics have been extensively studied, much less is known about how species of gut bacteria evolve over time. Here we introduce a model-based framework for quantifying evolutionary dynamics within and across hosts using a panel of metagenomic samples. We use this approach to study evolution in ∼30 prevalent species in the human gut. Although the patterns of between-host diversity are consistent with quasi-sexual evolution and purifying selection on long timescales, we identify new genealogical signatures that challenge standard population genetic models of these processes. Within hosts, we find that genetic differences that accumulate over ∼6 month timescales are only rarely attributable to replacement by distantly related strains. Instead, the resident strains more commonly acquire a smaller number of putative evolutionary changes, in which nucleotide variants or gene gains or losses rapidly sweep to high frequency. By comparing these mutations with the typical between-host differences, we find evidence that some sweeps are seeded by recombination, in addition to new mutations. However, comparisons of adult twins suggest that replacement eventually overwhelms evolution over multi-decade timescales, hinting at fundamental limits to the extent of local adaptation. Together, our results suggest that gut bacteria can evolve on human-relevant timescales, and they highlight the connections between these short-term evolutionary dynamics and longer-term evolution across hosts.

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The Aphid X Chromosome Is a Dangerous Place for Functionally Important Genes: Diverse Evolution of Hemipteran Genomes Based on Chromosome-Level Assemblies

Molecular Biology and Evolution ◽

10.1093/molbev/msaa095 ◽

2020 ◽

Vol 37 (8) ◽

pp. 2357-2368 ◽

Cited By ~ 2

Author(s):

Yiyuan Li ◽

Bo Zhang ◽

Nancy A Moran

Keyword(s):

Sex Determination ◽

Sex Chromosome ◽

Purifying Selection ◽

Life Cycles ◽

Gene Content ◽

Sequence Evolution ◽

Opposite Pattern ◽

Evolutionary Forces ◽

Sex Determination System ◽

Chromosome Level

Abstract Different evolutionary forces shape gene content and sequence evolution on autosomes versus sex chromosomes. Location on a sex chromosome can favor male-beneficial or female-beneficial mutations depending on the sex determination system and selective pressure on different sexual morphs. An X0 sex determination can lead to autosomal enrichment of male-biased genes, as observed in some hemipteran insect species. Aphids share X0 sex determination; however, models predict the opposite pattern, due to their unusual life cycles, which alternate between all-female asexual generations and a single sexual generation. Predictions include enrichment of female-biased genes on autosomes and of male-biased genes on the X, in contrast to expectations for obligately sexual species. Robust tests of these models require chromosome-level genome assemblies for aphids and related hemipterans with X0 sex determination and obligate sexual reproduction. In this study, we built the first chromosome-level assembly of a psyllid, an aphid relative with X0 sex determination and obligate sexuality, and compared it with recently resolved chromosome-level assemblies of aphid genomes. Aphid and psyllid X chromosomes differ strikingly. In aphids, female-biased genes are strongly enriched on autosomes and male-biased genes are enriched on the X. In psyllids, male-biased genes are enriched on autosomes. Furthermore, functionally important gene categories of aphids are enriched on autosomes. Aphid X-linked genes and male-biased genes are under relaxed purifying selection, but gene content and order on the X is highly conserved, possibly reflecting constraints imposed by unique chromosomal mechanisms associated with the unusual aphid life cycle.

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Evolutionary dynamics of sex-biased gene expression in a young XY system: Insights from the brown algae

10.1101/2021.08.12.455804 ◽

2021 ◽

Author(s):

William J Hatchett ◽

Alexander O Jueterbock ◽

Martina Kopp ◽

James A Coyer ◽

Susana M Coelho ◽

...

Keyword(s):

Gene Expression ◽

Brown Algae ◽

Evolutionary Dynamics ◽

Regulation Of Gene Expression ◽

Sequence Evolution ◽

Turnover Rates ◽

Evolution Of Sex ◽

High Turnover ◽

Evolutionary Forces ◽

Flagellar Proteins

The sex-dependent regulation of gene expression is considered to be the underlying cause of often extensive, sexually dimorphic traits between males and females. Although the nature and degree of sex-biased gene expression has been well-documented in several animal and plant systems, far less is known about the commonality, conservation, recruitment mechanisms and evolution of sex-biased genes in more distant eukaryotic groups. Brown algae are of particular interest for empirical studies on the evolution of sex-biased gene expression, as they have been evolving independently from animals and plants for over one billion years. Here we focus on two brown algal dioecious species, Fucus serratus and Fucus vesiculosus, where male heterogamety (XX/XY) has recently emerged. Using RNA-seq, we study sex-biased gene expression and discuss different evolutionary forces responsible for the evolution of sex-biased genes. We find that both species evolved masculinized transcriptomes, with sex-biased genes allocated mainly to male reproductive tissue, but virtually absent in vegetative tissues. Conserved male-biased genes were enriched in functions related to gamete production, along with sperm competition and include two flagellar proteins under positive selection. In contrast to female-biased genes, which show high turnover rates, male-biased genes reveal remarkable conservation of bias and expression levels between the two species. As observed in other XY systems, male-biased genes also display accelerated rates of coding sequence evolution compared to female-biased or unbiased genes. Our results imply that evolutionary forces affect male and female sex-biased genes differently on structural and regulatory levels. Similarly to evolutionary distant plant and animal lineages, sex-biased gene expression in Fucus evolved during the transition to dioecy to resolve intra-locus sexual conflict arising from anisogamy.

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Divergent and convergent evolution of housekeeping genes in human–pig lineage

PeerJ ◽

10.7717/peerj.4840 ◽

2018 ◽

Vol 6 ◽

pp. e4840 ◽

Cited By ~ 4

Author(s):

Kai Wei ◽

Tingting Zhang ◽

Lei Ma

Keyword(s):

Active Sites ◽

Evolutionary Dynamics ◽

Purifying Selection ◽

Housekeeping Genes ◽

Neutral Evolution ◽

Structure Evolution ◽

Tissue Cell ◽

Sequencing Data ◽

Cellular Functions ◽

Species Specific

Housekeeping genes are ubiquitously expressed and maintain basic cellular functions across tissue/cell type conditions. The present study aimed to develop a set of pig housekeeping genes and compare the structure, evolution and function of housekeeping genes in the human–pig lineage. By using RNA sequencing data, we identified 3,136 pig housekeeping genes. Compared with human housekeeping genes, we found that pig housekeeping genes were longer and subjected to slightly weaker purifying selection pressure and faster neutral evolution. Common housekeeping genes, shared by the two species, achieve stronger purifying selection than species-specific genes. However, pig- and human-specific housekeeping genes have similar functions. Some species-specific housekeeping genes have evolved independently to form similar protein active sites or structure, such as the classical catalytic serine–histidine–aspartate triad, implying that they have converged for maintaining the basic cellular function, which allows them to adapt to the environment. Human and pig housekeeping genes have varied structures and gene lists, but they have converged to maintain basic cellular functions essential for the existence of a cell, regardless of its specific role in the species. The results of our study shed light on the evolutionary dynamics of housekeeping genes.

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Daphnia as a Model for Eco-evolutionary Dynamics

10.1093/oso/9780190620271.003.0016 ◽

2018 ◽

pp. 403-424

Author(s):

Matthew R. Walsh ◽

Michelle Packer ◽

Shannon Beston ◽

Collin Funkhouser ◽

Michael Gillis ◽

...

Keyword(s):

Life History ◽

Evolutionary Dynamics ◽

Model Organism ◽

Life History Evolution ◽

Ecological Processes ◽

Evolutionary Forces ◽

Evolutionary Changes ◽

History Evolution ◽

Ecological Importance ◽

The Many

Much research has shown that variation in ecological processes can drive rapid evolutionary changes over periods of years to decades. Such contemporary adaptation sets the stage for evolution to have reciprocal impacts on the properties of populations, communities, and ecosystems, with ongoing interactions between ecological and evolutionary forces. The importance and generality of these eco-evolutionary dynamics are largely unknown. In this chapter, we promote the use of water fleas (Daphnia sp.) as a model organism in the exploration of eco-evolutionary interactions in nature. The many characteristics of Daphnia that make them suitable for laboratory study in conjunction with their well-known ecological importance in lakes, position Daphnia to contribute new and important insights into eco-evolutionary dynamics. We first review the influence of key environmental stressors in Daphnia evolution. We then highlight recent work documenting the pathway from life history evolution to ecology using Daphnia as a model. This review demonstrates that much is known about the influence of ecology on Daphnia life history evolution, while research exploring the genomic basis of adaptation as well as the influence of Daphnia life history traits on ecological processes is beginning to accumulate.

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Evolutionary Trends in the Mitochondrial Genome of Archaeplastida: How Does the GC Bias Affect the Transition from Water to Land?

Plants ◽

10.3390/plants9030358 ◽

2020 ◽

Vol 9 (3) ◽

pp. 358

Author(s):

Joan Pedrola-Monfort ◽

David Lázaro-Gimeno ◽

Carlos G. Boluda ◽

Laia Pedrola ◽

Alfonso Garmendia ◽

...

Keyword(s):

Mitochondrial Genome ◽

Evolutionary Biology ◽

Repetitive Sequences ◽

Gc Content ◽

Nuclear Genome ◽

Nuclear Ribosomal Dna ◽

Sequence Evolution ◽

Evolutionary Trends ◽

Genome Length ◽

Evolutionary Patterns

Among the most intriguing mysteries in the evolutionary biology of photosynthetic organisms are the genesis and consequences of the dramatic increase in the mitochondrial and nuclear genome sizes, together with the concomitant evolution of the three genetic compartments, particularly during the transition from water to land. To clarify the evolutionary trends in the mitochondrial genome of Archaeplastida, we analyzed the sequences from 37 complete genomes. Therefore, we utilized mitochondrial, plastidial and nuclear ribosomal DNA molecular markers on 100 species of Streptophyta for each subunit. Hierarchical models of sequence evolution were fitted to test the heterogeneity in the base composition. The best resulting phylogenies were used for reconstructing the ancestral Guanine-Cytosine (GC) content and equilibrium GC frequency (GC*) using non-homogeneous and non-stationary models fitted with a maximum likelihood approach. The mitochondrial genome length was strongly related to repetitive sequences across Archaeplastida evolution; however, the length seemed not to be linked to the other studied variables, as different lineages showed diverse evolutionary patterns. In contrast, Streptophyta exhibited a powerful positive relationship between the GC content, non-coding DNA, and repetitive sequences, while the evolution of Chlorophyta reflected a strong positive linear relationship between the genome length and the number of genes.

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Evolutionary Dynamics of Sex Chromosomes of Paleognathous Birds

Genome Biology and Evolution ◽

10.1093/gbe/evz154 ◽

2019 ◽

Vol 11 (8) ◽

pp. 2376-2390 ◽

Cited By ~ 13

Author(s):

Luohao Xu ◽

Simon Yung Wa Sin ◽

Phil Grayson ◽

Scott V Edwards ◽

Timothy B Sackton

Keyword(s):

Sex Chromosomes ◽

Evolutionary Dynamics ◽

Chromosome Evolution ◽

Sex Chromosome ◽

Z Chromosome ◽

Recombination Suppression ◽

Evolutionary Forces ◽

Genomic Level ◽

Standard Models ◽

Pseudoautosomal Regions

Abstract Standard models of sex chromosome evolution propose that recombination suppression leads to the degeneration of the heterogametic chromosome, as is seen for the Y chromosome in mammals and the W chromosome in most birds. Unlike other birds, paleognaths (ratites and tinamous) possess large nondegenerate regions on their sex chromosomes (PARs or pseudoautosomal regions). It remains unclear why these large PARs are retained over >100 Myr, and how this retention impacts the evolution of sex chromosomes within this system. To address this puzzle, we analyzed Z chromosome evolution and gene expression across 12 paleognaths, several of whose genomes have recently been sequenced. We confirm at the genomic level that most paleognaths retain large PARs. As in other birds, we find that all paleognaths have incomplete dosage compensation on the regions of the Z chromosome homologous to degenerated portions of the W (differentiated regions), but we find no evidence for enrichments of male-biased genes in PARs. We find limited evidence for increased evolutionary rates (faster-Z) either across the chromosome or in differentiated regions for most paleognaths with large PARs, but do recover signals of faster-Z evolution in tinamou species with mostly degenerated W chromosomes, similar to the pattern seen in neognaths. Unexpectedly, in some species, PAR-linked genes evolve faster on average than genes on autosomes, suggested by diverse genomic features to be due to reduced efficacy of selection in paleognath PARs. Our analysis shows that paleognath Z chromosomes are atypical at the genomic level, but the evolutionary forces maintaining largely homomorphic sex chromosomes in these species remain elusive.

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Synteny-Guided Resolution of Gene Trees Clarifies the Functional Impact of Whole-Genome Duplications

Molecular Biology and Evolution ◽

10.1093/molbev/msaa149 ◽

2020 ◽

Vol 37 (11) ◽

pp. 3324-3337

Author(s):

Elise Parey ◽

Alexandra Louis ◽

Cédric Cabau ◽

Yann Guiguen ◽

Hugues Roest Crollius ◽

...

Keyword(s):

Gene Families ◽

Sequence Evolution ◽

Whole Genome ◽

Gene Trees ◽

Ensembl Database ◽

Whole Genome Duplications ◽

Gene Copies ◽

Genome Duplications ◽

Phenotypic Robustness ◽

New Gene

Abstract Whole-genome duplications (WGDs) have major impacts on the evolution of species, as they produce new gene copies contributing substantially to adaptation, isolation, phenotypic robustness, and evolvability. They result in large, complex gene families with recurrent gene losses in descendant species that sequence-based phylogenetic methods fail to reconstruct accurately. As a result, orthologs and paralogs are difficult to identify reliably in WGD-descended species, which hinders the exploration of functional consequences of WGDs. Here, we present Synteny-guided CORrection of Paralogies and Orthologies (SCORPiOs), a novel method to reconstruct gene phylogenies in the context of a known WGD event. WGDs generate large duplicated syntenic regions, which SCORPiOs systematically leverages as a complement to sequence evolution to infer the evolutionary history of genes. We applied SCORPiOs to the 320-My-old WGD at the origin of teleost fish. We find that almost one in four teleost gene phylogenies in the Ensembl database (3,394) are inconsistent with their syntenic contexts. For 70% of these gene families (2,387), we were able to propose an improved phylogenetic tree consistent with both the molecular substitution distances and the local syntenic information. We show that these synteny-guided phylogenies are more congruent with the species tree, with sequence evolution and with expected expression conservation patterns than those produced by state-of-the-art methods. Finally, we show that synteny-guided gene trees emphasize contributions of WGD paralogs to evolutionary innovations in the teleost clade.

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Chloroplast competition is controlled by lipid biosynthesis in evening primroses

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1811661116 ◽

2019 ◽

Vol 116 (12) ◽

pp. 5665-5674 ◽

Cited By ~ 12

Author(s):

Johanna Sobanski ◽

Patrick Giavalisco ◽

Axel Fischer ◽

Julia M. Kreiner ◽

Dirk Walther ◽

...

Keyword(s):

Molecular Mechanisms ◽

Regulatory Region ◽

Nuclear Genome ◽

Lipid Biosynthesis ◽

Metabolic Phenotype ◽

Uniparental Inheritance ◽

Biparental Inheritance ◽

Turnover Rates ◽

Evening Primrose ◽

Evolutionary Forces

In most eukaryotes, organellar genomes are transmitted preferentially by the mother, but molecular mechanisms and evolutionary forces underlying this fundamental biological principle are far from understood. It is believed that biparental inheritance promotes competition between the cytoplasmic organelles and allows the spread of so-called selfish cytoplasmic elements. Those can be, for example, fast-replicating or aggressive chloroplasts (plastids) that are incompatible with the hybrid nuclear genome and therefore maladaptive. Here we show that the ability of plastids to compete against each other is a metabolic phenotype determined by extremely rapidly evolving genes in the plastid genome of the evening primroseOenothera. Repeats in the regulatory region ofaccD(the plastid-encoded subunit of the acetyl-CoA carboxylase, which catalyzes the first and rate-limiting step of lipid biosynthesis), as well as inycf2(a giant reading frame of still unknown function), are responsible for the differences in competitive behavior of plastid genotypes. Polymorphisms in these genes influence lipid synthesis and most likely profiles of the plastid envelope membrane. These in turn determine plastid division and/or turnover rates and hence competitiveness. This work uncovers cytoplasmic drive loci controlling the outcome of biparental chloroplast transmission. Here, they define the mode of chloroplast inheritance, as plastid competitiveness can result in uniparental inheritance (through elimination of the “weak” plastid) or biparental inheritance (when two similarly “strong” plastids are transmitted).

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