Dynamics of gene duplication in the genomes of chlorophyll d-producing cyanobacteria: implications for the ecological niche.

Abstract:

:Gene duplication may be an important mechanism for the evolution of new functions and for the adaptive modulation of gene expression via dosage effects. Here, we analyzed the fate of gene duplicates for two strains of a novel group of cyanobacteria (genus Acaryochloris) that produces the far-red light absorbing chlorophyll d as its main photosynthetic pigment. The genomes of both strains contain an unusually high number of gene duplicates for bacteria. As has been observed for eukaryotic genomes, we find that the demography of gene duplicates can be well modeled by a birth-death process. Most duplicated Acaryochloris genes are of comparatively recent origin, are strain-specific, and tend to be located on different genetic elements. Analyses of selection on duplicates of different divergence classes suggest that a minority of paralogs exhibit near neutral evolutionary dynamics immediately following duplication but that most duplicate pairs (including those which have been retained for long periods) are under strong purifying selection against amino acid change. The likelihood of duplicate retention varied among gene functional classes, and the pronounced differences between strains in the pool of retained recent duplicates likely reflects differences in the nutrient status and other characteristics of their respective environments. We conclude that most duplicates are quickly purged from Acaryochloris genomes and that those which are retained likely make important contributions to organism ecology by conferring fitness benefits via gene dosage effects. The mechanism of enhanced duplication may involve homologous recombination between genetic elements mediated by paralogous copies of recA.

journal_name

Genome Biol Evol

authors

Miller SR,Wood AM,Blankenship RE,Kim M,Ferriera S

doi

10.1093/gbe/evr060

subject

Has Abstract

pub_date

2011-01-01 00:00:00

pages

601-13

issn

1759-6653

pii

evr060

journal_volume

3

pub_type

杂志文章
  • Evolution of proteasome regulators in eukaryotes.

    abstract::All living organisms require protein degradation to terminate biological processes and remove damaged proteins. One such machine is the 20S proteasome, a specialized barrel-shaped and compartmentalized multicatalytic protease. The activity of the 20S proteasome generally requires the binding of regulators/proteasome a...

    journal_title:Genome biology and evolution

    pub_type: 杂志文章

    doi:10.1093/gbe/evv068

    authors: Fort P,Kajava AV,Delsuc F,Coux O

    更新日期:2015-05-04 00:00:00

  • Life in an arsenic-containing gold mine: genome and physiology of the autotrophic arsenite-oxidizing bacterium rhizobium sp. NT-26.

    abstract::Arsenic is widespread in the environment and its presence is a result of natural or anthropogenic activities. Microbes have developed different mechanisms to deal with toxic compounds such as arsenic and this is to resist or metabolize the compound. Here, we present the first reference set of genomic, transcriptomic a...

    journal_title:Genome biology and evolution

    pub_type: 杂志文章

    doi:10.1093/gbe/evt061

    authors: Andres J,Arsène-Ploetze F,Barbe V,Brochier-Armanet C,Cleiss-Arnold J,Coppée JY,Dillies MA,Geist L,Joublin A,Koechler S,Lassalle F,Marchal M,Médigue C,Muller D,Nesme X,Plewniak F,Proux C,Ramírez-Bahena MH,Schenowitz C

    更新日期:2013-01-01 00:00:00

  • Evolutionary Rate Heterogeneity of Primary and Secondary Metabolic Pathway Genes in Arabidopsis thaliana.

    abstract::Primary metabolism is essential to plants for growth and development, and secondary metabolism helps plants to interact with the environment. Many plant metabolites are industrially important. These metabolites are produced by plants through complex metabolic pathways. Lack of knowledge about these pathways is hinderi...

    journal_title:Genome biology and evolution

    pub_type: 杂志文章

    doi:10.1093/gbe/evv217

    authors: Mukherjee D,Mukherjee A,Ghosh TC

    更新日期:2015-11-10 00:00:00

  • Partial dosage compensation in Strepsiptera, a sister group of beetles.

    abstract::Sex chromosomes have evolved independently in many different taxa, and so have mechanisms to compensate for expression differences on sex chromosomes in males and females. Different clades have evolved vastly different ways to achieve dosage compensation, including hypertranscription of the single X in male Drosophila...

    journal_title:Genome biology and evolution

    pub_type: 杂志文章

    doi:10.1093/gbe/evv008

    authors: Mahajan S,Bachtrog D

    更新日期:2015-01-18 00:00:00

  • Regulation of Large Number of Weak Targets-New Insights from Twin-microRNAs.

    abstract::Each animal microRNA (miRNA) targets many genes for repression. Down-regulation of most of these targets is weak and has no detectable individual phenotypic effect. Whether this extensive weak repression is biologically relevant is a central issue in the debate on miRNA functionality. In the "small (target) pool" view...

    journal_title:Genome biology and evolution

    pub_type: 杂志文章

    doi:10.1093/gbe/evy079

    authors: Zhao Y,Lin P,Liufu Z,Yang H,Lyu Y,Shen X,Wu CI,Tang T

    更新日期:2018-04-01 00:00:00

  • Protein subcellular relocalization in the evolution of yeast singleton and duplicate genes.

    abstract::Gene duplication is the primary source of new genes, but the mechanisms underlying the functional divergence and retention of duplicate genes are not well understood. Because eukaryotic proteins are localized to subcellular structures and localization can be altered by a single amino acid replacement, it was recently ...

    journal_title:Genome biology and evolution

    pub_type: 信件

    doi:10.1093/gbe/evp021

    authors: Qian W,Zhang J

    更新日期:2009-07-22 00:00:00

  • Comparative Genomic Analysis of Acanthamoeba Endosymbionts Highlights the Role of Amoebae as a "Melting Pot" Shaping the Rickettsiales Evolution.

    abstract::Amoebae have been considered as a genetic "melting pot" for its symbionts, facilitating genetic exchanges of the bacteria that co-inhabit the same host. To test the "melting pot" hypothesis, we analyzed six genomes of amoeba endosymbionts within Rickettsiales, four of which belong to Holosporaceae family and two to Ca...

    journal_title:Genome biology and evolution

    pub_type: 杂志文章

    doi:10.1093/gbe/evx246

    authors: Wang Z,Wu M

    更新日期:2017-11-01 00:00:00

  • Developmental Constraints on Genome Evolution in Four Bilaterian Model Species.

    abstract::Developmental constraints on genome evolution have been suggested to follow either an early conservation model or an "hourglass" model. Both models agree that late development strongly diverges between species, but debate on which developmental period is the most conserved. Here, based on a modified "Transcriptome Age...

    journal_title:Genome biology and evolution

    pub_type: 杂志文章

    doi:10.1093/gbe/evy177

    authors: Liu J,Robinson-Rechavi M

    更新日期:2018-09-01 00:00:00

  • Teff, an Orphan Cereal in the Chloridoideae, Provides Insights into the Evolution of Storage Proteins in Grasses.

    abstract::Seed storage proteins (SSP) in cereals provide essential nutrition for humans and animals. Genes encoding these proteins have undergone rapid evolution in different grass species. To better understand the degree of divergence, we analyzed this gene family in the subfamily Chloridoideae, where the genome of teff (Eragr...

    journal_title:Genome biology and evolution

    pub_type: 杂志文章

    doi:10.1093/gbe/evw117

    authors: Zhang W,Xu J,Bennetzen JL,Messing J

    更新日期:2016-06-13 00:00:00

  • Evolutionary Dynamics of Chloroplast Genomes in Low Light: A Case Study of the Endolithic Green Alga Ostreobium quekettii.

    abstract::Some photosynthetic organisms live in extremely low light environments. Light limitation is associated with selective forces as well as reduced exposure to mutagens, and over evolutionary timescales it can leave a footprint on species' genomes. Here, we present the chloroplast genomes of four green algae (Bryopsidales...

    journal_title:Genome biology and evolution

    pub_type: 杂志文章

    doi:10.1093/gbe/evw206

    authors: R Marcelino V,Cremen MC,Jackson CJ,Larkum AA,Verbruggen H

    更新日期:2016-10-05 00:00:00

  • Evolutionary Remodeling of the Cell Envelope in Bacteria of the Planctomycetes Phylum.

    abstract::Bacteria of the Planctomycetes phylum have many unique cellular features, such as extensive membrane invaginations and the ability to import macromolecules. These features raise intriguing questions about the composition of their cell envelopes. In this study, we have used microscopy, phylogenomics, and proteomics to ...

    journal_title:Genome biology and evolution

    pub_type: 杂志文章

    doi:10.1093/gbe/evaa159

    authors: Mahajan M,Seeger C,Yee B,Andersson SGE

    更新日期:2020-09-01 00:00:00

  • Evolutionary Analysis of Bile Acid-Conjugating Enzymes Reveals a Complex Duplication and Reciprocal Loss History.

    abstract::To fulfill their physiological functions, bile acids are conjugated with amino acids. In humans, conjugation is catalyzed by bile acid coenzyme A: amino acid N-acyltransferase (BAAT), an enzyme with a highly conserved catalytic triad in its active site. Interestingly, the conjugated amino acids are highly variable amo...

    journal_title:Genome biology and evolution

    pub_type: 杂志文章

    doi:10.1093/gbe/evz238

    authors: Kirilenko BM,Hagey LR,Barnes S,Falany CN,Hiller M

    更新日期:2019-11-01 00:00:00

  • Adaptation and Conservation throughout the Drosophila melanogaster Life-Cycle.

    abstract::Previous studies of the evolution of genes expressed at different life-cycle stages of Drosophila melanogaster have not been able to disentangle adaptive from nonadaptive substitutions when using nonsynonymous sites. Here, we overcome this limitation by combining whole-genome polymorphism data from D. melanogaster and...

    journal_title:Genome biology and evolution

    pub_type: 杂志文章

    doi:10.1093/gbe/evz086

    authors: Coronado-Zamora M,Salvador-Martínez I,Castellano D,Barbadilla A,Salazar-Ciudad I

    更新日期:2019-05-01 00:00:00

  • Nonrandom survival of gene conversions among yeast ribosomal proteins duplicated through genome doubling.

    abstract::By comparing the patterns of evolution in the coding and upstream noncoding regions of yeast ribosomal protein (RP) genes duplicated in a genome duplication, we find that although nonsynonymous sites in the coding sequences show strong evidence for the fixation of recent gene conversion events, similar patterns are le...

    journal_title:Genome biology and evolution

    pub_type: 杂志文章

    doi:10.1093/gbe/evq067

    authors: Evangelisti AM,Conant GC

    更新日期:2010-01-01 00:00:00

  • Nephromyces Encodes a Urate Metabolism Pathway and Predicted Peroxisomes, Demonstrating That These Are Not Ancient Losses of Apicomplexans.

    abstract::The phylum Apicomplexa is a quintessentially parasitic lineage, whose members infect a broad range of animals. One exception to this may be the apicomplexan genus Nephromyces, which has been described as having a mutualistic relationship with its host. Here we analyze transcriptome data from Nephromyces and its parasi...

    journal_title:Genome biology and evolution

    pub_type: 杂志文章

    doi:10.1093/gbe/evy251

    authors: Paight C,Slamovits CH,Saffo MB,Lane CE

    更新日期:2019-01-01 00:00:00

  • Whole genome comparisons of ergot fungi reveals the divergence and evolution of species within the genus Claviceps are the result of varying mechanisms driving genome evolution and host range expansion.

    abstract::The genus Claviceps has been known for centuries as an economically important fungal genera for pharmacology and agricultural research. Only recently have researchers begun to unravel the evolutionary history of the genus, with origins in South America and classification of four distinct sections through ecological, m...

    journal_title:Genome biology and evolution

    pub_type: 杂志文章

    doi:10.1093/gbe/evaa267

    authors: Wyka SA,Mondo SJ,Liu M,Dettman J,Nalam V,Broders KD

    更新日期:2021-01-29 00:00:00

  • Sex Chromosome Dosage Compensation in Heliconius Butterflies: Global yet Still Incomplete?

    abstract::The evolution of heterogametic sex chromosomes is often-but not always-accompanied by the evolution of dosage compensating mechanisms that mitigate the impact of sex-specific gene dosage on levels of gene expression. One emerging view of this process is that such mechanisms may only evolve in male-heterogametic (XY) s...

    journal_title:Genome biology and evolution

    pub_type: 杂志文章

    doi:10.1093/gbe/evv156

    authors: Walters JR,Hardcastle TJ,Jiggins CD

    更新日期:2015-09-02 00:00:00

  • Rapid evolution of piRNA pathway in the teleost fish: implication for an adaptation to transposon diversity.

    abstract::The Piwi-interacting RNA (piRNA) pathway is responsible for germline specification, gametogenesis, transposon silencing, and genome integrity. Transposable elements can disrupt genome and its functions. However, piRNA pathway evolution and its adaptation to transposon diversity in the teleost fish remain unknown. This...

    journal_title:Genome biology and evolution

    pub_type: 杂志文章

    doi:10.1093/gbe/evu105

    authors: Yi M,Chen F,Luo M,Cheng Y,Zhao H,Cheng H,Zhou R

    更新日期:2014-05-19 00:00:00

  • Phylogenomic data support a seventh order of Methylotrophic methanogens and provide insights into the evolution of Methanogenesis.

    abstract::Increasing evidence from sequence data from various environments, including the human gut, suggests the existence of a previously unknown putative seventh order of methanogens. The first genomic data from members of this lineage, Methanomassiliicoccus luminyensis and "Candidatus Methanomethylophilus alvus," provide in...

    journal_title:Genome biology and evolution

    pub_type: 信件

    doi:10.1093/gbe/evt128

    authors: Borrel G,O'Toole PW,Harris HM,Peyret P,Brugère JF,Gribaldo S

    更新日期:2013-01-01 00:00:00

  • Being Aquifex aeolicus: Untangling a hyperthermophile's checkered past.

    abstract::Lateral gene transfer (LGT) is an important factor contributing to the evolution of prokaryotic genomes. The Aquificae are a hyperthermophilic bacterial group whose genes show affiliations to many other lineages, including the hyperthermophilic Thermotogae, the Proteobacteria, and the Archaea. Previous phylogenomic an...

    journal_title:Genome biology and evolution

    pub_type: 杂志文章

    doi:10.1093/gbe/evt195

    authors: Eveleigh RJ,Meehan CJ,Archibald JM,Beiko RG

    更新日期:2013-01-01 00:00:00

  • In Silico Identification of Candidate Genes for Fertility Restoration in Cytoplasmic Male Sterile Perennial Ryegrass (Lolium perenne L.).

    abstract::Perennial ryegrass (Lolium perenne L.) is widely used for forage production in both permanent and temporary grassland systems. To increase yields in perennial ryegrass, recent breeding efforts have been focused on strategies to more efficiently exploit heterosis by hybrid breeding. Cytoplasmic male sterility (CMS) is ...

    journal_title:Genome biology and evolution

    pub_type: 杂志文章

    doi:10.1093/gbe/evw047

    authors: Sykes T,Yates S,Nagy I,Asp T,Small I,Studer B

    更新日期:2017-02-01 00:00:00

  • The Tritryps Comparative Repeatome: Insights on Repetitive Element Evolution in Trypanosomatid Pathogens.

    abstract::The major human pathogens Trypanosoma cruzi, Trypanosoma brucei, and Leishmania major are collectively known as the Tritryps. The initial comparative analysis of their genomes has uncovered that Tritryps share a great number of genes, but repetitive DNA seems to be extremely variable between them. However, the in-dept...

    journal_title:Genome biology and evolution

    pub_type: 信件

    doi:10.1093/gbe/evz017

    authors: Pita S,Díaz-Viraqué F,Iraola G,Robello C

    更新日期:2019-02-01 00:00:00

  • Draft Genome Sequences of Two Closely Related Aflatoxigenic Aspergillus Species Obtained from the Ivory Coast.

    abstract::Aspergillus ochraceoroseus and Aspergillus rambellii were isolated from soil detritus in Taï National Park, Ivory Coast, Africa. The Type strain for each species happens to be the only representative ever sampled. Both species secrete copious amounts of aflatoxin B1 and sterigmatocystin, because each of their genomes ...

    journal_title:Genome biology and evolution

    pub_type: 杂志文章

    doi:10.1093/gbe/evv246

    authors: Moore GG,Mack BM,Beltz SB

    更新日期:2015-12-03 00:00:00

  • Insect-Symbiont Gene Expression in the Midgut Bacteriocytes of a Blood-Sucking Parasite.

    abstract::Animals interact with a diverse array of both beneficial and detrimental microorganisms. In insects, these symbioses in many cases allow feeding on nutritionally unbalanced diets. It is, however, still not clear how are obligate symbioses maintained at the cellular level for up to several hundred million years. Exact ...

    journal_title:Genome biology and evolution

    pub_type: 杂志文章

    doi:10.1093/gbe/evaa032

    authors: Husnik F,Hypsa V,Darby A

    更新日期:2020-04-01 00:00:00

  • Conserved meiotic machinery in Glomus spp., a putatively ancient asexual fungal lineage.

    abstract::Arbuscular mycorrhizal fungi (AMF) represent an ecologically important and evolutionarily intriguing group of symbionts of land plants, currently thought to have propagated clonally for over 500 Myr. AMF produce multinucleate spores and may exchange nuclei through anastomosis, but meiosis has never been observed in th...

    journal_title:Genome biology and evolution

    pub_type: 杂志文章

    doi:10.1093/gbe/evr089

    authors: Halary S,Malik SB,Lildhar L,Slamovits CH,Hijri M,Corradi N

    更新日期:2011-01-01 00:00:00

  • The Combined Effect of Oseltamivir and Favipiravir on Influenza A Virus Evolution.

    abstract::Influenza virus inflicts a heavy death toll annually and resistance to existing antiviral drugs has generated interest in the development of agents with novel mechanisms of action. Favipiravir is an antiviral drug that acts by increasing the genome-wide mutation rate of influenza A virus (IAV). Potential synergistic b...

    journal_title:Genome biology and evolution

    pub_type: 杂志文章

    doi:10.1093/gbe/evx138

    authors: Ormond L,Liu P,Matuszewski S,Renzette N,Bank C,Zeldovich K,Bolon DN,Kowalik TF,Finberg RW,Jensen JD,Wang JP

    更新日期:2017-07-01 00:00:00

  • Whole Genome Sequencing and Assembly of the Asian Honey Bee Apis dorsata.

    abstract::The Asian honey bee (Apis dorsata) is distinct from its more widely distributed cousin Apis mellifera by a few key characteristics. Most prominently, A. dorsata, nest in the open by forming a colony clustered around the honeycomb, whereas A. mellifera nest in concealed cavities. Additionally, the worker and reproducti...

    journal_title:Genome biology and evolution

    pub_type: 杂志文章

    doi:10.1093/gbe/evz277

    authors: Oppenheim S,Cao X,Rueppel O,Krongdang S,Phokasem P,DeSalle R,Goodwin S,Xing J,Chantawannakul P,Rosenfeld JA

    更新日期:2020-01-01 00:00:00

  • The Impact of Natural Selection on the Evolution and Function of Placentally Expressed Galectins.

    abstract::Immunity genes have repeatedly experienced natural selection during mammalian evolution. Galectins are carbohydrate-binding proteins that regulate diverse immune responses, including maternal-fetal immune tolerance in placental pregnancy. Seven human galectins, four conserved across vertebrates and three specific to p...

    journal_title:Genome biology and evolution

    pub_type: 杂志文章

    doi:10.1093/gbe/evz183

    authors: Ely ZA,Moon JM,Sliwoski GR,Sangha AK,Shen XX,Labella AL,Meiler J,Capra JA,Rokas A

    更新日期:2019-09-01 00:00:00

  • A model for the effect of homologous recombination on microbial diversification.

    abstract::The effect of homologous recombination (HR) on the evolution of microbial genomes remains contentious as competing hypotheses seek to explain the evolutionary dynamics of microbial species. Evidence for HR between microbial genomes is widespread, and this process has been proposed to act as a cohesive force that can c...

    journal_title:Genome biology and evolution

    pub_type: 杂志文章

    doi:10.1093/gbe/evr110

    authors: Doroghazi JR,Buckley DH

    更新日期:2011-01-01 00:00:00

  • Transcriptional Interference Promotes Rapid Expression Divergence of Drosophila Nested Genes.

    abstract::Nested genes are the most common form of protein-coding overlap in eukaryotic genomes. Previous studies have shown that nested genes accumulate rapidly over evolutionary time, typically via the insertion of short young duplicate genes into long introns. However, the evolutionary relationship between nested genes remai...

    journal_title:Genome biology and evolution

    pub_type: 信件

    doi:10.1093/gbe/evw237

    authors: Assis R

    更新日期:2016-10-23 00:00:00