Genome erosion in a nitrogen-fixing vertically transmitted endosymbiotic multicellular cyanobacterium.

PubWeight™: 1.40‹?› | Rank: Top 5%

🔗 View Article (PMC 2900214)

Published in PLoS One on July 08, 2010

Authors

Liang Ran1, John Larsson, Theoden Vigil-Stenman, Johan A A Nylander, Karolina Ininbergs, Wei-Wen Zheng, Alla Lapidus, Stephen Lowry, Robert Haselkorn, Birgitta Bergman

Author Affiliations

1: Department of Botany, Stockholm University, Stockholm, Sweden.

Articles citing this

Evolutionary transitions in bacterial symbiosis. Proc Natl Acad Sci U S A (2011) 1.69

Genome fluctuations in cyanobacteria reflect evolutionary, developmental and adaptive traits. BMC Evol Biol (2011) 1.69

Insights from 20 years of bacterial genome sequencing. Funct Integr Genomics (2015) 1.27

Genomes of Stigonematalean cyanobacteria (subsection V) and the evolution of oxygenic photosynthesis from prokaryotes to plastids. Genome Biol Evol (2013) 1.22

Biological nitrogen fixation in non-legume plants. Ann Bot (2013) 1.22

Evolution of an endofungal lifestyle: Deductions from the Burkholderia rhizoxinica genome. BMC Genomics (2011) 1.05

Cyanobacteria produce a high variety of hepatotoxic peptides in lichen symbiosis. Proc Natl Acad Sci U S A (2012) 1.04

Evidence for the widespread distribution of CRISPR-Cas system in the Phylum Cyanobacteria. RNA Biol (2013) 0.99

The percentage of bacterial genes on leading versus lagging strands is influenced by multiple balancing forces. Nucleic Acids Res (2012) 0.97

Genomic deletions disrupt nitrogen metabolism pathways of a cyanobacterial diatom symbiont. Nat Commun (2013) 0.96

Massively convergent evolution for ribosomal protein gene content in plastid and mitochondrial genomes. Genome Biol Evol (2013) 0.93

Evolution of small prokaryotic genomes. Front Microbiol (2015) 0.91

Between two fern genomes. Gigascience (2014) 0.90

Crowdfunding the Azolla fern genome project: a grassroots approach. Gigascience (2014) 0.90

Complete genome of a nonphotosynthetic cyanobacterium in a diatom reveals recent adaptations to an intracellular lifestyle. Proc Natl Acad Sci U S A (2014) 0.90

Genome-derived insights into the biology of the hepatotoxic bloom-forming cyanobacterium Anabaena sp. strain 90. BMC Genomics (2012) 0.89

Bacterial leaf symbiosis in angiosperms: host specificity without co-speciation. PLoS One (2011) 0.89

Prokaryotic caspase homologs: phylogenetic patterns and functional characteristics reveal considerable diversity. PLoS One (2012) 0.86

Bacterial endosymbiosis in a chordate host: long-term co-evolution and conservation of secondary metabolism. PLoS One (2013) 0.84

Candidatus Frankia Datiscae Dg1, the Actinobacterial Microsymbiont of Datisca glomerata, Expresses the Canonical nod Genes nodABC in Symbiosis with Its Host Plant. PLoS One (2015) 0.83

A Brief Review: The Z-curve Theory and its Application in Genome Analysis. Curr Genomics (2014) 0.83

The mitochondrial and chloroplast genomes of the haptophyte Chrysochromulina tobin contain unique repeat structures and gene profiles. BMC Genomics (2014) 0.81

Local hopping mobile DNA implicated in pseudogene formation and reductive evolution in an obligate cyanobacteria-plant symbiosis. BMC Genomics (2015) 0.80

Evidence of horizontal gene transfer between obligate leaf nodule symbionts. ISME J (2016) 0.79

Diversification of DnaA dependency for DNA replication in cyanobacterial evolution. ISME J (2015) 0.79

Multiple Modes of Cell Death Discovered in a Prokaryotic (Cyanobacterial) Endosymbiont. PLoS One (2013) 0.79

The intracellular Scots pine shoot symbiont Methylobacterium extorquens DSM13060 aggregates around the host nucleus and encodes eukaryote-like proteins. MBio (2015) 0.79

Dinitrogen fixation is restricted to the terminal heterocysts in the invasive cyanobacterium Cylindrospermopsis raciborskii CS-505. PLoS One (2013) 0.79

Regulation of Three Nitrogenase Gene Clusters in the Cyanobacterium Anabaena variabilis ATCC 29413. Life (Basel) (2014) 0.78

The composition of the global and feature specific cyanobacterial core-genomes. Front Microbiol (2015) 0.78

The genome and transcriptome of Trichormus sp. NMC-1: insights into adaptation to extreme environments on the Qinghai-Tibet Plateau. Sci Rep (2016) 0.78

Diverse roles of the GlcP glucose permease in free-living and symbiotic cyanobacteria. Plant Signal Behav (2013) 0.76

Sequence variability of Rhizobiales orthologs and relationship with physico-chemical characteristics of proteins. Biol Direct (2011) 0.75

Metabolic Adaptation, a Specialized Leaf Organ Structure and Vascular Responses to Diurnal N2 Fixation by Nostoc azollae Sustain the Astonishing Productivity of Azolla Ferns without Nitrogen Fertilizer. Front Plant Sci (2017) 0.75

Highly Iterated Palindromic Sequences (HIPs) and Their Relationship to DNA Methyltransferases. Life (Basel) (2015) 0.75

The Cosmic Zoo: The (Near) Inevitability of the Evolution of Complex, Macroscopic Life. Life (Basel) (2016) 0.75

The evolution of host-symbiont dependence. Nat Commun (2017) 0.75

High abundance and expression of transposases in bacteria from the Baltic Sea. ISME J (2017) 0.75

The Role of the N-Terminal Domains of Bacterial Initiator DnaA in the Assembly and Regulation of the Bacterial Replication Initiation Complex. Genes (Basel) (2017) 0.75

Articles cited by this

MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res (2004) 168.89

RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics (2006) 87.59

Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics (2010) 42.80

A rapid bootstrap algorithm for the RAxML Web servers. Syst Biol (2008) 38.22

OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res (2003) 33.03

OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups. Nucleic Acids Res (2006) 11.43

Phosphoenolpyruvate:carbohydrate phosphotransferase systems of bacteria. Microbiol Rev (1993) 11.25

ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res (2006) 9.58

De novo identification of repeat families in large genomes. Bioinformatics (2005) 7.95

PCR primers to amplify 16S rRNA genes from cyanobacteria. Appl Environ Microbiol (1997) 6.70

Genome sequence of the endocellular obligate symbiont of tsetse flies, Wigglesworthia glossinidia. Nat Genet (2002) 5.91

The DOE-JGI Standard Operating Procedure for the Annotations of Microbial Genomes. Stand Genomic Sci (2009) 5.50

DNAPlotter: circular and linear interactive genome visualization. Bioinformatics (2008) 5.49

Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus. Proc Natl Acad Sci U S A (2002) 5.48

The dynamics and time scale of ongoing genomic erosion in symbiotic bacteria. Science (2009) 4.25

Determination of the core of a minimal bacterial gene set. Microbiol Mol Biol Rev (2004) 4.14

Reassessing the first appearance of eukaryotes and cyanobacteria. Nature (2008) 3.67

Ori-Finder: a web-based system for finding oriCs in unannotated bacterial genomes. BMC Bioinformatics (2008) 3.65

Strict host-symbiont cospeciation and reductive genome evolution in insect gut bacteria. PLoS Biol (2006) 3.62

The bacterial phosphoenolpyruvate: glycose phosphotransferase system. Annu Rev Biochem (1990) 3.53

Genomic changes following host restriction in bacteria. Curr Opin Genet Dev (2004) 2.87

Where are the pseudogenes in bacterial genomes? Trends Microbiol (2001) 2.24

The Paleoproterozoic snowball Earth: a climate disaster triggered by the evolution of oxygenic photosynthesis. Proc Natl Acad Sci U S A (2005) 2.14

Pseudogenes, junk DNA, and the dynamics of Rickettsia genomes. Mol Biol Evol (2001) 1.95

The smallest known genomes of multicellular and toxic cyanobacteria: comparison, minimal gene sets for linked traits and the evolutionary implications. PLoS One (2010) 1.77

Host-symbiont co-speciation and reductive genome evolution in gut symbiotic bacteria of acanthosomatid stinkbugs. BMC Biol (2009) 1.76

Genes of cyanobacterial origin in plant nuclear genomes point to a heterocyst-forming plastid ancestor. Mol Biol Evol (2008) 1.62

Genome evolution in cyanobacteria: the stable core and the variable shell. Proc Natl Acad Sci U S A (2008) 1.58

Regulation of glutamine synthetase activity and synthesis in free-living and symbiotic Anabaena spp. J Bacteriol (1982) 1.56

Differences in mRNA levels in Anabaena living freely or in symbiotic association with Azolla. EMBO J (1986) 1.55

How do endosymbionts become organelles? Understanding early events in plastid evolution. Bioessays (2007) 1.36

Integrating Markov clustering and molecular phylogenetics to reconstruct the cyanobacterial species tree from conserved protein families. Mol Biol Evol (2008) 1.29

patS minigenes inhibit heterocyst development of Anabaena sp. strain PCC 7120. J Bacteriol (2004) 1.13

Transcriptional analysis and mutation of a dnaA-like gene in Synechocystis sp. strain PCC 6803. J Bacteriol (1998) 1.07

Genomes at the interface between bacteria and organelles. Philos Trans R Soc Lond B Biol Sci (2003) 0.97

Variability in benthic diazotrophy and cyanobacterial diversity in a tropical intertidal lagoon. FEMS Microbiol Ecol (2008) 0.89

Cellular responses in the cyanobacterial symbiont during its vertical transfer between plant generations in the Azolla microphylla symbiosis. New Phytol (2009) 0.86

DNA polymerase I in constitutive stable DNA replication in Escherichia coli. J Bacteriol (1997) 0.85

Dinitrogenase reductase (Fe-protein) of nitrogenase in the cyanobacterial symbionts of three Azolla species: Localization and sequence of appearance during heterocyst differentiation. Planta (1988) 0.80

Does my genome look big in this? Nat Rev Microbiol (2008) 0.80

Articles by these authors

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature (2009) 15.06

Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. Nat Methods (2007) 7.73

Genome sequence of Bacillus cereus and comparative analysis with Bacillus anthracis. Nature (2003) 7.05

Assembling single-cell genomes and mini-metagenomes from chimeric MDA products. J Comput Biol (2013) 6.90

Complete sequence and comparative genome analysis of the dairy bacterium Streptococcus thermophilus. Nat Biotechnol (2004) 5.40

The genome sequence of the facultative intracellular pathogen Brucella melitensis. Proc Natl Acad Sci U S A (2001) 5.39

A bioinformatician's guide to metagenomics. Microbiol Mol Biol Rev (2008) 4.33

The Wolbachia genome of Brugia malayi: endosymbiont evolution within a human pathogenic nematode. PLoS Biol (2005) 4.28

Patterns and implications of gene gain and loss in the evolution of Prochlorococcus. PLoS Genet (2007) 4.25

Genome sequencing reveals complex secondary metabolome in the marine actinomycete Salinispora tropica. Proc Natl Acad Sci U S A (2007) 4.04

The genomic basis of trophic strategy in marine bacteria. Proc Natl Acad Sci U S A (2009) 3.72

One bacterial cell, one complete genome. PLoS One (2010) 3.69

Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography. Genome Res (2006) 3.53

Genes encoding plastid acetyl-CoA carboxylase and 3-phosphoglycerate kinase of the Triticum/Aegilops complex and the evolutionary history of polyploid wheat. Proc Natl Acad Sci U S A (2002) 3.51

Complete genome sequence of Kytococcus sedentarius type strain (541). Stand Genomic Sci (2009) 3.30

Genome sequence and analysis of the oral bacterium Fusobacterium nucleatum strain ATCC 25586. J Bacteriol (2002) 3.18

High-resolution metagenomics targets specific functional types in complex microbial communities. Nat Biotechnol (2008) 2.99

Comparison of the complete genome sequences of Pseudomonas syringae pv. syringae B728a and pv. tomato DC3000. Proc Natl Acad Sci U S A (2005) 2.85

Methylotrophy in Methylobacterium extorquens AM1 from a genomic point of view. J Bacteriol (2003) 2.81

The plant cell wall-decomposing machinery underlies the functional diversity of forest fungi. Science (2011) 2.67

The genome of deep-sea vent chemolithoautotroph Thiomicrospira crunogena XCL-2. PLoS Biol (2006) 2.43

Complete genome sequence of the industrial bacterium Bacillus licheniformis and comparisons with closely related Bacillus species. Genome Biol (2004) 2.41

The fast changing landscape of sequencing technologies and their impact on microbial genome assemblies and annotation. PLoS One (2012) 2.25

A korarchaeal genome reveals insights into the evolution of the Archaea. Proc Natl Acad Sci U S A (2008) 2.16

The cyanobacterial genome core and the origin of photosynthesis. Proc Natl Acad Sci U S A (2006) 2.11

Novel features of the polysaccharide-digesting gliding bacterium Flavobacterium johnsoniae as revealed by genome sequence analysis. Appl Environ Microbiol (2009) 2.11

International integrated database for the evaluation of severe sepsis and drotrecogin alfa (activated) therapy: analysis of efficacy and safety data in a large surgical cohort. Surgery (2006) 2.05

Environmental genomics reveals a single-species ecosystem deep within Earth. Science (2008) 1.98

Complete genome sequence of Meiothermus ruber type strain (21). Stand Genomic Sci (2010) 1.96

The genomes of the fungal plant pathogens Cladosporium fulvum and Dothistroma septosporum reveal adaptation to different hosts and lifestyles but also signatures of common ancestry. PLoS Genet (2012) 1.95

Genomic islands link secondary metabolism to functional adaptation in marine Actinobacteria. ISME J (2009) 1.94

Diverse taxa of cyanobacteria produce beta-N-methylamino-L-alanine, a neurotoxic amino acid. Proc Natl Acad Sci U S A (2005) 1.92

Living with genome instability: the adaptation of phytoplasmas to diverse environments of their insect and plant hosts. J Bacteriol (2006) 1.89

Tracing the impact of the Andean uplift on Neotropical plant evolution. Proc Natl Acad Sci U S A (2009) 1.86

Whole-genome shotgun optical mapping of Rhodospirillum rubrum. Appl Environ Microbiol (2005) 1.83

Genome analysis of the anaerobic thermohalophilic bacterium Halothermothrix orenii. PLoS One (2009) 1.83

Genome of the epsilonproteobacterial chemolithoautotroph Sulfurimonas denitrificans. Appl Environ Microbiol (2007) 1.82

Complete genome sequence of Pedobacter heparinus type strain (HIM 762-3). Stand Genomic Sci (2009) 1.82

Recombinant human platelet-activating factor acetylhydrolase for treatment of severe sepsis: results of a phase III, multicenter, randomized, double-blind, placebo-controlled, clinical trial. Crit Care Med (2004) 1.80

The Methanosarcina barkeri genome: comparative analysis with Methanosarcina acetivorans and Methanosarcina mazei reveals extensive rearrangement within methanosarcinal genomes. J Bacteriol (2006) 1.79

The complete genome sequence of Cupriavidus metallidurans strain CH34, a master survivalist in harsh and anthropogenic environments. PLoS One (2010) 1.78

Genes coding for hepatotoxic heptapeptides (microcystins) in the cyanobacterium Anabaena strain 90. Appl Environ Microbiol (2004) 1.76

The evolution of host specialization in the vertebrate gut symbiont Lactobacillus reuteri. PLoS Genet (2011) 1.75

Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche. Proc Natl Acad Sci U S A (2012) 1.74

Whole-genome comparative analysis of three phytopathogenic Xylella fastidiosa strains. Proc Natl Acad Sci U S A (2002) 1.73

Phylogenetic analysis of the acetyl-CoA carboxylase and 3-phosphoglycerate kinase loci in wheat and other grasses. Plant Mol Biol (2002) 1.73

N2 fixation by unicellular bacterioplankton from the Atlantic and Pacific oceans: phylogeny and in situ rates. Appl Environ Microbiol (2004) 1.69

Genome fluctuations in cyanobacteria reflect evolutionary, developmental and adaptive traits. BMC Evol Biol (2011) 1.69

Genome sequence and analysis of the soil cellulolytic actinomycete Thermobifida fusca YX. J Bacteriol (2007) 1.67

Localized plasticity in the streamlined genomes of vinyl chloride respiring Dehalococcoides. PLoS Genet (2009) 1.61

Comparative genomics of Ceriporiopsis subvermispora and Phanerochaete chrysosporium provide insight into selective ligninolysis. Proc Natl Acad Sci U S A (2012) 1.61

A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans. Genome Biol (2008) 1.60

The enigmatic planctomycetes may hold a key to the origins of methanogenesis and methylotrophy. Mol Biol Evol (2004) 1.56

Carbon and nitrogen fluxes associated with the cyanobacterium Aphanizomenon sp. in the Baltic Sea. ISME J (2010) 1.55

Exploring the symbiotic pangenome of the nitrogen-fixing bacterium Sinorhizobium meliloti. BMC Genomics (2011) 1.55

Recombinant platelet-activating factor acetylhydrolase to prevent acute respiratory distress syndrome and mortality in severe sepsis: Phase IIb, multicenter, randomized, placebo-controlled, clinical trial. Crit Care Med (2003) 1.53

Deinococcus geothermalis: the pool of extreme radiation resistance genes shrinks. PLoS One (2007) 1.52

The genome sequence of the psychrophilic archaeon, Methanococcoides burtonii: the role of genome evolution in cold adaptation. ISME J (2009) 1.40

Comparative genomics of xylose-fermenting fungi for enhanced biofuel production. Proc Natl Acad Sci U S A (2011) 1.39

Complete genome sequence of Eggerthella lenta type strain (IPP VPI 0255). Stand Genomic Sci (2009) 1.34

Analysis of factorial time-course microarrays with application to a clinical study of burn injury. Proc Natl Acad Sci U S A (2010) 1.33

Complete genome sequence of Spirosoma linguale type strain (1). Stand Genomic Sci (2010) 1.32

Evidence for production of the phytohormone indole-3-acetic acid by cyanobacteria. Planta (2002) 1.31

Inactivation of patS and hetN causes lethal levels of heterocyst differentiation in the filamentous cyanobacterium Anabaena sp. PCC 7120. Mol Microbiol (2005) 1.31

Draft sequencing and comparative genomics of Xylella fastidiosa strains reveal novel biological insights. Genome Res (2002) 1.31

The complete multipartite genome sequence of Cupriavidus necator JMP134, a versatile pollutant degrader. PLoS One (2010) 1.31

Transfer of a cyanobacterial neurotoxin within a temperate aquatic ecosystem suggests pathways for human exposure. Proc Natl Acad Sci U S A (2010) 1.30

Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations. Genome Res (2009) 1.29

Genome analysis of F. nucleatum sub spp vincentii and its comparison with the genome of F. nucleatum ATCC 25586. Genome Res (2003) 1.28

Genome sequence of Thermofilum pendens reveals an exceptional loss of biosynthetic pathways without genome reduction. J Bacteriol (2008) 1.27

The genetically remote pathogenic strain NVH391-98 of the Bacillus cereus group is representative of a cluster of thermophilic strains. Appl Environ Microbiol (2007) 1.25

Sequencing of multiple clostridial genomes related to biomass conversion and biofuel production. J Bacteriol (2010) 1.25

Genome of Methylobacillus flagellatus, molecular basis for obligate methylotrophy, and polyphyletic origin of methylotrophy. J Bacteriol (2007) 1.25

Genome sequence of the Fleming strain of Micrococcus luteus, a simple free-living actinobacterium. J Bacteriol (2009) 1.25

Complete genome sequence of the Medicago microsymbiont Ensifer (Sinorhizobium) medicae strain WSM419. Stand Genomic Sci (2010) 1.24

Single-site mutations in the carboxyltransferase domain of plastid acetyl-CoA carboxylase confer resistance to grass-specific herbicides. Proc Natl Acad Sci U S A (2007) 1.22

Complete genome sequence of Chitinophaga pinensis type strain (UQM 2034). Stand Genomic Sci (2010) 1.21

Trichodesmium--a widespread marine cyanobacterium with unusual nitrogen fixation properties. FEMS Microbiol Rev (2012) 1.20

Complete genome sequence of the photosynthetic purple nonsulfur bacterium Rhodobacter capsulatus SB 1003. J Bacteriol (2010) 1.18

Complete genome sequence of Brachybacterium faecium type strain (Schefferle 6-10). Stand Genomic Sci (2009) 1.17

Genomic characterization of methanomicrobiales reveals three classes of methanogens. PLoS One (2009) 1.17

Facile recovery of individual high-molecular-weight, low-copy-number natural plasmids for genomic sequencing. Appl Environ Microbiol (2006) 1.16

Complete genome sequences for the anaerobic, extremely thermophilic plant biomass-degrading bacteria Caldicellulosiruptor hydrothermalis, Caldicellulosiruptor kristjanssonii, Caldicellulosiruptor kronotskyensis, Caldicellulosiruptor owensensis, and Caldicellulosiruptor lactoaceticus. J Bacteriol (2011) 1.16

Genome sequence of the Arctic methanotroph Methylobacter tundripaludum SV96. J Bacteriol (2011) 1.15

Complete genome sequence of Segniliparus rotundus type strain (CDC 1076). Stand Genomic Sci (2010) 1.15

Complete genome sequence of Atopobium parvulum type strain (IPP 1246). Stand Genomic Sci (2009) 1.14

Comparative genomics of the white-rot fungi, Phanerochaete carnosa and P. chrysosporium, to elucidate the genetic basis of the distinct wood types they colonize. BMC Genomics (2012) 1.14

Microarray analysis of gene expression during bacteriophage T4 infection. Virology (2002) 1.13

The genome sequence of Geobacter metallireducens: features of metabolism, physiology and regulation common and dissimilar to Geobacter sulfurreducens. BMC Microbiol (2009) 1.13

Complete genome sequence of the filamentous anoxygenic phototrophic bacterium Chloroflexus aurantiacus. BMC Genomics (2011) 1.13

Complete genome sequence of Cryptobacterium curtum type strain (12-3). Stand Genomic Sci (2009) 1.12

Complete genome sequence of the aerobic marine methanotroph Methylomonas methanica MC09. J Bacteriol (2011) 1.12

The carboxyltransferase activity of the apicoplast acetyl-CoA carboxylase of Toxoplasma gondii is the target of aryloxyphenoxypropionate inhibitors. J Biol Chem (2002) 1.12

Metagenomes of Mediterranean coastal lagoons. Sci Rep (2012) 1.11

Metabolic analysis of the soil microbe Dechloromonas aromatica str. RCB: indications of a surprisingly complex life-style and cryptic anaerobic pathways for aromatic degradation. BMC Genomics (2009) 1.10

Complete genome sequence of Streptosporangium roseum type strain (NI 9100). Stand Genomic Sci (2010) 1.10

Massive changes in genome architecture accompany the transition to self-fertility in the filamentous fungus Neurospora tetrasperma. Genetics (2011) 1.10