ArticleThe ISME journal2015
Evolutionary origin of a streamlined marine bacterioplankton lineage.
Article in The ISME journal, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Challenges, adaptations, and biotechnological potential of oligophilic bacteria.Antonie van Leeuwenhoek · 2025Review
- Extensive and diverse lanthanide-dependent metabolism in the ocean.The ISME journal · 2025Article
- Promiscuous and genome-wide recombination underlies the sequence-discrete species of the SAR11 lineage in the deep ocean.The ISME journal · 2025Article
- Genome reduction occurred in early Prochlorococcus with an unusually low effective population size.The ISME journal · 2024Article
- Ecophysiology and genomics of the brackish water adapted SAR11 subclade IIIa.The ISME journal · 2023Article
- Isolation and Genomics ofMicrobiology spectrum · 2023Article
- Site-and-branch-heterogeneous analyses of an expanded dataset favour mitochondria as sister to known Alphaproteobacteria.Nature ecology & evolution · 2022Article
- Estimating the Divergence Times of Alphaproteobacteria Based on Mitochondrial Endosymbiosis and Eukaryotic Fossils.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Six-State Amino Acid Recoding is not an Effective Strategy to Offset Compositional Heterogeneity and Saturation in Phylogenetic Analyses.Systematic biology · 2021Article
- Dating Alphaproteobacteria evolution with eukaryotic fossils.Nature communications · 2021Article
- Phosphate-limited ocean regions select for bacterial populations enriched in the carbon-phosphorus lyase pathway for phosphonate degradation.Environmental microbiology · 2019Article
- An updated phylogeny of theeLife · 2019Article
- Insights into origin and evolution of α-proteobacterial gene transfer agents.Virus evolution · 2017Article
- Excess of non-conservative amino acid changes in marine bacterioplankton lineages with reduced genomes.Nature microbiology · 2017Article
- Endosymbiotic calcifying bacteria across sponge species and oceans.Scientific reports · 2017Article
- Article
- Trace Metal Acquisition by Marine Heterotrophic Bacterioplankton with Contrasting Trophic Strategies.Applied and environmental microbiology · 2016Article
- Expansion of Cultured Bacterial Diversity by Large-Scale Dilution-to-Extinction Culturing from a Single Seawater Sample.Microbial ecology · 2016Article
- The use of evolutionary approaches to understand single cell genomes.Frontiers in microbiology · 2015Article
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1 author.
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No grant is acknowledged in the PubMed record.
Abstract
Planktonic bacterial lineages with streamlined genomes are prevalent in the ocean. The base composition of their DNA is often highly biased towards low G+C content, a possible source of systematic error in phylogenetic reconstruction. A total of 228 orthologous protein families were sampled that are shared among major lineages of Alphaproteobacteria, including the marine free-living SAR11 clade and the obligate endosymbiotic Rickettsiales. These two ecologically distinct lineages share genome sizes of <1.5 Mbp and genomic G+C content of <30%. Statistical analyses showed that only 28 protein families are composition-homogeneous, whereas the other 200 families significantly violate the composition-homogeneous assumption included in most phylogenetic methods. RAxML analysis based on the concatenation of 24 ribosomal proteins that fall into the heterogeneous protein category clustered the SAR11 and Rickettsiales lineages at the base of the Alphaproteobacteria tree, whereas that based on the concatenation of 28 homogeneous proteins (including 19 ribosomal proteins) disassociated the lineages and placed SAR11 at the base of the non-endosymbiotic lineages. When the two data sets were concatenated, only a model that accounted for compositional bias yielded a tree identical to the tree built with composition-homogeneous proteins. Ancestral genome analysis suggests that the first evolved SAR11 cell had a small genome streamlined from its ancestor by a factor of two and coinciding with an ecological transition, followed by further gradual streamlining towards the extant SAR11 populations.
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