Horizontal Gene Transfer in Bacterial and Archaeal Complete Genomes

Garcı́a-Vallvé, Santiago; Romeu, Anton; Palau, Jaume

doi:10.1101/gr.130000

Cited by 327 publications

(244 citation statements)

References 39 publications

Supporting

Mentioning

228

Contrasting

Unclassified

Order By: Relevance

“…0.01, using Spearman test). This estimate for the fraction of foreign genes per genome is consistent with other studies using similar methods (Garcia-Vallve et al 2000;Nakamura et al 2004).…”

Section: A Directed Network Of Recent Lgtsupporting

confidence: 81%

“…Therefore, GC content may be used to detect the foreign origin of a gene (Garcia-Vallve et al 2000;Nakamura et al 2004). The statistical analysis of GC content is favored over codon usage because it is more statistically robust due to the smaller relative standard errors of the estimates resulting from a larger sample size (nucleotides vs. codons) and smaller number of states (two vs. 61).…”

Section: Identification Of Recently Acquired Genesmentioning

confidence: 99%

“…In the case of prokaryote genome sequence data, the LGT donor-recipient relationships are not known a priori, but they can be estimated for recently acquired DNA sequences through analyses of codon bias, GC content, and nucleotide pattern frequencies (Garcia-Vallve et al 2000;Nakamura et al 2004). …”

mentioning

confidence: 99%

See 2 more Smart Citations

Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes

Popa

Hazkani‐Covo²,

Landan³

et al. 2011

Genome Res.

227

204

View full text Add to dashboard Cite

Lateral gene transfer (LGT) plays a major role in prokaryote evolution with only a few genes that are resistant to it; yet the nature and magnitude of barriers to lateral transfer are still debated. Here, we implement directed networks to investigate donor-recipient events of recent lateral gene transfer among 657 sequenced prokaryote genomes. For 2,129,548 genes investigated, we detected 446,854 recent lateral gene transfer events through nucleotide pattern analysis. Among these, donor-recipient relationships could be specified through phylogenetic reconstruction for 7% of the pairs, yielding 32,028 polarized recent gene acquisition events, which constitute the edges of our directed networks. We find that the frequency of recent LGT is linearly correlated both with genome sequence similarity and with proteome similarity of donor-recipient pairs. Genome sequence similarity accounts for 25% of the variation in gene-transfer frequency, with proteome similarity adding only 1% to the variability explained. The range of donor-recipient GC content similarity within the network is extremely narrow, with 86% of the LGTs occurring between donor-recipient pairs having #5% difference in GC content. Hence, genome sequence similarity and GC content similarity are strong barriers to LGT in prokaryotes. But they are not insurmountable, as we detected 1530 recent transfers between distantly related genomes. The directed network revealed that recipient genomes of distant transfers encode proteins of nonhomologous end-joining (NHEJ; a DNA repair mechanism) far more frequently than the recipient lacking that mechanism. This implicates NHEJ in genes spread across distantly related prokaryotes through bypassing the donor-recipient sequence similarity barrier.

show abstract

Section: A Directed Network Of Recent Lgtsupporting

confidence: 81%

Section: Identification Of Recently Acquired Genesmentioning

confidence: 99%

See 1 more Smart Citation

Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes

Popa

Hazkani‐Covo²,

Landan³

et al. 2011

Genome Res.

227

204

View full text Add to dashboard Cite

show abstract

“…In support of our results, the ‘ quinone oxidoreductase ’ (PSNMU‐V1.4_AUG‐EV‐PASAV3_0025570.1) was already known to be derived from HGT in diatoms (Nosenko & Bhattacharya, 2007). In addition, a significant difference ( t ‐test, P = 0.014) in the GC content for HGT genes compared with all P. multistriata genes supports their foreign origin (Garcia‐Vallvé et al ., 2000) (Fig. S9).…”

Section: Resultsmentioning

confidence: 99%

Finding a partner in the ocean: molecular and evolutionary bases of the response to sexual cues in a planktonic diatom

et al. 2017

View full text Add to dashboard Cite

Summary Microalgae play a major role as primary producers in aquatic ecosystems. Cell signalling regulates their interactions with the environment and other organisms, yet this process in phytoplankton is poorly defined. Using the marine planktonic diatom Pseudo‐nitzschia multistriata, we investigated the cell response to cues released during sexual reproduction, an event that demands strong regulatory mechanisms and impacts on population dynamics.We sequenced the genome of P. multistriata and performed phylogenomic and transcriptomic analyses, which allowed the definition of gene gains and losses, horizontal gene transfers, conservation and evolutionary rate of sex‐related genes. We also identified a small number of conserved noncoding elements.Sexual reproduction impacted on cell cycle progression and induced an asymmetric response of the opposite mating types. G protein‐coupled receptors and cyclic guanosine monophosphate (cGMP) are implicated in the response to sexual cues, which overall entails a modulation of cell cycle, meiosis‐related and nutrient transporter genes, suggesting a fine control of nutrient uptake even under nutrient‐replete conditions.The controllable life cycle and the genome sequence of P. multistriata allow the reconstruction of changes occurring in diatoms in a key phase of their life cycle, providing hints on the evolution and putative function of their genes and empowering studies on sexual reproduction.

show abstract

“…Usually, hydrophobic interactions have been detected to occur between amino acids that have a polar side-chain. These amino acids mostly have T and C at their second codon position (such as Phe, Leu, Ile, Val, Pro and Ala; García 2005), which corresponds to the base composition pattern of B. cenocepacia . Furthermore, protein hydrophobicity has ever been considered to be associated with the transport and binding function, such as bidirectional cholesterol transfer (Cheruku et al 2006), anchoring to membranes (Ferrante and Gorski 2007) and controlling the stop-transfer function (Barré et al 2005).…”

Section: Discussionmentioning

confidence: 99%

Analysis of genomic characters reveals that four distinct gene clusters are correlated with different functions in Burkholderia cenocepacia AU 1054

Yuan

Yang

Ren

et al. 2013

Appl Microbiol Biotechnol

View full text Add to dashboard Cite

Possessing three circular chromosomes is a distinct genomic characteristic of Burkholderia cenocepacia AU 1054, a clinically important pathogen in cystic fibrosis. In this study, base composition, codon usage and functional role category were analyzed in the B. cenocepacia AU 1054 genome. Although no bias in the base and codon usage was detected between any two chromosomes, function differences did exist in the genes of each chromosome. Similar base composition and differential functional role categories indicated that genes on these three chromosomes were relatively stable and that a proper division of labor was established. Based on variations in the base or codon usage, four small gene clusters were observed in all of the genes. Multivariate analysis revealed that protein hydrophobicity played a predominant role in shaping base usage bias, while horizontal gene transfer and the gene expression level were the two most important factors that affected the codon usage bias. Interestingly, we also found that these gene clusters were correlated with different biological functions: (i) 45 pyrimidine-leadingcodon preferred genes were predominantly involved in regulatory function; (ii) most drug resistance-related genes involved in 826 genes that coding for hydrophobic proteins; (iii) most of the 111 horizontal transfer genes were responsible for genomic plasticity; and (iv) 73 highly expressed genes (predicted by their codon adaptation index values) showed environmental adaptation to cystic fibrosis. Our results showed that genes with base or codon usage bias were affected by mutational pressure and natural selection, and their functions could contribute to drug assistance and transmissible activity in B. cenocepacia.

show abstract

Horizontal Gene Transfer in Bacterial and Archaeal Complete Genomes

Cited by 327 publications

References 39 publications

Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes

Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes

Finding a partner in the ocean: molecular and evolutionary bases of the response to sexual cues in a planktonic diatom

Analysis of genomic characters reveals that four distinct gene clusters are correlated with different functions in Burkholderia cenocepacia AU 1054

Contact Info

Product

Resources

About