Pangenome evidence for extensive interdomain horizontal transfer affecting lineage coreandshell genes inuncultured planktonic thaumarchaeota and euryarchaeota

Genome Biology and Evolution

Volumn 6, Issue 7, 2014, Pages 1549-1563

  Deschamps, Philippe ^a   Zivanovic, Yvan ^a   Moreira, David ^a   Rodriguez Valera, Francisco ^b   Lopez García, Purificación ^a  

^a CNRS   (France)

^b MIGUEL HERNÁNDEZ UNIVERSITY   (Spain)

Author keywords

Ammonia oxidizing archaea; Euryarchaeota; Horizontal gene transfer; Thaumarchaeota; Uncultured archaea

Indexed keywords

ARCHAEON; EURYARCHAEOTA; GENE LIBRARY; GENETICS; GENOME; HORIZONTAL GENE TRANSFER; MOLECULAR EVOLUTION; PHYLOGENY;

ARCHAEA; EURYARCHAEOTA; EVOLUTION, MOLECULAR; GENE TRANSFER, HORIZONTAL; GENOME; GENOMIC LIBRARY; PHYLOGENY;

EID: 84926123404     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evu127     Document Type: Article

References (57)

1. Abby SS, Tannier E, Gouy M, Daubin V (2012) Lateral gene transfer as a support for the tree of life. Proc Natl Acad Sci U S A (109: 4962-4967.
2. Alonso-Saez L, et al (2012) Role for urea in nitrification by polar marine Archaea. Proc Natl Acad Sci U S A (109: 17989-17994.
3. Altschul SF, et al (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25: 3389-3402.
4. Baker BJ, et al (2013) Community transcriptomic assembly reveals microbes that contribute to deep-sea carbon and nitrogen cycling. ISME J. 7: 1962-1973.
5. Baltrus DA (2013) Exploring the costs of horizontal gene transfer. Trends Ecol Evol. 28: 489-495.
6. Bano N, Ruffin S, Ransom B, Hollibaugh JT (2004) Phylogenetic composition of Arctic Ocean archaeal assemblages and comparison with Antarctic assemblages. Appl Environ Microbiol. 70: 781-789.
7. Blainey PC, Mosier AC, Potanina A, Francis CA, Quake SR (2011) Genome of a low-salinity ammonia-oxidizing archaeon determined by singlecell and metagenomic analysis. PLoS One 6: e16626.
8. Brochier-Armanet C, Boussau B, Gribaldo S, Forterre P (2008) Mesophilic Crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota. Nat Rev Microbiol. 6: 245-252.
9. Brochier-Armanet C, et al (2011) Complete-fosmid and fosmid-end sequences reveal frequent horizontal gene transfers in marine uncultured planktonic archaea. ISME J. 5: 1291-1302.
10. Creevey CJ, Doerks T, Fitzpatrick DA, Raes J, Bork P (2011) Universally distributed single-copy genes indicate a constant rate of horizontal transfer. PLoS One 6: e22099.
11. Criscuolo A, Gribaldo S (2010) BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments. BMC Evol Biol. 10: 210.
12. de la Torre JR, Walker CB, Ingalls AE, Konneke M, Stahl DA (2008) Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol. Environ Microbiol. 10: 810-818.
13. DeLong EF (1992) Archaea in coastal marine environments. Proc Natl Acad Sci U S A. 89: 5685-5689.
14. DeLong EF, et al (2006) Community genomics among stratified microbial assemblages in the ocean's interior. Science 311: 496-503.
15. Eisen JA (1998) Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis. Genome Res. 8: 163-167.
16. Frigaard NU, Martinez A, Mincer TJ, DeLong EF (2006) Proteorhodopsin lateral gene transfer between marine planktonic Bacteria and Archaea. Nature 439: 847-850.
17. Fuhrman JA, Davis AA (1997) Widespread Archaea and novel Bacteria from the deep sea as shown by 16S rRNA gene sequences. Mar Ecol Prog Ser. 150: 275-285.
18. Fuhrman JA, McCallum K, Davis AA (1992) Novel major archaebacterial group from marine plankton. Nature 356: 148-149.
19. Garcia-Vallve S, Palau J, Romeu A (1999) Horizontal gene transfer in glycosyl hydrolases inferred from codon usage in Escherichia coli and Bacillus subtilis. Mol Biol Evol. 16: 1125-1134.
20. Ghai R, et al (2010) Metagenome of the Mediterranean deep chlorophyll maximum studied by direct and fosmid library 454 pyrosequencing. ISME J. 4: 1154-1166.
21. Gogarten JP, Doolittle WF, Lawrence JG (2002) Prokaryotic evolution in light of gene transfer. Mol Biol Evol. 19: 2226-2238.
22. Gophna U, Ofran Y (2011) Lateral acquisition of genes is affected by the friendliness of their products. Proc Natl Acad Sci U S A (108: 343-348.
23. Heyer LJ, Kruglyak S, Yooseph S (1999) Exploring expression data: identification and analysis of coexpressed genes. Genome Res. 9: 1106-1115.
24. Huang Y, Gilna P, Li W (2009) Identification of ribosomal RNA genes in metagenomic fragments. Bioinformatics 25: 1338-1340.
25. Hyatt D, et al (2010) Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11: 119.
26. Isambert H, Stein RR (2009) On the need for widespread horizontal gene transfers under genome size constraint. Biol Direct. 4: 28.
27. Iverson V, et al (2012) Untangling genomes from metagenomes: revealing an uncultured class of marine Euryarchaeota. Science 335: 587-590.
28. Kanhere A, Vingron M (2009) Horizontal gene transfers in prokaryotes show differential preferences for metabolic and translational genes. BMC Evol Biol. 9: 9.
29. Karner MB, DeLong EF, Karl DM (2001) Archaeal dominance in the mesopelagic zone of the Pacific Ocean. Nature 409: 507-510.
30. Katoh K, Kuma K, Toh H, Miyata T (2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 33: 511-518.
31. Konneke M, et al (2005) Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437: 543-546.
32. Koski LB, Golding GB (2001) The closest BLAST hit is often not the nearest neighbor. J Mol Evol. 52: 540-542.
33. Leininger S, et al (2006) Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 442: 806-809.
34. López-García P, Brochier C, Moreira D, Rodríguez- Valera F (2004) Comparative analysis of a genome fragment of an uncultivated mesopelagic crenarchaeote reveals multiple horizontal gene transfers. Environ Microbiol. 6: 19-34.
35. López-García P, Moreira D, López-López A, Rodríguez-Valera F (2001) A novel haloarchaeal-related lineage iswidely distributed in deep oceanic regions. Environ Microbiol. 3: 72-78.
36. Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25: 955-964.
37. Marchler-Bauer A, et al (2005) CDD: a conserved domain database for protein classification. Nucleic Acids Res. 33: D192-D196.
38. Martin-Cuadrado AB, et al (2007) Metagenomics of the deep Mediterranean, a warm bathypelagic habitat. PLoS One 2: e914.
39. Martin-Cuadrado AB, et al (2008) Hindsight in the relative abundance, metabolic potential and genome dynamics of uncultivated marine archaea from comparativemetagenomic analyses of bathypelagic plankton of different oceanic regions. ISME J (2: 865-886.
40. Moreira D, Rodriguez-Valera F, Lopez-Garcia P (2004) Analysis of a genome fragment of a deep-sea uncultivated Group II euryarchaeote containing 16S rDNA, a spectinomycin-like operon and several energy metabolism genes. Environ Microbiol. 6: 959-969.
41. Nelson-Sathi S, et al (2012) Acquisition of 1,000 eubacterial genes physiologically transformed a methanogen at the origin of Haloarchaea. Proc Natl Acad Sci U S A (109: 20537-20542.
42. Nicol GW, Schleper C (2006) Ammonia-oxidising Crenarchaeota: important players in the nitrogen cycle? Trends Microbiol. 14: 207-212.
43. Ochman H, Lawrence JG, Groisman EA (2000) Lateral gene transfer and the nature of bacterial innovation. Nature 405: 299-304.
44. Pester M, Schleper C, Wagner M (2011) The Thaumarchaeota: an emerging view of their phylogeny and ecophysiology. Curr Opin Microbiol. 14: 300-306.Price MN, Dehal PS, Arkin AP (2009) FastTree: computing large minimum evolution trees with profiles instead of a distancematrix.Mol Biol Evol. 26: 1641-1650.
45. Price MN, Dehal PS, Arkin AP (2009) FastTree: computing large minimum evolution trees with profiles instead of a distancematrix.Mol Biol Evol. 26: 1641-1650.
46. Ragon M, Van Driessche AE, Garcia-Ruiz JM, Moreira D, Lopez-Garcia P (2013) Microbial diversity in the deep-subsurface hydrothermal aquifer feeding the giant gypsum crystal-bearing Naica Mine, Mexico. Front Microbiol. 4: 37.
47. Raychaudhuri S, Stuart JM, Altman RB (2000) Principal components analysis to summarize microarray experiments: application to sporulation time series. Pac Symp Biocomput. 455-466.
48. Rice P, Longden I, Bleasby A (2000) EMBOSS: The European molecular biology open software suite. Trends Genet. 16: 276-277.
49. Rinke C, et al (2013) Insights into the phylogeny and coding potential of microbial dark matter. Nature 499: 431-437.
50. Saeed AI, et al (2003) TM4: a free, open-source system formicroarray data management and analysis. Biotechniques 34: 374-378.
51. Schleper C, Jurgens G, Jonuscheit M (2005) Genomic studies of uncultivated archaea. Nat Rev Microbiol. 3: 479-488.
52. Spang A, et al (2012) The genome of the ammonia-oxidizing Candidatus Nitrososphaera gargensis: insights into metabolic versatility and environmental adaptations. Environ Microbiol. 14: 3122-3145.
53. Teeling H, Meyerdierks A, Bauer M, Amann R, Glockner FO (2004. Application of tetranucleotide frequencies for the assignment of genomic fragments. Environ Microbiol. 6: 938-947.
54. Teeling H, Waldmann J, Lombardot T, Bauer M, Glockner FO (2004) TETRA: a web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences. BMC Bioinformatics 5: 163.
55. Treangen TJ, Rocha EP (2011) Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes. PLoS Genet. 7: e1001284.
56. Walker CB, et al (2010) Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea. Proc Natl Acad Sci U S A (107: 8818-8823.
57. Wolf YI, Makarova KS, Yutin N, Koonin EV (2012) Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer. Biol Direct. 7: 46.