ATGC: a Database of Orthologous Genes from Closely Related Prokaryotic Genomes and a Research Platform for Microevolution of Prokaryotes

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2008 Oct 11

PMID 18845571

Citations 40

Authors

Pavel S Novichkov

Igor Ratnere

Yuri I Wolf

Eugene V Koonin

Inna Dubchak

Affiliations

Soon will be listed here.

Abstract

The database of Alignable Tight Genomic Clusters (ATGCs) consists of closely related genomes of archaea and bacteria, and is a resource for research into prokaryotic microevolution. Construction of a data set with appropriate characteristics is a major hurdle for this type of studies. With the current rate of genome sequencing, it is difficult to follow the progress of the field and to determine which of the available genome sets meet the requirements of a given research project, in particular, with respect to the minimum and maximum levels of similarity between the included genomes. Additionally, extraction of specific content, such as genomic alignments or families of orthologs, from a selected set of genomes is a complicated and time-consuming process. The database addresses these problems by providing an intuitive and efficient web interface to browse precomputed ATGCs, select appropriate ones and access ATGC-derived data such as multiple alignments of orthologous proteins, matrices of pairwise intergenomic distances based on genome-wide analysis of synonymous and nonsynonymous substitution rates and others. The ATGC database will be regularly updated following new releases of the NCBI RefSeq. The database is hosted by the Genomics Division at Lawrence Berkeley National laboratory and is publicly available at http://atgc.lbl.gov.

Citing Articles

Prophages and plasmids can display opposite trends in the types of accessory genes they carry.

Takeuchi N, Hamada-Zhu S, Suzuki H Proc Biol Sci. 2023; 290(2001):20231088.

PMID: 37339743 PMC: 10281811. DOI: 10.1098/rspb.2023.1088.

HGD: an integrated homologous gene database across multiple species.

Duan G, Wu G, Chen X, Tian D, Li Z, Sun Y Nucleic Acids Res. 2022; 51(D1):D994-D1002.

PMID: 36318261 PMC: 9825607. DOI: 10.1093/nar/gkac970.

SARS-CoV-2-Encoded MiRNAs Inhibit Host Type I Interferon Pathway and Mediate Allelic Differential Expression of Susceptible Gene.

Zhu Y, Zhang Z, Song J, Qian W, Gu X, Yang C Front Immunol. 2022; 12:767726.

PMID: 35003084 PMC: 8733928. DOI: 10.3389/fimmu.2021.767726.

In-depth serum virome analysis in patients with acute liver failure with indeterminate etiology.

Ren Y, Xu Y, Lee W, Di Bisceglie A, Fan X Arch Virol. 2019; 165(1):127-135.

PMID: 31741097 PMC: 6957702. DOI: 10.1007/s00705-019-04466-9.

Strong Purifying Selection Is Associated with Genome Streamlining in Epipelagic Marinimicrobia.

Martinez-Gutierrez C, Aylward F Genome Biol Evol. 2019; 11(10):2887-2894.

PMID: 31539038 PMC: 6798728. DOI: 10.1093/gbe/evz201.

References

Koonin E, Wolf Y . Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world. Nucleic Acids Res. 2008; 36(21):6688-719. PMC: 2588523. DOI: 10.1093/nar/gkn668. View

Darling A, Miklos I, Ragan M . Dynamics of genome rearrangement in bacterial populations. PLoS Genet. 2008; 4(7):e1000128. PMC: 2483231. DOI: 10.1371/journal.pgen.1000128. View

Tatusov R, Natale D, Garkavtsev I, Tatusova T, Shankavaram U, Rao B . The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res. 2000; 29(1):22-8. PMC: 29819. DOI: 10.1093/nar/29.1.22. View

Jordan I, Kondrashov F, Rogozin I, Tatusov R, Wolf Y, Koonin E . Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and eukaryotic proteins. Genome Biol. 2002; 2(12):RESEARCH0053. PMC: 64838. DOI: 10.1186/gb-2001-2-12-research0053. View

Li L, Stoeckert Jr C, Roos D . OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 2003; 13(9):2178-89. PMC: 403725. DOI: 10.1101/gr.1224503. View

Zmasek C, Eddy S . RIO: analyzing proteomes by automated phylogenomics using resampled inference of orthologs. BMC Bioinformatics. 2002; 3:14. PMC: 116988. DOI: 10.1186/1471-2105-3-14. View

Wolf Y, Rogozin I, Grishin N, Tatusov R, Koonin E . Genome trees constructed using five different approaches suggest new major bacterial clades. BMC Evol Biol. 2001; 1:8. PMC: 60490. DOI: 10.1186/1471-2148-1-8. View

Edgar R . MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004; 32(5):1792-7. PMC: 390337. DOI: 10.1093/nar/gkh340. View

Frazer K, Pachter L, Poliakov A, Rubin E, Dubchak I . VISTA: computational tools for comparative genomics. Nucleic Acids Res. 2004; 32(Web Server issue):W273-9. PMC: 441596. DOI: 10.1093/nar/gkh458. View

10.

Edgar R . MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics. 2004; 5:113. PMC: 517706. DOI: 10.1186/1471-2105-5-113. View

11.

Altschul S, Gish W, Miller W, Myers E, Lipman D . Basic local alignment search tool. J Mol Biol. 1990; 215(3):403-10. DOI: 10.1016/S0022-2836(05)80360-2. View

12.

Tatusov R, Koonin E, Lipman D . A genomic perspective on protein families. Science. 1997; 278(5338):631-7. DOI: 10.1126/science.278.5338.631. View

13.

Yang Z . PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci. 1997; 13(5):555-6. DOI: 10.1093/bioinformatics/13.5.555. View

14.

Alm E, Huang K, Price M, Koche R, Keller K, Dubchak I . The MicrobesOnline Web site for comparative genomics. Genome Res. 2005; 15(7):1015-22. PMC: 1172046. DOI: 10.1101/gr.3844805. View

15.

Koonin E . Orthologs, paralogs, and evolutionary genomics. Annu Rev Genet. 2005; 39:309-38. DOI: 10.1146/annurev.genet.39.073003.114725. View

16.

Rocha E, Smith J, Hurst L, Holden M, Cooper J, Smith N . Comparisons of dN/dS are time dependent for closely related bacterial genomes. J Theor Biol. 2005; 239(2):226-35. DOI: 10.1016/j.jtbi.2005.08.037. View

17.

Charlesworth J, Eyre-Walker A . The rate of adaptive evolution in enteric bacteria. Mol Biol Evol. 2006; 23(7):1348-56. DOI: 10.1093/molbev/msk025. View

18.

Mau B, Glasner J, Darling A, Perna N . Genome-wide detection and analysis of homologous recombination among sequenced strains of Escherichia coli. Genome Biol. 2006; 7(5):R44. PMC: 1779527. DOI: 10.1186/gb-2006-7-5-r44. View

19.

DeSantis T, Hugenholtz P, Larsen N, Rojas M, Brodie E, Keller K . Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol. 2006; 72(7):5069-72. PMC: 1489311. DOI: 10.1128/AEM.03006-05. View

20.

Fulton D, Li Y, Laird M, Horsman B, Roche F, Brinkman F . Improving the specificity of high-throughput ortholog prediction. BMC Bioinformatics. 2006; 7:270. PMC: 1524997. DOI: 10.1186/1471-2105-7-270. View