TRGdb: a Universal Resource For the Exploration Of taxonomically Restricted Genes In bacteria

Overview

Journal Database (Oxford)

Specialty Biology

Date 2023 Aug 9

PMID 37555549

Authors

Andrzej Zielezinski

Wojciech Dobrychlop

Wojciech M Karlowski

Affiliations

Soon will be listed here.

Abstract

The TRGdb database is a resource dedicated to taxonomically restricted genes (TRGs) in bacteria. It provides a comprehensive collection of genes that are specific to different genera and species, according to the latest release of bacterial taxonomy. The user interface allows for easy browsing and searching as well as sequence similarity exploration. The website also provides information on each TRG protein sequence, including its level of disorder, complexity and tendency to aggregate. TRGdb is a valuable resource for gaining a deeper understanding of the TRG-associated, unique features, and characteristics of bacterial organisms. Database URL www.combio.pl/trgdb.

References

Som A . Causes, consequences and solutions of phylogenetic incongruence. Brief Bioinform. 2014; 16(3):536-48. DOI: 10.1093/bib/bbu015. View

Siew N, Fischer D . Unravelling the ORFan Puzzle. Comp Funct Genomics. 2008; 4(4):432-41. PMC: 2447361. DOI: 10.1002/cfg.311. View

Daubin V, Ochman H . Bacterial genomes as new gene homes: the genealogy of ORFans in E. coli. Genome Res. 2004; 14(6):1036-42. PMC: 419781. DOI: 10.1101/gr.2231904. View

Johnson B, Tsutsui N . Taxonomically restricted genes are associated with the evolution of sociality in the honey bee. BMC Genomics. 2011; 12:164. PMC: 3072959. DOI: 10.1186/1471-2164-12-164. View

Chen S, Krinsky B, Long M . New genes as drivers of phenotypic evolution. Nat Rev Genet. 2013; 14(9):645-60. PMC: 4236023. DOI: 10.1038/nrg3521. View

Virtanen P, Gommers R, Oliphant T, Haberland M, Reddy T, Cournapeau D . SciPy 1.0: fundamental algorithms for scientific computing in Python. Nat Methods. 2020; 17(3):261-272. PMC: 7056644. DOI: 10.1038/s41592-019-0686-2. View

Fischer D, Eisenberg D . Finding families for genomic ORFans. Bioinformatics. 1999; 15(9):759-62. DOI: 10.1093/bioinformatics/15.9.759. View

Martinez-Gutierrez C, Aylward F . Phylogenetic Signal, Congruence, and Uncertainty across Bacteria and Archaea. Mol Biol Evol. 2021; 38(12):5514-5527. PMC: 8662615. DOI: 10.1093/molbev/msab254. View

Zile K, Dessimoz C, Wurm Y, Masel J . Only a Single Taxonomically Restricted Gene Family in the Drosophila melanogaster Subgroup Can Be Identified with High Confidence. Genome Biol Evol. 2020; 12(8):1355-1366. PMC: 8059200. DOI: 10.1093/gbe/evaa127. View

10.

Toll-Riera M, Castelo R, Bellora N, Alba M . Evolution of primate orphan proteins. Biochem Soc Trans. 2009; 37(Pt 4):778-82. DOI: 10.1042/BST0370778. View

11.

Fernandez-Escamilla A, Rousseau F, Schymkowitz J, Serrano L . Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins. Nat Biotechnol. 2004; 22(10):1302-6. DOI: 10.1038/nbt1012. View

12.

Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K . BLAST+: architecture and applications. BMC Bioinformatics. 2009; 10:421. PMC: 2803857. DOI: 10.1186/1471-2105-10-421. View

13.

Siew N, Fischer D . Analysis of singleton ORFans in fully sequenced microbial genomes. Proteins. 2003; 53(2):241-51. DOI: 10.1002/prot.10423. View

14.

Prangishvili D, Garrett R, Koonin E . Evolutionary genomics of archaeal viruses: unique viral genomes in the third domain of life. Virus Res. 2006; 117(1):52-67. DOI: 10.1016/j.virusres.2006.01.007. View

15.

Meszaros B, Erdos G, Dosztanyi Z . IUPred2A: context-dependent prediction of protein disorder as a function of redox state and protein binding. Nucleic Acids Res. 2018; 46(W1):W329-W337. PMC: 6030935. DOI: 10.1093/nar/gky384. View

16.

Steinegger M, Soding J . MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nat Biotechnol. 2017; 35(11):1026-1028. DOI: 10.1038/nbt.3988. View

17.

Fukuchi S, Nishikawa K . Estimation of the number of authentic orphan genes in bacterial genomes. DNA Res. 2004; 11(4):219-31, 311-313. View

18.

Sollars E, Harper A, Kelly L, Sambles C, Ramirez-Gonzalez R, Swarbreck D . Genome sequence and genetic diversity of European ash trees. Nature. 2016; 541(7636):212-216. DOI: 10.1038/nature20786. View

19.

Chin K, Ruan S, Wang A, Chou S . XC5848, an ORFan protein from Xanthomonas campestris, adopts a novel variant of Sm-like motif. Proteins. 2007; 68(4):1006-10. DOI: 10.1002/prot.21375. View

20.

Edwards R, Rohwer F . Viral metagenomics. Nat Rev Microbiol. 2005; 3(6):504-10. DOI: 10.1038/nrmicro1163. View