Widespread of horizontal gene transfer in the human genome

BMC Genomics

Volumn 18, Issue 1, 2017, Pages

  Huang, Wenze ^a   Tsai, Lillian ^b   Li, Yulong ^a   Hua, Nan ^a,c   Sun, Chen ^a,c   Wei, Chaochun ^a,c  

^a SHANGHAI JIAO TONG UNIVERSITY   (China)

^b HARVARD COLLEGE   (United States)

^c SHANGHAI CENTER FOR BIOINFORMATION TECHNOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BINDING AND RELATED PHENOMENA; CHROMATIN; CHROMOSOME; DNA BASE COMPOSITION; GENETIC ANALYSIS; HISTONE MODIFICATION; HOMOLOGOUS SEQUENCE; HORIZONTAL GENE TRANSFER; HUMAN; HUMAN GENOME; ION BINDING; LONG INTERSPERSED REPEAT; LONG TERMINAL REPEAT; NONHUMAN; PHYLOGENETIC TREE; PREDICTION; SEQUENCE ANALYSIS; SHORT INTERSPERSED REPEAT; VERTEBRATE; BIOLOGY; DNA SEQUENCE; GENETICS; HUMAN CHROMOSOME; MOLECULAR EVOLUTION; PHYLOGENY;

BASE COMPOSITION; CHROMOSOMES, HUMAN; COMPUTATIONAL BIOLOGY; EVOLUTION, MOLECULAR; GENE TRANSFER, HORIZONTAL; GENOME, HUMAN; HUMANS; PHYLOGENY; SEQUENCE ANALYSIS, DNA;

EID: 85016985108     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/s12864-017-3649-y     Document Type: Article

References (31)

1. Freeman VJ. Studies on the virulence of bacteriophage-infected strains of Corynebacterium diphtheriae. Journal of bacteriology. 1951;61(6):675-88.
2. Syvanen M. Cross-species gene transfer; implications for a new theory of evolution. Journal of theoretical biology. 1985;112(2):333-43.
3. Jain R, Rivera MC, Lake JA. Horizontal gene transfer among genomes: the complexity hypothesis. Proceedings of the National Academy of Sciences of the United States of America. 1999;96(7):3801-6.
4. Barlow M. What antimicrobial resistance has taught us about horizontal gene transfer. Methods in molecular biology. 2009;532:397-411.
5. Gyles C, Boerlin P. Horizontally transferred genetic elements and their role in pathogenesis of bacterial disease. Veterinary pathology. 2014;51(2):328-40.
6. Rossi F, Rizzotti L, Felis GE, Torriani S. Horizontal gene transfer among microorganisms in food: current knowledge and future perspectives. Food microbiology. 2014;42:232-43.
7. Chan CX, Bhattacharya D, Reyes-Prieto A. Endosymbiotic and horizontal gene transfer in microbial eukaryotes: Impacts on cell evolution and the tree of life. Mobile genetic elements. 2012;2(2):101-5.
8. Keeling PJ. Role of horizontal gene transfer in the evolution of photosynthetic eukaryotes and their plastids. Methods in molecular biology. 2009;532:501-15.
9. Pace 2nd JK, Gilbert C, Clark MS, Feschotte C. Repeated horizontal transfer of a DNA transposon in mammals and other tetrapods. Proceedings of the National Academy of Sciences of the United States of America. 2008;105(44):17023-8.
10. Crisp A, Boschetti C, Perry M, Tunnacliffe A, Micklem G. Expression of multiple horizontally acquired genes is a hallmark of both vertebrate and invertebrate genomes. Genome biology. 2015;16:50.
11. Gilbert C, Cordaux R. Horizontal transfer and evolution of prokaryote transposable elements in eukaryotes. Genome biology and evolution. 2013;5(5):822-32.
12. El Baidouri M, Carpentier MC, Cooke R, Gao D, Lasserre E, Llauro C, Mirouze M, Picault N, Jackson SA, Panaud O. Widespread and frequent horizontal transfers of transposable elements in plants. Genome research. 2014;24(5):831-8.
13. Walsh AM, Kortschak RD, Gardner MG, Bertozzi T, Adelson DL. Widespread horizontal transfer of retrotransposons. Proceedings of the National Academy of Sciences of the United States of America. 2013;110(3):1012-6.
14. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, et al. Initial sequencing and analysis of the human genome. Nature. 2001;409(6822):860-921.
15. Ernst J, Kellis M. Discovery and characterization of chromatin states for systematic annotation of the human genome. Nature biotechnology. 2010;28(8):817-25.
16. Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, Epstein CB, Zhang X, Wang L, Issner R, Coyne M, et al. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature. 2011;473(7345):43-9.
17. Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proceedings of the National Academy of Sciences of the United States of America. 2003;100(20):11484-9.
18. Karolchik D, Barber GP, Casper J, Clawson H, Cline MS, Diekhans M, Dreszer TR, Fujita PA, Guruvadoo L, Haeussler M, et al. The UCSC Genome Browser database: 2014 update. Nucleic acids research. 2014;42(Database issue):D764-770.
19. Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pacific Symposium on Biocomputing Pacific Symposium on Biocomputing. 2002;7:115-26.
20. Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome research. 2003;13(1):103-7.
21. Flicek P, Amode MR, Barrell D, Beal K, Billis K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fitzgerald S, et al. Ensembl 2014. Nucleic acids research. 2014;42(Database issue):D749-755.
22. da Huang W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature protocols. 2009;4(1):44-57.
23. da Huang W, Sherman BT, Lempicki RA. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic acids research. 2009;37(1):1-13.
24. Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K. High-resolution profiling of histone methylations in the human genome. Cell. 2007;129(4):823-37.
25. Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF, Roskin KM, Baertsch R, Rosenbloom K, Clawson H, Green ED, et al. Aligning multiple genomic sequences with the threaded blockset aligner. Genome research. 2004;14(4):708-15.
26. Murphy WJ, Eizirik E, O'Brien SJ, Madsen O, Scally M, Douady CJ, Teeling E, Ryder OA, Stanhope MJ, de Jong WW, et al. Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science. 2001;294(5550):2348-51.
27. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Molecular biology and evolution. 2013;30(12):2725-9.
28. Hill T, Nordstrom KJ, Thollesson M, Safstrom TM, Vernersson AK, Fredriksson R, Schioth HB. SPRIT: Identifying horizontal gene transfer in rooted phylogenetic trees. BMC evolutionary biology. 2010;10:42.
29. Brant SV, Loker ES. Can specialized pathogens colonize distantly related hosts? Schistosome evolution as a case study. PLoS pathogens. 2005;1(3):167-9.
30. Schaack S, Gilbert C, Feschotte C. Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution. Trends in ecology & evolution. 2010;25(9):537-46.
31. Schistosoma japonicum Genome S, Functional Analysis C: The Schistosoma japonicum genome reveals features of host-parasite interplay. Nature 2009, 460(7253):345-351.