Genome-wide analyses of recombination suggest that giardia intestinalis assemblages represent different species

Molecular Biology and Evolution

Volumn 29, Issue 10, 2012, Pages 2895-2898

  Xu, Feifei ^a   Jerlström Hultqvist, Jon ^a   Andersson, Jan O ^a  

^a UPPSALA UNIVERSITY   (Sweden)

Author keywords

diplomonads; protists; sex; substitution rate

Indexed keywords

AMINO ACID SUBSTITUTION; ARTICLE; GENE CONVERSION; GENETIC ASSOCIATION; GENETIC ISOLATION BY DISTANCE; GIARDIA LAMBLIA; NONHUMAN; PHYLOGENY; RECOMBINATION REPAIR;

BASE PAIRING; GENOME; GIARDIA LAMBLIA; RECOMBINATION, GENETIC; SEQUENCE HOMOLOGY, NUCLEIC ACID; SPECIES SPECIFICITY;

DIPLOMONADIDA; GIARDIA; GIARDIA INTESTINALIS; PROTISTA;

EID: 84865966881     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/mss107     Document Type: Article

References (25)

1. Andersson JO. 2012. Double peaks reveal rare diplomonad sex. Trends Parasitol. 28:46-52.
2. Birky CW Jr. 2010. Giardia sex? Yes, but how and how much? Trends Parasitol. 26:70-74.
3. Bruen TC, Philippe H, Bryant D. 2006. A simple and robust statistical test for detecting the presence of recombination. Genetics 172:2665-2681.
4. Caccio SM, Ryan U. 2008. Molecular epidemiology of giardiasis. Mol Biochem Parasitol. 160:75-80.
5. Cooper MA, Adam RD, Worobey M, Sterling CR. 2007. Population genetics provides evidence for recombination in Giardia. Curr Biol. 17:1984-1988. (Pubitemid 350088486)
6. de Queiroz K. 2007. Species concepts and species delimitation. Syst Biol. 56:879-886. (Pubitemid 350129638)
7. Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32: 1792-1797. (Pubitemid 38832724)
8. Franzén O, Jerlström-Hultqvist J, Castro E, Sherwood E, Ankarklev J, Reiner D, Palm D, Andersson JO, Andersson B, Svärd S. 2009. Draft genome sequencing of Giardia intestinalis assemblage B isolate GS: are human giardiasis caused by two different species? PLoS Pathog. 5(8):e1000560.
9. Guy L, Kultima JR, Andersson SGE. 2010. genoPlotR: comparative gene and genome visualization in R. Bioinformatics 26: 2334-2335.
10. Hao W. 2010. OrgConv: detection of gene conversion using consensus sequences and its application in plant mitochondrial and chloroplast homologs. BMC Bioinformatics 11:114.
11. Jerlström-Hultqvist J, Franzén O, Ankarklev J, Xu F, Nohynkova E, Andersson JO, Svärd SG, Andersson B. 2010. Genome analysis and comparative genomics of a Giardia intestinalis assemblage E isolate. BMC Genomics 11:543.
12. Klasson L, Westberg J, Sapountzis P, et al. (12 co-authors). 2009. The mosaic genome structure of the Wolbachia wRi strain infecting Drosophila simulans. Proc Natl Acad Sci USA. 106:5725-5730.
13. Lasek-Nesselquist E, Welch DM, Thompson RC, Steuart RF, Sogin ML. 2009. Genetic exchange within and between assemblages of Giardia duodenalis. J Eukaryot Microbiol. 56:504-518.
14. Logsdon JM Jr. 2008. Evolutionary genetics: sex happens in Giardia. Curr Biol. 18:R66-R68.
15. Martin D, Rybicki E. 2000. RDP: detection of recombination amongst aligned sequences. Bioinformatics 16:562-563.
16. Monis PT, Caccio SM, Thompson RC. 2009. Variation in Giardia: towards a taxonomic revision of the genus. Trends Parasitol. 25:93-100.
17. Morrison HG, McArthur AG, Gillin FD, et al. (29 co-authors). 2007. Genomic minimalism in the early diverging intestinal parasite Giardia lamblia. Science 317:1921-1926. (Pubitemid 47509437)
18. Posada D. 2002. Evaluation of methods for detecting recombination from DNA sequences: empirical data. Mol Biol Evol. 19:708-717. (Pubitemid 34521302)
19. Posada D, Crandall KA. 2001. Evaluation of methods for detecting recombination from DNA sequences: computer simulations. Proc Natl Acad Sci USA. 98:13757-13762. (Pubitemid 33115971)
20. Ramesh MA, Malik SB, Logsdon JM Jr. 2005. A phylogenomic inventory of meiotic genes; evidence for sex in Giardia and an early eukaryotic origin of meiosis. Curr Biol. 15:185-191.
21. Sawyer S. 1989. Statistical tests for detecting gene conversion. Mol Biol Evol. 6:526-538. (Pubitemid 19210235)
22. Smith JM. 1992. Analyzing the mosaic structure of genes. J Mol Evol. 34:126-129.
23. Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688-2690. (Pubitemid 44642609)
24. Teodorovic S, Braverman JM, Elmendorf HG. 2007. Unusually low levels of genetic variation among Giardia lamblia isolates. Eukaryot Cell. 6:1421-1430. (Pubitemid 47257711)
25. Yang Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci. 13:555-556. (Pubitemid 27480216)