Rapidly evolving genes in pathogens: Methods for detecting positive selection and examples among fungi, bacteria, viruses and protists Discussion

被引:89
作者
Aguileta, Gabriela [1 ,2 ]
Refregier, Guislaine [1 ,2 ]
Yockteng, Roxana [3 ]
Fournier, Elisabeth [4 ]
Giraud, Tatiana [1 ,2 ]
机构
[1] Univ Paris 11, F-91405 Orsay, France
[2] CNRS, F-91405 Orsay, France
[3] CNRS, MNHN, UMR 7205, Dept Syst & Evolut, F-75005 Paris, France
[4] BGPI, UMR, TA A 54K, F-34398 Montpellier 5, France
关键词
Avirulence genes; Toxins; Antigens; Effector; Elicitor; Resistance genes; Polymorphism; Genomic scan; Gene-for-gene; Parasite; Plasmodium; AMINO-ACID SITES; MAJOR-HISTOCOMPATIBILITY-COMPLEX; EPISODIC ADAPTIVE EVOLUTION; ANCESTRAL POPULATION SIZES; CODON-SUBSTITUTION MODELS; MCDONALD-KREITMAN TEST; NATURAL-SELECTION; DIVERSIFYING SELECTION; NUCLEOTIDE SUBSTITUTION; MOLECULAR EVOLUTION;
D O I
10.1016/j.meegid.2009.03.010
中图分类号
R51 [传染病];
学科分类号
100401 ;
摘要
The ongoing coevolutionary struggle between hosts and pathogens, with hosts evolving to escape pathogen infection and pathogens evolving to escape host defences, can generate an 'arm srace', i.e. the, occurrence of recurrent selective sweeps that each favours a novel resistance or virulence allele that goes to fixation. Host-pathogen coevolution can alternatively lead to a 'trench warfare', i.e., balancing selection, maintaining certain alleles at loci involved in host-pathogen recognition over long time scales. Recently, technological and methodological progress has enabled detection of footprints of selection directly on genes, which can provide useful insights into the processes of coevolution. This knowledge can also have practical applications, for instance development of vaccines or drugs. Here we review the methods for detecting genes under positive selection using divergence data (i.e., the ratio of nonsynonymous to synonymous substitution rates, d(N)/d(S)). We also review methods for detecting selection using polymorphisms, such as methods based on F-ST measures, frequency spectrum, linkage disequilibrium and haplotype structure. In the second part, we review examples where targets of selection have been identified in pathogens using these tests. Genes under positive selection in pathogens have mostly been sought among viruses, bacteria and protists, because of their paramount importance for human health. Another focus is on fungal pathogens owing to their agronomic importance. We finally discuss promising directions in pathogen studies, such as detecting selection in non-coding regions. (C) 2009 Elsevier B.V. All rights reserved.
引用
收藏
页码:656 / 670
页数:15
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