Duplication is more common among laterally transferred genes than among indigenous genes

被引:50
作者
Hooper, SD [1 ]
Berg, OG [1 ]
机构
[1] Uppsala Univ, Dept Mol Evolut, SE-75236 Uppsala, Sweden
关键词
D O I
10.1186/gb-2003-4-8-r48
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
Background: Recent developments in the understanding of paralogous evolution have prompted a focus not only on obviously advantageous genes, but also on genes that can be considered to have a weak or sporadic impact on the survival of the organism. Here we examine the duplicative behavior of a category of genes that can be considered to be mostly transient in the genome, namely laterally transferred genes. Using both a compositional method and a gene-tree approach, we identify a number of proposed laterally transferred genes and study their nucleotide composition and frequency of duplication. Results: It is found that duplications are significantly overrepresented among potential laterally transferred genes compared to the indigenous ones. Furthermore, the GC(3) distribution of potential laterally transferred genes was found to be largely uniform in some genomes, suggesting an import from a broad range of donors. Conclusions: The results are discussed not in a context of strongly optimized established genes, but rather of genes with weak or ancillary functions. The importance of duplication may therefore depend on the variability and availability of weak genes for which novel functions may be discovered. Therefore, lateral transfer may accelerate the evolutionary process of duplication by bringing foreign genes that have mainly weak or no function into the genome.
引用
收藏
页数:9
相关论文
共 35 条
[1]  
ALTSCHUL SF, 1990, J MOL BIOL, V215, P403, DOI 10.1006/jmbi.1990.9999
[2]   Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles [J].
Aravind, L ;
Tatusov, RL ;
Wolf, YI ;
Walker, DR ;
Koonin, EV .
TRENDS IN GENETICS, 1998, 14 (11) :442-444
[3]   Genome and virulence determinants of high virulence community-acquired MRSA [J].
Baba, T ;
Takeuchi, F ;
Kuroda, M ;
Yuzawa, H ;
Aoki, K ;
Oguchi, A ;
Nagai, Y ;
Iwama, N ;
Asano, K ;
Naimi, T ;
Kuroda, H ;
Cui, L ;
Yamamoto, K ;
Hiramatsu, K .
LANCET, 2002, 359 (9320) :1819-1827
[4]   Evolution of microbial genomes: Sequence acquisition and loss [J].
Berg, OG ;
Kurland, CG .
MOLECULAR BIOLOGY AND EVOLUTION, 2002, 19 (12) :2265-2276
[5]   The complete genome sequence of Escherichia coli K-12 [J].
Blattner, FR ;
Plunkett, G ;
Bloch, CA ;
Perna, NT ;
Burland, V ;
Riley, M ;
ColladoVides, J ;
Glasner, JD ;
Rode, CK ;
Mayhew, GF ;
Gregor, J ;
Davis, NW ;
Kirkpatrick, HA ;
Goeden, MA ;
Rose, DJ ;
Mau, B ;
Shao, Y .
SCIENCE, 1997, 277 (5331) :1453-+
[6]   Phylogenetic classification and the universal tree [J].
Doolittle, WF .
SCIENCE, 1999, 284 (5423) :2124-2128
[7]   Horizontal gene transfer in bacterial and archaeal complete genomes [J].
Garcia-Vallvé, S ;
Romeu, A ;
Palau, J .
GENOME RESEARCH, 2000, 10 (11) :1719-1725
[8]   Prokaryotic evolution in light of gene transfer [J].
Gogarten, JP ;
Doolittle, WF ;
Lawrence, JG .
MOLECULAR BIOLOGY AND EVOLUTION, 2002, 19 (12) :2226-2238
[9]   Intragenomic base content variation is a potential source of biases when searching for horizontally transferred genes [J].
Guindon, S ;
Perrière, G .
MOLECULAR BIOLOGY AND EVOLUTION, 2001, 18 (09) :1838-1840
[10]   On the nature of gene innovation: Duplication patterns in microbial genomes [J].
Hooper, SD ;
Berg, OG .
MOLECULAR BIOLOGY AND EVOLUTION, 2003, 20 (06) :945-954