The rarity of gene shuffling in conserved genes

Abstract

Background: Among three sources of evolutionary innovation in gene function - point mutations, gene duplications, and gene shuffling (recombination between dissimilar genes) - gene shuffling is the most potent one. However, surprisingly little is known about its incidence on a genome-wide scale.

Results: We have studied shuffling in genes that are conserved between distantly related species. Specifically, we estimated the incidence of gene shuffling in ten organisms from the three domains of life: eukaryotes, eubacteria, and archaea, considering only genes showing significant sequence similarity in pairwise genome comparisons. We found that successful gene shuffling is very rare among such conserved genes. For example, we could detect only 48 successful gene-shuffling events in the genome of the fruit fly Drosophila melanogaster which have occurred since its common ancestor with the worm Caenorhabditis elegans more than half a billion years ago.

Conclusion: The incidence of gene shuffling is roughly an order of magnitude smaller than the incidence of single-gene duplication in eukaryotes, but it can approach or even exceed the gene-duplication rate in prokaryotes. If true in general, this pattern suggests that gene shuffling may not be a major force in reshaping the core genomes of eukaryotes. Our results also cast doubt on the notion that introns facilitate gene shuffling, both because prokaryotes show an appreciable incidence of gene shuffling despite their lack of introns and because we find no statistical association between exon-intron boundaries and recombined domains in the two multicellular genomes we studied.

Figure 1

Identifying gene shuffling. (a) Gene shuffling and how it changes gene structure. The three scenarios of 'domain insertion' represent insertions of domains from gene 2 into gene 1. The reciprocal insertions (gene 1 into gene 2) are not shown. (b) Distinguishing true from spurious recombination events. In a spurious recombination event, reference genome R1 has two separate genes, where both T and R2 have a single, shuffled gene. The most parsimonious explanation for this observation is that the shuffled gene was present in R1 but was lost since R1's divergence from T.

Figure 2

Representative examples of shuffled genes identified. (a) Bacillus anthracis M23/M37 peptidase BA1903, the result of a domain exchange between B. cereus genes BC5234 (12098), a N-acetylmuramoyl-L-alanine amidase and BC1480(08460.1), another M23/M37 peptidase. (b) A fusion of the fission yeast genes his7 (a phosphoribosyl-AMP cyclohydrolase) and his2 (a histidinol dehydrogenase) to produce the budding yeast his4 gene, which is involved in histidine biosynthesis. The budding yeast gene appears to combine the functions of the two fission yeast genes [35]. (c) The fruit fly gene Aats-tyr is a tyrosyl-tRNA synthetase (Flybase annotation) [36]. It is a probable recombination product of a predicted worm methionyl-tRNA synthetase gene mrs-1 (WormBase annotation) [37] and a second worm gene Y105E8A.19 of unknown function. (d) C. elegans gene ceh-20, which encodes a homeodomain protein. This gene appears to be the result of a domain exchange between the Drosophila genes exd (extradenticle, also a homeodomain protein) and Pkg21D (cGMP-dependant protein kinase). (e) E. coli b4343, a hypothetical protein apparently formed via a domain exchange between Salmonella genes STY4850 (annotated as a DEAD-box helicase-related protein) and STY4851 (hypothetical protein). The numbers in the recombinant gene box are amino-acid positions in the protein product, indicating the portion of the protein derived from each of its 'parental' proteins.

Figure 3

Association between recombined sequence domains and Pfam structural domains. The horizontal axis shows the starting and ending positions of the sequence domains in recombined genes (in amino acids, relative to the translation start site of the gene). The vertical axis shows the starting and ending positions of the Pfam domain closest to each recombined sequence domain.

Figure 4

Incidence of gene shuffling relative to various other mutational events. (a) Gene duplication, (b) silent nucleotide substitutions, and (c) amino-acid changing nucleotide substitutions for the species pairs indicated on the horizontal axis. Note the scale breaks on the vertical axes.

Figure 5

Similarity in sequence divergence between regions of shuffled genes. The amino-acid divergences (K_a) of recombined domains to their respective parental counterparts are correlated. One outlying observation (K_a1 = 3.26 and K_a2 = 0.36) is not shown in this plot but was included in the calculation of correlation coefficients. Excluding this observation increases the Pearson correlation coefficient to 0.61 and leaves the Spearman correlation coefficient unchanged (P < 0.0001 for both).