Reductive genome evolution in Buchnera aphidicola

Abstract

We have sequenced the genome of the intracellular symbiont Buchnera aphidicola from the aphid Baizongia pistacea. This strain diverged 80-150 million years ago from the common ancestor of two previously sequenced Buchnera strains. Here, a field-collected, nonclonal sample of insects was used as source material for laboratory procedures. As a consequence, the genome assembly unveiled intrapopulational variation, consisting of approximately 1,200 polymorphic sites. Comparison of the 618-kb (kbp) genome with the two other Buchnera genomes revealed a nearly perfect gene-order conservation, indicating that the onset of genomic stasis coincided closely with establishment of the symbiosis with aphids, approximately 200 million years ago. Extensive genome reduction also predates the synchronous diversification of Buchnera and its host; but, at a slower rate, gene loss continues among the extant lineages. A computational study of protein folding predicts that proteins in Buchnera, as well as proteins of other intracellular bacteria, are generally characterized by smaller folding efficiency compared with proteins of free living bacteria. These and other degenerative genomic features are discussed in light of compensatory processes and theoretical predictions on the long-term evolutionary fate of symbionts like Buchnera.

Figure 1

Comparison of the linearized Buchnera genomes from B. pistaciae, A. pisum, and S. graminum. Nucleotide numbering, marked in 100 kb, starts from the respective origins of replication. Genes above and below lines are transcribed from forward and reverse strands, respectively. Blue, genes present in all genomes; black, RNAs; light green, pseudogenes; pink, inversions; orange, genes unique among the three genomes; red, genes absent only in BBp; dark green, genes absent only in BAp; violet, genes absent only in BSg; yellow, genes chromosomally encoded in BBp and plasmid encoded in BAp and BSg. Hatched lines highlight the inversions in BBp. A map of the 2.4-kb plasmid of BBp is presented in Fig. 5.

Figure 2

Numerical comparison of the gene content of Buchnera BBp, BAp, and BSg genomes. Solid boxes, genes present; hatched boxes, pseudogenes; open boxes, genes absent. Asterisked numbers denote genes that were putatively lost or inactivated in parallel in independent lineages. Arrows indicate estimated divergence times (5).

Figure 3

Relation between number of events of gene loss and pseudogene formation from the LCSA genome and genomic position of affected genes. The 635 chromosomally encoded genes of the reconstructed LCSA genome were numbered from the putative origin of replication onwards and arranged into 13 bins of ≈50 genes. Green bars represent total numbers per bin of deletion events from all three Buchnera genomes. Yellow bars represent total numbers per bin of pseudogene formation.

Figure 4

Relation between average protein stability parameter α for 11 proteins in 40 bacterial species and their average sequence similarity to the reference structure of each protein. Bacterial lifestyles are indicated as follows: black dots, free-living bacteria and facultative pathogens; red triangles, obligate parasites; blue squares, Buchnera strains (see Materials and Methods for protein families and species included).