Plant development

Mutations in the pale aleurone color1 regulatory gene of the Zea mays anthocyanin pathway have distinct phenotypes relative to the functionally similar TRANSPARENT TESTA GLABRA1 gene in Arabidopsis thaliana. Carey, C. C. et al. Plant Cell 16, 450–464 (2004)

This article reports the cloning and characterization of the pale aleurone color 1 (pac1) locus, which regulates the synthesis of anthocyanin in the maize seed. An experimental comparison of pac1 function and that of similar genes in Arabidopsis thaliana and Petunia hybrida highlights important differences in how the regulation of this pathway has evolved between monocots and dicots. For example, in monocots such as maize, the regulators of the biosynthetic genes are not under each other's control, as in dicots.

Evolution

Codon usage between genomes is constrained by genome-wide mutational processes. Chen, S. L. et al. Proc. Natl Acad. Sci. USA 101, 3480–3485 (2004)

In this article, Chen et al. use a new method to examine whether mutational forces or coding-region-specific selective forces are most important for shaping genome-wide codon bias. They found that genome-wide codon bias is well characterized by just two parameters — genome G+C content and nearest-neighbour nucleotide bias — and is determined primarily by mutational processes. The selective forces that act on translated sequences are only secondary determinants of codon bias.

Genomics

Community structure and metabolism through reconstruction of microbial genomes from the environment. Tyson, G. W. et al. Nature 428, 37–43 (2004)

Environmental genome shotgun sequencing of the Sargasso Sea. Venter, J. C. et al. Science 4 Mar 2004 (10.1126/science.1093857)

Our inability to culture most microorganisms has prevented detailed studies of microbial communities. This problem is solved in two new studies that report shotgun sequencing of microbial communities directly from environmental samples. Tyson et al. reconstructed near-complete genomes from two bacterial groups and partial genomes from the three other dominant members of a well-characterized simple microbial community. By contrast, Venter et al. got smaller amounts of sequence from at least 1,800 genomes from the Sargasso Sea microbial community. The broader approach of Venter et al. identifies numerous new bacterial groups and genes, whereas the intensive genomic characterization of Tyson et al. provides insights into the evolution of, and metabolic interactions within, a complete community. The challenge for the future is to obtain such detailed insights into microbial communities as complex as the Sargasso Sea.