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This Week in Genome Biology: May 6, 2009

In Genome Biology this week, scientists at the University of Rochester studied the evolution of R1 and R2 retrotransposons across 12 Drosophila genomes. These specifically insert into the 28S rRNA genes. They found that most copies of R1 and R2 in each species were found to exhibit less than 0.2% sequence divergence, suggesting that all copies are relatively new. In looking at target DNA cleavage and synthesis, they found that each active element generates its own independent lineage and that both R1 and R2 use "imprecise, rapidly evolving mechanisms" for second strand synthesis.

Researchers used genome-scale pH modeling and transcriptome analysis to look at how environmental pH levels affect the production of organic acids in the filamentous fungus Aspergillus niger. Looking across three pH levels, they found four pH-regulated secondary metabolite gene clusters. Integrating this with functional data, they pinpointed candidate genes for all steps of the pal/pacC pH signaling pathway.

Tel Aviv University scientists have created the first global network of gene co-evolution in fungi. Using two measures, the relative evolutionary rate pattern and the copy number pattern, they looked at the co-evolution of genes in nine fungal species. Two fundamental patterns of co-evolution of conserved genes emerged, they say: cooperative and reciprocal. "Only genes co-evolving cooperatively functionally backup each other," they write.

Finally, Steven Salzberg's group published its assembly of the genome of the sequenced domestic cow, Bos taurus. They mapped the 35 million hierarchical and whole-genome shotgun sequencing reads into an assembly of 2.86 billion base pairs that has "multiple improvements over previous assemblies," they write, namely that it is more accurate – it covers more of the genome, closes thousands of gaps, and corrects many indel and translocation errors. In light of two new assemblies, an opinion piece chimes in on how best to serve the scientific community when it comes to releasing data. And another paper examines the lactation genome, comparing cow milk and mammary genes to those of platypus, opossum, and four other placental mammals: human, dog, mouse, and rat.