Bat Genomes: Bats are of great interest because of their ability to fly and as hosts for infectious disease. Zhang et al. (p. 456 , published online 20 December) sequenced the genomes of two distantly related bat species, David's Myotis and Black flying fox. Analysis of the two genomes revealed likely changes that accompanied the evolution of bats, including selection for increased expression of genes involved in the oxidative phosphorylation pathway needed to generate the energy required for flight. Furthermore, while some immune genes have been lost, others are under positive selection, which may potentially explain bats' status as viral reservoirs.

Significance: Here we provide what is, to our knowledge, the first gene map of the type I IFN region of any bat species with the sequence of the type I IFN locus of the Australian black flying fox,Pteropus alecto.The bat IFN locus contains fewer IFN genes compared with any other mammal sequenced to date, including only threeIFN-αgenes. We also demonstrate that batIFN-αgenes are constitutively expressed in unstimulated bat tissues and cells and that their expression is unaffected by viral infection. This unusual pattern ofIFN-αexpression has not been described in any other species to our knowledge and has important implications for the role of innate immunity in the ability of bats to coexist with viruses in the absence of disease.

Bats are natural hosts to numerous viruses and have ancient origins, having diverged from other eutherian mammals early in evolution. These characteristics place them in an important position to provide insights into the evolution of the mammalian immune system and antiviral immunity. We describe the first detailed partial map of a bat (Pteropus alecto) MHC-I region with comparative analysis of the MHC-I region and genes. The bat MHC-I region is highly condensed, yet relatively conserved in organisation and is unusual in that MHC-I genes are present within only one of the three highly conserved class I duplication blocks. We hypothesise that MHC-I genes first originated in the β duplication block and subsequently duplicated in a step-wise manner across the MHC-I region during mammalian evolution. Furthermore, bat MHC-I genes contain unique insertions within their peptide-binding grooves potentially affecting the peptide repertoire presented to T cells, which may have implications for the ability of bats to control infection without overt disease.

We report the resequencing and revised annotation of the Mycobacterium avium subsp. paratuberculosis K10 genome. A total of 90 single-nucleotide errors and a 51-bp indel in the original K10 genome were corrected, and the whole genome annotation was revised. Correction of these sequencing errors resulted in 28 frameshift alterations. The amended genome sequence is accessible via the supplemental section of study SRR060191 in the NCBI Sequence Read Archive and will serve as a valuable reference genome for future studies.