Type I interferons in Myotis lucifugus and Pteropus vampyrus
We used the protein-coding portions of the human genes IFNA2, IFNK, IFNB, and IFNE, the bovine gene IFNT, and murine gene IFNZ in blast searches against the whole genome shotgun sequence trace archives for Pteropus vampyrus and Myotis lucifugus. The sequences retrieved in each of the blast searches were then assembled using the methods described above.
We obtained unique final assemblies for IFNB in each bat. Each of these final assemblies contained an intact ORF which, when BLASTed against the NCBI nucleotide sequence database, returned multiple hits on the corresponding gene in several mammals. The greatest similarity was to horse, pig, and cow sequences, with about 80% nucleotide identity.
Myotis produced two final assemblies for IFNE, both of which contain intact ORFs and appear, on close examination, to be genuinely distinct sequences. Pteropus produced a single final assembly, which had an intact ORF.
The sequencing traces returned in the search on IFNA2 produced multiple final assemblies that fall into three distinct families with clear similarity to IFNA, IFNW, and IFND (Table 1), respectively.
Table 1 Summary of Final Assemblies in Myotis lucifugus and Pteropus vampyrus.
Species Family #assemblies #Intact ORFs #Pseudogenes #Partial length (AA)
M. lucifugus IFNB 1 1 0 0 186
IFNE 2 2 0 0 193
IFNK 2 2 0 0 208
IFNA 2 0 2 0 -
IFNW 25 12 7 9 195
IFND 19 11 3 5 1711
P. vampyrus IFNB 1 1 0 0 185
IFNE 1 1 0 0 193
IFNK 1 1 0 0 201
IFNA 7 7 0 0 189
IFNW 28 18 8 1 1852
IFND 14 5 7 2 1713
1. two genes encode polypeptides of length 190
2. one at 187 and two at 195
3. one at 170
No relevant hits to murine IFNZ were found in either chiropteran genome. No hits to bovine IFNT beyond those already obtained using other queries were found.

Chiropteran Type II interferon
In mammals, the type I interferons have a single exon of fewer than 700 bases. IFNG, the type II interferon, has multiple exons. We used our methods to infer the type-II interferon genes in the two bats by using the full-length human IFNG gene comprising introns and exons (4972 bases, NC_000012 REGION: complement(68548550..68553521)). Our methods produced a single assembly in each bat (Additional File 1). All exons were clearly identifiable and all intronic splice signals were conserved. Table 2 shows the sequence similarity among the human and bat sequences.
Table 2 DNA sequence similarity among human (Has) IFNG and inferred bat (Mlu, Pva) IFNG assemblies for exons (above the diagonal), and introns (below the diagonal).
species Hsa Mlu Pva
Has ID 0.752 0.784
Mlu 0.655 ID 0.832
Pva 0.711 0.696 ID