Cross-Species Genome-Wide Analysis Reveals Molecular and Functional Diversity of the Unconventional Interferon-? Subtype

Shields, Lauren E.; Jennings, Jordan; Liu, Qinfang; Lee, Jinhwa; Ma, Wenjun; Blecha, Frank; Miller, Laura C.; Sang, Yongming

A combinative procedure was used to identify IFN genes (including both predictable IFN-coding genes and pseudogenes) in animal genomes (9, 10, 13) . Single and grouped sequences, or hidden Markov model (HMM) profiles generated using sequence alignments with identified IFN peptide sequences in fish, birds, mammals, and amphibians, were used to query of genome assemblies available mainly through NCBI (http:// www.ncbi.nlm.nih.gov/genome/80, and Ensembl (http://useast. ensembl.org/index.html), and sometimes through a speciesconcentrated database such as at Xenbase (http://www.xenbase. org/). Protein BLAST searches were conducted using the default algorithm parameters with BLOSUM62 matrix and Expected thresholds (E) <10 or 1. Resultant IFN homologs in each species were further used as query entries to inspect other more diversified IFN homologs in that species, which may generally have less pairwise identity (<40%) to cross-species IFN homologs.