Genomic Identification of Chemokines and Cytokines in Opossum

Abstract

The cytokine repertoire of marsupials is largely unknown. The sequencing of the opossum genome has expedited the identification of many immune genes. However, many genes have not been identified using automated annotation pipelines because of high levels of sequence divergence. To fill gaps in our knowledge of the cytokine gene complement in marsupials, we searched the genome assembly of the gray short-tailed opossum for chemokine, interleukin, colony-stimulating factor, tumor necrosis factor, and transforming growth factor genes. In particular, we focused on genes that were not previously identified through Ensembl's automatic annotations. We report that the vast majority of cytokines are conserved, with direct orthologs between therian species. The major exceptions are chemokine genes, which show lineage-specific duplication/loss. Thirty-six chemokines were identified in opossum, including a lineage-specific expansion of macrophage inflammatory protein family genes. Divergent cytokines IL7, IL9, IL31, IL33, and CSF2 were identified. This is the first time IL31 and IL33 have been described outside of eutherian species. The high levels of similarities between the cytokine gene repertoires of therians suggest that the marsupial immune response is highly similar to eutherians.