Genome structure of MHC Class II β gene from Humboldt penguin ( Spheniscus humboldti)

Abstract

Endangered penguins are in need of the genetic management to estimate the risk for loss of genetic diversity from populations resulting from habitat fragmentation or inbreeding. However, as for genome diversity in penguin species, there are limited reports and it is insufficient to give useful and appropriate information. In the present study, we obtained the full length sequence of the MHC class II gene, which is expected to be a useful genetic marker for biodiversity in conservation genetics. The 4.4 kb genome region containing two novel genes was determined for nucleotide sequences using genomic DNA extracted from Humboldt penguin, by using the inverse PCR method. Homology analysis of MHC class II genes with those from other birds suggested that the novel two genes were alpha and beta genes. In addition, phylogenetic analysis suggested that the beta gene of penguins was clustered with the beta genes from waterfowl. These observations provide basic information on the structure of MHC class II locus to relieve the genetic diversity of penguin species.