454 sequencing reveals extreme complexity of the class ii major histocompatibility complex in the collared flycatcher454测序揭示极端复杂性二类主要组织相容性复合体的成卷的捕蝇草.pdfVIP

Zagalska-Neubauer et al. BMC Evolutionary Biology 2010, 10:395 /1471-2148/10/395 RESEARCH ARTICLE Open Access 454 sequencing reveals extreme complexity of the class II Major Histocompatibility Complex in the collared flycatcher 1,2† 1† 1 3 1 Magdalena Zagalska-Neubauer , Wiesław Babik , Michał Stuglik , Lars Gustafsson , Mariusz Cichoń , Jacek Radwan 1* Abstract Background: Because of their functional significance, the Major Histocompatibility Complex (MHC) class I and II genes have been the subject of continuous interest in the fields of ecology, evolution and conservation. In some vertebrate groups MHC consists of multiple loci with similar alleles; therefore, the multiple loci must be genotyped simultaneously. In such complex systems, understanding of the evolutionary patterns and their causes has been limited due to challenges posed by genotyping. Results: Here we used 454 amplicon sequencing to characterize MHC class IIB exon 2 variation in the collared flycatcher, an important organism in evolutionary and immuno-ecological studies. On the basis of over 152,000 sequencing reads we identified 194 putative alleles in 237 individuals. We found an extreme complexity of the MHC class IIB in the collared flycatchers, with our estimates pointing to the presence of at least nine expressed loci and a large, though difficult to estimate precisely, number of pseudogene loci. Many similar alleles occurred in the pseudogenes indicating either a series of recent duplications or extensive concerted evolution. The expressed alleles showed unambiguous signals of historical selection and the occurrence of apparent interlocus exchange of alleles. Placing the collared flycatcher’s MHC sequences in the co