Evolutionary Analysis and Expression Profiling of Zebra Finch Immune Genes

Abstract

Genes of the immune system are generally considered to evolve rapidly due to host–parasite coevolution. They are therefore of great interest in evolutionary biology and molecular ecology. In this study, we manually annotated 144 avian immune genes from the zebra finch (Taeniopygia guttata) genome and conducted evolutionary analyses of these by comparing them with their orthologs in the chicken (Gallus gallus). Genes classified as immune receptors showed elevated dN/dS ratios compared with other classes of immune genes. Immune genes in general also appear to be evolving more rapidly than other genes, as inferred from a higher dN/dS ratio compared with the rest of the genome. Furthermore, ten genes (of 27) for which sequence data were available from at least three bird species showed evidence of positive selection acting on specific codons. From transcriptome data of eight different tissues, we found evidence for expression of 106 of the studied immune genes, with primary expression of most of these in bursa, blood, and spleen. These immune-related genes showed a more tissue-specific expression pattern than other genes in the zebra finch genome. Several of the avian immune genes investigated here provide strong candidates for in-depth studies of molecular adaptation in birds.

Structural and functional annotation of the porcine immunome

“…These results confirm that positively selected genes in swine are enriched for roles in defense and immunity in mammals, as already shown in human [1], cow [9], five other mammals [69], as well as birds like the Zebra finch [70]. Other functions are also reported as privileged targets for an accelerated evolutionary rate of related genes in mammals, such as reproduction, taste perception, chemosensory reception [69], and olfaction, as recently shown in pig [44].…”

Contrasting patterns of selection and drift between two categories of immune genes in prairie‐chickens

“…; Ekblom et al . ). In particular, genes of the adaptive immune system, such as the major histocompatibility complex (MHC), are involved in recognition of specific antigens and experience strong selection as a consequence of host–pathogen co‐evolution (‘immune‐receptor’ genes).…”

“…; Ekblom et al . ). With the rapid increase in novel pathogens that may threaten local populations with extinction (Smith et al .…”

Characterization of the house sparrow (Passer domesticus) transcriptome: a resource for molecular ecology and immunogenetics

“…; Ekblom et al . ). The strong signs of selection, together with a high degree of genetic variation in some immune genes, have made them an appropriate target for studying functional genetic variation.…”