title: The genome sequence and insights into the immunogenetics of the bananaquit (Passeriformes: Coereba flaveola).
abstract: Avian genomics, especially of non-model species, is in its infancy relative to mammalian genomics. Here, we describe the sequencing, assembly, and annotation of a new avian genome, that of the bananaquit Coereba flaveola (Passeriformes: Thraupidae). We produced ∼30-fold coverage of the genome with an assembly size of ca. 1.2 Gb, including approximately 16,500 annotated genes. Passerine birds, such as the bananaquit, are commonly infected by avian malarial parasites (Haemosporida), which presumably drive adaptive evolution of immunogenetic loci within the host genome. In the context of our research on the distribution of avian Haemosporida, we specifically characterized immune loci, including toll-like receptor (TLR) and major histocompatibility complex (MHC) genes. Additionally, we identified novel molecular markers in the form of single nucleotide polymorphisms (SNPs), both genome-wide and within identified immune loci. We discovered nine TLR genes and four MHC genes and identified five other TLR- or MHC- associated genes. Genome-wide, over 6 million high-quality SNPs were annotated, including 568 within TLR genes and 102 in MHC genes. This newly described genome and immune characterization expands the knowledge base for avian genomics and phylogenetics and allows for immune genotyping in the bananaquit, providing tools for the investigation of host-parasite coevolution.
authors.affiliation: Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN, USA. jantonid@purdue.edu.
authors.forename: Jennifer
authors.identifier: 0000-0002-6118-6342
authors.initials: J
authors.lastname: Antonides
authors.affiliation: Department of Biology, University of Missouri at St Louis, St Louis, MO, USA.
authors.forename: Robert
authors.initials: R
authors.lastname: Ricklefs
authors.affiliation: Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN, USA.|Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.
authors.forename: J Andrew
authors.initials: JA
authors.lastname: DeWoody
mesh_terms: D000818:Animals; D005075:Biological Evolution; D014644:Genetic Variation / Q000235:genetics*; D016678:Genome; D023281:Genomics; D005838:Genotype; D007125:Immunogenetics; D008285:Major Histocompatibility Complex / Q000235:genetics*; D058977:Molecular Sequence Annotation; D046109:Passeriformes / Q000235:genetics* / Q000276:immunology*; D051193:Toll-Like Receptors / Q000235:genetics*
chemical_list: D051193:Toll-Like Receptors
keywords: Avian genomics; Immune system; Major histocompatibility complex; Single nucleotide polymorphisms; Toll-like receptor