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The genome sequence and insights into the immunogenetics of the bananaquit (Passeriformes: Coereba flaveola)

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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.

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Acknowledgements

We thank the Purdue Genomics Core Facility for the technical advice, Maria Pil from the Ricklefs Lab for the assistance with sample preparation, and members of the DeWoody Lab for the review of this manuscript. Funding was provided to JAD by Purdue through the University Faculty Scholar program and a seed grant from Purdue’s Department of Forestry and Natural Resources and to JA by a fellowship (P200A090324) in the area of Ecological and Environmental Engineering via the Department of Education’s Graduate Assistance in Area of National Need (GAANN) program.

Data management

The filtered sequencing reads, genome assembly, and annotated SNPs are available from NCBI (Bioproject ID: PRJNA353240). The genome annotation and sequences of transcripts and proteins can be found on Dryad (doi 10.5061/dryad.8182t).

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Authors and Affiliations

  1. Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN, USA

    Jennifer Antonides & J. Andrew DeWoody

  2. Department of Biology, University of Missouri at St Louis, St Louis, MO, USA

    Robert Ricklefs

  3. Department of Biological Sciences, Purdue University, West Lafayette, IN, USA

    J. Andrew DeWoody

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  1. Jennifer Antonides
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Correspondence to Jennifer Antonides.

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Antonides, J., Ricklefs, R. & DeWoody, J.A. The genome sequence and insights into the immunogenetics of the bananaquit (Passeriformes: Coereba flaveola). Immunogenetics 69, 175–186 (2017). https://doi.org/10.1007/s00251-016-0960-8

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