Bananaquit (Coereba flaveola) proteins

Fasta file for the annotated proteins from bananaquit genome sequencing and assembly (NCBI Bioproject ID: PRJNA353240)

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

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

Bananaquit (Coereba flaveola) genome annotation

Structural and functional annotation (.gff) file for the genes, exons, and CDS from bananaquit genome sequencing and assembly (NCBI Bioproject ID: PRJNA353240)

Bananaquit (Coereba flaveola) transcripts

Fasta file for the annotated transcripts from bananaquit genome sequencing and assembly (NCBI Bioproject ID: PRJNA353240)

Bioproject ID: PRJNA353240

NCBI Bioproject including sequencing reads, genome assembly, annotated SNPs, and BioSamples

TV_gene_flow

Sampled landscapes, surface metrics measured, and genetic distance measured between beetle populations. This data file is used for the GAMM model

T.velutinus.SSR10

Genotypes for individual beetles collected from all study sites. Scores are the 10 SSRs