High-coverage sequencing and annotated assemblies of the budgerigar genome

Area of Science:

• * Genomics
• * Ornithology
• * Behavioral Neuroscience

Background:

• * Parrots exhibit advanced vocal learning and cognitive abilities, including speech imitation and understanding referential meaning.
• * The genetic underpinnings of these complex behaviors in parrots remain largely unknown.
• * A robust parrot genome assembly is crucial for genetic investigations.

Purpose of the Study:

• * To generate a high-quality genome assembly for the budgerigar (Melopsittacus undulatus), a widely studied parrot species.
• * To provide a valuable genomic resource for understanding the genetic basis of complex behavioral traits in parrots.
• * To advance genome technology development for avian research.

Main Methods:

• * Whole genome sequencing using multiple technologies (PacBio single-molecule sequencing) and chromosome optical mapping.
• * Hybrid assembly of genomic data to create large genomic scaffolds.
• * Annotation of assemblies using protein and transcriptome data from budgerigars, chickens, and zebra finches.

Main Results:

• * Creation of three hybrid budgerigar genome assemblies, achieving large genomic scaffold sizes.
• * Assemblies demonstrate high quality, comparable or superior to existing bird genome assemblies (chicken, zebra finch).
• * The assemblies enable analysis of challenging genomic regions and gene promoter regions relevant to vocal learning.

Conclusions:

• * The budgerigar genome assembly provides a valuable resource for studying the genomics of complex behaviors.
• * This work facilitates research into the genetic basis of vocal learning and other advanced traits in parrots.
• * The developed genomic data and methods contribute to both genome technology and avian behavioral genetics research.