Improved zebra finch brain transcriptome identifies novel proteins with sex differences

•In this study, we utilized the publicly available RNA-seq data generated from Illumina-based short-reads and PacBio single-molecule real-time (SMRT) long-reads to assess the zebra finch brain transcriptome.•To analyze the high-throughput RNA-seq data, we adopted a hybrid bioinformatic approach combining short and long-read pipelines.•We added 220 novel genes and 8134 transcript variants to the Ensembl annotation, and predicted a new proteome based on the refined annotation.•Using mass-spectrometry of zebra finch caudal telencephalon, we validated 18 different novel proteins.•Our results provide additional resources for future studies of zebra finches utilizing this improved bird genome annotation and proteome.