Improved zebra finch brain transcriptome identifies novel proteins with sex differences

Gene. 2022 Nov 15;843:146803. doi: 10.1016/j.gene.2022.146803. Epub 2022 Aug 9.

Abstract

The zebra finch (Taeniopygia guttata), a representative oscine songbird species, has been widely studied to investigate behavioral neuroscience, most notably the neurobiological basis of vocal learning, a rare trait shared in only a few animal groups including humans. In 2019, an updated zebra finch genome annotation (bTaeGut1_v1.p) was released from the Ensembl database and is substantially more comprehensive than the first version published in 2010. 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 bird transcriptome. To analyze the high-throughput RNA-seq data, we adopted a hybrid bioinformatic approach combining short and long-read pipelines. From our analysis, we added 220 novel genes and 8,134 transcript variants to the Ensembl annotation, and predicted a new proteome based on the refined annotation. We further validated 18 different novel proteins by using mass-spectrometry data generated from zebra finch caudal telencephalon tissue. Our results provide additional resources for future studies of zebra finches utilizing this improved bird genome annotation and proteome.

Keywords: RNA-seq; SMRT-seq; Song-system; Zebra finch.

MeSH terms

  • Animals
  • Brain
  • Female
  • Finches* / genetics
  • Humans
  • Male
  • Proteome / genetics
  • Sex Characteristics
  • Transcriptome / genetics
  • Vocalization, Animal

Substances

  • Proteome