Normalized long read RNA sequencing in chicken reveals transcriptome complexity similar to human

Richard I Kuo, Elizabeth Tseng, Lel Eory, Ian R Paton, Alan L Archibald, David W Burt

Research output: Contribution to journalArticlepeer-review

Abstract

BACKGROUND: Despite the significance of chicken as a model organism, our understanding of the chicken transcriptome is limited compared to human. This issue is common to all non-human vertebrate annotations due to the difficulty in transcript identification from short read RNAseq data. While previous studies have used single molecule long read sequencing for transcript discovery, they did not perform RNA normalization and 5'-cap selection which may have resulted in lower transcriptome coverage and truncated transcript sequences.

RESULTS: We sequenced normalised chicken brain and embryo RNA libraries with Pacific Bioscience Iso-Seq. 5' cap selection was performed on the embryo library to provide methodological comparison. From these Iso-Seq sequencing projects, we have identified 60 k transcripts and 29 k genes within the chicken transcriptome. Of these, more than 20 k are novel lncRNA transcripts with ~3 k classified as sense exonic overlapping lncRNA, which is a class that is underrepresented in many vertebrate annotations. The relative proportion of alternative transcription events revealed striking similarities between the chicken and human transcriptomes while also providing explanations for previously observed genomic differences.

CONCLUSIONS: Our results indicate that the chicken transcriptome is similar in complexity compared to human, and provide insights into other vertebrate biology. Our methodology demonstrates the potential of Iso-Seq sequencing to rapidly expand our knowledge of transcriptomics.

Original languageEnglish
Article number323 (2017)
Pages (from-to)1-19
Number of pages20
JournalBMC Genomics
Volume18
Issue number1
Early online date24 Apr 2017
DOIs
Publication statusE-pub ahead of print - 24 Apr 2017

Keywords

  • Iso-Seq
  • PacBio
  • Single molecule long read sequencing
  • Transcriptome sequencing
  • RNAseq
  • Chicken
  • Avian
  • Gallus gallus
  • Genome annotation
  • Coding RNA
  • Non-coding RNA

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