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

Area of Science:

• Genomics
• Transcriptomics
• Comparative Biology

Background:

• Chicken is a vital model organism, but its transcriptome is poorly understood compared to humans.
• Short-read RNA sequencing presents challenges for accurate transcript identification in non-human vertebrates.
• Previous long-read sequencing efforts lacked RNA normalization and 5'-cap selection, potentially limiting transcriptome coverage.

Purpose of the Study:

• To comprehensively characterize the chicken transcriptome using advanced sequencing techniques.
• To compare the complexity and features of the chicken transcriptome with that of humans.
• To establish a robust methodology for avian transcriptomic analysis.

Main Methods:

• Utilized Pacific Biosciences Iso-Seq single-molecule, long-read sequencing on normalized chicken brain and embryo RNA libraries.
• Performed 5' cap selection on the embryo library for methodological comparison.
• Analyzed sequencing data to identify and quantify transcripts and genes.

Main Results:

• Identified 60,000 transcripts and 29,000 genes in the chicken transcriptome.
• Discovered over 20,000 novel long non-coding RNA (lncRNA) transcripts, including approximately 3,000 sense exonic overlapping lncRNAs.
• Revealed significant similarities in alternative transcription events between chicken and human transcriptomes.

Conclusions:

• The chicken transcriptome is comparable in complexity to the human transcriptome.
• The findings offer insights into vertebrate biology and explain previously observed genomic differences.
• Iso-Seq sequencing is a powerful tool for rapidly advancing transcriptomic knowledge.