The zebrafish (Danio rerio) is one of the most important model organisms worldwide. Due to its advantages, including high reproductive rate, external fertilization, rapid embryonic development, and abundant genetic manipulation techniques, it has been widely used in human disease and developmental research. However, existing zebrafish genome annotations mainly rely on computational predictions and short-read sequencing data, leaving large unannotated regions in the genome that severely limit further research progress. 

In a study published in BMC Biology, a research team led by Professor HE Shunping from the Institute of Hydrobiology (IHB) of the Chinese Academy of Sciences identified 2,113 novel genes and 33,018 novel isoforms in zebrafish embryos using high-resolution full-length RNA sequencing. This discovery significantly advances the understanding of transcriptome complexity during vertebrate development.

Using the PacBio Sequel II platform, the researchers conducted high-resolution full-length transcriptome sequencing across 21 stages of early zebrafish embryonic development. Based on these data, they reannotated the zebrafish genome. This approach led to the discovery of a large number of previously undiscovered novel genes and isoforms in the zebrafish genome, significantly improving both the accuracy and completeness of zebrafish genome annotation. 

The researchers sequenced samples from 21 embryonic developmental stages, generating an average of 26,754,033 subreads and 748,081 circular consensus sequences (CCS) per stage. Through strict quality control and analysis, they discovered 2,113 previously unannotated novel genes and 33,018 novel isoforms. Multi-platform validation confirmed the reliability of these newly discovered genes and isoforms.

By analyzing the dynamic expression patterns of transcripts across 21 developmental stages, the researchers revealed alternative splicing events at different stages. During early embryonic development, particularly from the 1k-cell to oblong stage and from the oblong to dome stage, alternative splicing events increased significantly before gradually decreasing. These dynamic changes indicate that alternative splicing plays an important role in zebrafish embryonic development. 

Additionally, conservation analysis revealed that although lncRNAs exhibited low conservation across species, they may have important regulatory functions in embryonic development. 

This study not only provides the zebrafish research community with significantly improved high-resolution transcriptome annotation of embryonic development, but also offers valuable resources for understanding the molecular mechanisms of zebrafish embryonic development. By revealing numerous novel genes and isoforms as well as dynamic changes in alternative splicing events, this study establishes a solid foundation for future studies on zebrafish development and gene regulation.

(Editor: MA Yun)