Zebrafish (Danio rerio) is one of the most important model organisms which has been widely used in human disease and developmental research due to its high reproductive rate, external fertilization, and rapid embryonic development. However, existing zebrafish genome annotations mainly rely on computational predictions and short-read sequencing data. 

In a study published in BMC Biology, a research team led by Prof. 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, significantly advancing the understanding of transcriptome complexity during vertebrate development.

Using the PacBio Sequel II platform, 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, 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 indicated that alternative splicing plays an important role in zebrafish embryonic development. 

In addition, 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. It provides a solid foundation for future studies on zebrafish development and gene regulation.