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Related Experiment Video

Updated: Feb 7, 2026

Amplicon Sequencing using the Long-Read Sequencing Technologies

Amplicon Sequencing using the Long-Read Sequencing Technologies

Published on: August 29, 2025

High resolution annotation of zebrafish transcriptome using long-read sequencing.

German Nudelman^1,2, Antonio Frasca³, Brandon Kent⁴

¹Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.

Genome Research

|August 1, 2018

Summary

This summary is machine-generated.

Long-read sequencing improved zebrafish transcriptome annotation, revealing novel transcripts and isoforms crucial for early development and zygotic genome activation (ZGA). This enhances our understanding of zebrafish gene expression.

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Ultra-long Read Sequencing for Whole Genomic DNA Analysis

Ultra-long Read Sequencing for Whole Genomic DNA Analysis

Published on: March 15, 2019

Area of Science:

Molecular Biology
Genomics
Developmental Biology

Background:

Zebrafish are a key model organism for biological research.
Current zebrafish transcriptome annotation is limited by short-read sequencing, especially for dynamic gene expression during zygotic genome activation (ZGA).

Purpose of the Study:

To improve zebrafish transcriptome annotation accuracy and coverage using long-read sequencing.
To identify novel transcripts and isoforms expressed before and after ZGA.

Main Methods:

Utilized the SMRT (Single Molecule, Real-Time) long-read sequencing platform.
Analyzed zebrafish embryonic transcriptomes before and after ZGA.
Employed computational validation (structural prediction, homology, functional conservation) and short-read sequencing for confirmation.
Validated novel splicing events, including a transcript spanning mir-430 elements, via PCR.

Main Results:

Identified 2539 novel transcripts from unannotated loci and 1835 new isoforms of annotated genes.
Discovered new homologs, paralogs, noncoding RNAs, and isoform switching events.
Validated several novel isoforms and an 8-kb transcript associated with mir-430, a key developmental regulator.

Conclusions:

Long-read sequencing significantly enhances zebrafish transcriptome annotation.
The study reveals greater complexity and novelty in the zebrafish transcriptome, particularly around ZGA.
Provides a valuable, improved resource for zebrafish research and understanding early development.