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Updated: Apr 8, 2026

Metabolic Labeling of the Nascent Transcriptome in Xenopus Early Embryogenesis

Metabolic Labeling of the Nascent Transcriptome in Xenopus Early Embryogenesis

Published on: March 27, 2026

Benchmarking Transcriptome Quantification Methods for Duplicated Genes in Xenopus laevis.

¹Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, University of Texas, Austin, Tex., USA; Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea.

Cytogenetic and Genome Research

|June 27, 2015

Summary

This summary is machine-generated.

RNA sequencing (RNA-seq) can distinguish expression of duplicated genes in Xenopus. Long paired-end reads and specific mapping strategies improve accuracy for studying gene evolution in organisms with duplicated genomes.

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Xenopus laevis as a Model to Identify Translation Impairment

Xenopus laevis as a Model to Identify Translation Impairment

Published on: September 27, 2015

Area of Science:

Genomics
Bioinformatics
Evolutionary Biology

Background:

Xenopus is a key model for vertebrate genome duplication studies.
Advancements in sequencing necessitate refined analytical methods for duplicated genes.
Understanding gene duplication's functional impact requires accurate expression analysis.

Purpose of the Study:

Evaluate computational methods for quantifying gene expression from RNA-seq data in Xenopus.
Assess the ability of RNA-seq to discriminate expression of highly similar duplicated genes.
Provide guidelines for analyzing RNA-seq data in organisms with duplicated genomes.

Main Methods:

Utilized two independent Xenopus laevis egg RNA-seq datasets.
Employed two reference databases for duplicated genes.
Compared various computational methods, including different read lengths and mapping software (bowtie, BWA, GSNAP, STAR), focusing on mapping quality scores.

Main Results:

RNA-seq can measure expression levels of similar duplicated genes, with long paired-end reads being more informative than short single-end reads.
Bowtie reported fewer unique hits compared to BWA, GSNAP, and STAR based on mapping quality scores.
Expression levels and ratios of duplicated genes were consistently estimated among replicates using unique hits and mapping quality scores.

Conclusions:

RNA-seq effectively discriminates expression of individual gene copies within duplicated pairs.
The chosen computational approach provides a reliable method for studying gene expression in Xenopus and other organisms with duplicated genomes.
This evaluation serves as a guide for future RNA-seq analyses in the context of genome duplication.