Related Experiment Video
Updated: Jun 23, 2026
10:41
Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved (Non-model) Organisms
Published on: May 9, 2017
An approach to transcriptome analysis of non-model organisms using short-read sequences
Lesley J Collins1, Patrick J Biggs, Claudia Voelckel
1Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand. L.J.Collins@massey.ac.nz
Summary
This study introduces a new transcriptome analysis method for non-model organisms lacking reference genomes. The approach successfully identified duplicate genes in polyploid plants using related model organisms for reference.
Area of Science:
- Genomics
- Bioinformatics
- Plant Science
Background:
- High-throughput short-read sequencing is standard for transcriptome analysis when a reference genome is available.
- Analyzing transcriptomes of non-model organisms without a reference genome presents significant challenges.
Purpose of the Study:
- To develop and validate a novel computational approach for transcriptome analysis in organisms lacking a reference genome.
- To demonstrate the applicability of this method for identifying gene duplicates in polyploid species.
Main Methods:
- Utilized a combination of sequence mapping and de novo assembly tools.
- Employed a closely related model organism's genome (Arabidopsis thaliana) as a reference for a non-model polyploid plant (Pachycladon enysii).
- Analyzed data from Solexa sequencing.
Main Results:
- Successfully determined duplicate genes within the polyploid genome by leveraging the reference genome of a related diploid species.
- Validated the effectiveness of the combined mapping and assembly strategy.
Conclusions:
- The presented approach enables robust transcriptome analysis for non-model organisms, expanding the utility of high-throughput sequencing.
- This method overcomes limitations previously associated with the absence of a specific reference genome.
Related Concept Videos
03:21RNA-seq
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
02:24Ribosome Profiling
Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...