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Related Concept Videos

RNA-seq03:21

RNA-seq

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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. 
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The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
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Updated: Jun 16, 2025

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved Non-model Organisms
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Trans2express - de novo transcriptome assembly pipeline optimized for gene expression analysis.

Aleksandra M Kasianova1,2, Aleksey A Penin1, Mikhail I Schelkunov1,2

  • 1Institute for Information Transmission, Russian Academy of Sciences, Moscow, Russia.

Plant Methods
|August 16, 2024
PubMed
Summary

Trans2express is a new pipeline for de novo hybrid transcriptome assembly, producing high-quality gene expression data for plants. This tool aids in characterizing transcriptomes and analyzing gene expression, especially in non-model species.

Keywords:
De novo transcriptome assemblyAssembly pipelineLongest isoformOnline toolTrans2express

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Area of Science:

  • Plant genomics
  • Transcriptome sequencing
  • Bioinformatics tools

Background:

  • De novo genome assembly is challenging for large, complex plant genomes.
  • Transcriptome assembly is an alternative but faces challenges like isoforms and uneven expression.
  • Existing transcriptome assemblers struggle to produce high-quality assemblies for downstream analysis.

Purpose of the Study:

  • To develop a robust pipeline for de novo hybrid transcriptome assembly.
  • To create a web-based tool (Trans2express) for efficient transcriptome analysis.
  • To improve the quality of transcriptome assemblies for gene expression studies, particularly in non-model plants.

Main Methods:

  • Developed Trans2express, a pipeline using rnaSPAdes for hybrid transcriptome assembly.
  • Implemented postprocessing filtration steps for enhanced assembly quality.
  • Tested the pipeline on Arabidopsis thaliana and three non-model plant species using Illumina and Oxford Nanopore data.

Main Results:

  • Trans2express achieved high-quality transcriptome assembly, with 86.1% of Arabidopsis genes assembled as single contigs.
  • The assembled transcriptomes showed high congruence with genome-based analyses for gene expression levels.
  • Effective differential gene expression analysis was demonstrated for both model and non-model plants.

Conclusions:

  • Trans2express provides a protocol for de novo hybrid transcriptome assembly, aiming for single transcript recovery per gene.
  • The protocol and web tool are expected to advance transcriptome characterization and gene expression analysis in non-model plants.
  • Trans2express will be a valuable resource for plant biologists studying gene expression and transcriptomes.