Trans2express - de novo transcriptome assembly pipeline optimized for gene expression analysis

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.