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

Authors :
Aleksandra M. Kasianova
Aleksey A. Penin
Mikhail I. Schelkunov
Artem S. Kasianov
Maria D. Logacheva
Anna V. Klepikova
Source :
Plant Methods, Vol 20, Iss 1, Pp 1-11 (2024)
Publication Year :
2024
Publisher :
BMC, 2024.

Abstract

Abstract Background As genomes of many eukaryotic species, especially plants, are large and complex, their de novo sequencing and assembly is still a difficult task despite progress in sequencing technologies. An alternative to genome assembly is the assembly of transcriptome, the set of RNA products of the expressed genes. While a bunch of de novo transcriptome assemblers exists, the challenges of transcriptomes (the existence of isoforms, the uneven expression levels across genes) complicates the generation of high-quality assemblies suitable for downstream analyses. Results We developed Trans2express – a web-based tool and a pipeline of de novo hybrid transcriptome assembly and postprocessing based on rnaSPAdes with a set of subsequent filtrations. The pipeline was tested on Arabidopsis thaliana cDNA sequencing data obtained using Illumina and Oxford Nanopore Technologies platforms and three non-model plant species. The comparison of structural characteristics of the transcriptome assembly with reference Arabidopsis genome revealed the high quality of assembled transcriptome with 86.1% of Arabidopsis expressed genes assembled as a single contig. We tested the applicability of the transcriptome assembly for gene expression analysis. For both Arabidopsis and non-model species the results showed high congruence of gene expression levels and sets of differentially expressed genes between analyses based on genome and based on the transcriptome assembly. Conclusions We present Trans2express – a protocol for de novo hybrid transcriptome assembly aimed at recovering of a single transcript per gene. We expect this protocol to promote the characterization of transcriptomes and gene expression analysis in non-model plants and web-based tool to be of use to a wide range of plant biologists.

Details

Language :
English
ISSN :
17464811
Volume :
20
Issue :
1
Database :
Directory of Open Access Journals
Journal :
Plant Methods
Publication Type :
Academic Journal
Accession number :
edsdoj.85cfb395a5ab4b9ea6755079ab7ca0f5
Document Type :
article
Full Text :
https://doi.org/10.1186/s13007-024-01255-7