A gene expression microarray for Nicotiana benthamiana based on de novo transcriptome sequence assembly.

Area of Science:

• Plant molecular biology
• Transcriptomics
• Bioinformatics

Background:

• Nicotiana benthamiana is crucial for studying plant-pathogen interactions and gene silencing.
• Transcriptome exploration has been limited by insufficient sequence data and analysis tools like DNA microarrays.
• Despite advances, DNA microarrays remain valuable for gene expression studies due to cost-effectiveness and lower bioinformatics demands.

Purpose of the Study:

• To design and validate a gene expression microarray for Nicotiana benthamiana.
• To improve the analysis of N. benthamiana gene expression and transcriptome.
• To provide a cost-effective tool for researchers studying this plant model.

Main Methods:

• Designed a microarray with 103,747 probes based on N. benthamiana transcriptome versions v.3 and v.5.
• Determined the sense strand of transcriptome contigs using homology searches and a test microarray.
• Developed the Nb-105k microarray on the Agilent eArray platform and hybridized with RNA from N. benthamiana roots and leaves.

Main Results:

• The Nb-105k microarray demonstrated high specificity and sensitivity for detecting differential gene expression.
• Identified the sense strand for 106,684 transcriptome contigs, enhancing functional annotation.
• The microarray data can identify incorrectly assembled contigs in transcriptome assemblies by detecting expression inconsistencies.

Conclusions:

• A comprehensive oligonucleotide microarray design for N. benthamiana transcriptome research is now available.
• The new microarray empowers the N. benthamiana research community to leverage gene expression analysis.
• The sense orientation determination method can be applied to update transcriptomes of other non-model organisms.