Comparing RNA‐Seq and microarray gene expression data in two zones of the Arabidopsis root apex relevant to spaceflight

Abstract

Premise of the StudyThe root apex is an important region involved in environmental sensing, but comprises a very small part of the root. Obtaining root apex transcriptomes is therefore challenging when the samples are limited. The feasibility of using tiny root sections for transcriptome analysis was examined, comparing RNA sequencing (RNA‐Seq) to microarrays in characterizing genes that are relevant to spaceflight.Methods Arabidopsis thaliana Columbia ecotype (Col‐0) roots were sectioned into Zone 1 (0.5 mm; root cap and meristematic zone) and Zone 2 (1.5 mm; transition, elongation, and growth‐terminating zone). Differential gene expression in each was compared.ResultsBoth microarrays and RNA‐Seq proved applicable to the small samples. A total of 4180 genes were differentially expressed (with fold changes of 2 or greater) between Zone 1 and Zone 2. In addition, 771 unique genes and 19 novel transcriptionally active regions were identified by RNA‐Seq that were not detected in microarrays. However, microarrays detected spaceflight‐relevant genes that were missed in RNA‐Seq.DiscussionSingle root tip subsections can be used for transcriptome analysis using either RNA‐Seq or microarrays. Both RNA‐Seq and microarrays provided novel information. These data suggest that techniques for dealing with small, rare samples from spaceflight can be further enhanced, and that RNA‐Seq may miss some spaceflight‐relevant changes in gene expression.

Root Transcriptomic Analysis Reveals Global Changes Induced by Systemic Infection of Solanum lycopersicum with Mild and Severe Variants of Potato Spindle Tuber Viroid

“…Other studies concluded that these two methods complement each other, for example, in a study of the Chlamydomonas reinhardtii hydrogen production process [56], transcriptome profiling of wild-type and hrpX mutant strains of the ƴ-Proteobacterium Xanthomonas citri [58], and Mesorhizobium huakuii 7653R that occurs symbiotically with a host plant ( Astragalus sinicus ) or as free-living cell in the soil [59]. Moreover, comparative analysis of gene expression in two zones of the Arabidopsis root apex relevant to spaceflight showed how genes with low expression levels can be missed by RNA-seq analysis performed at a generally accepted read depth [60].…”

Test of Arabidopsis Space Transcriptome: A Discovery Environment to Explore Multiple Plant Biology Spaceflight Experiments

“…Many spaceflight samples are also preserved on orbit in the chemical fixative RNAlater and so TOAST includes a dataset on the effects of RNAlater on Arabidopsis seedlings (GLDS-38). In addition, as there are several spaceflight studies that present data on root responses to spaceflight, a root tip transcriptome (Krishnamurthy et al, 2018) and root tissue gene expression mapping (Birnbaum et al, 2003) are also included for comparative analyses.…”

Meta-analysis of the space flight and microgravity response of the Arabidopsis plant transcriptome

“…5a–c ). Krishnamurthy et al 17 have compared microarray and RNA-seq analyses of identical samples from Arabidopsis roots, concluding that although the two approaches broadly agreed (on ~66% of ~6400 DEGs in their study), RNA-seq analysis revealed significantly more DEGs. Thus, in our study the RNA-seq is likely providing a broader dataset within which to find enriched Gene Ontologies likely leading to the increased number of groupings found by our analysis.…”