TagSeq for gene expression in non-model plants: A pilot study at the Santa Rita Experimental Range NEON core site.

Hannah E Marx,Stephen Scheidt,Katrina M Dlugosch,Michael S Barker

doi:10.1002/aps3.11398

Abstract

PremiseTagSeq is a cost‐effective approach for gene expression studies requiring a large number of samples. To date, TagSeq studies in plants have been limited to those with a high‐quality reference genome. We tested the suitability of reference transcriptomes for TagSeq in non‐model plants, as part of a study of natural gene expression variation at the Santa Rita Experimental Range National Ecological Observatory Network (NEON) core site.MethodsTissue for TagSeq was sampled from multiple individuals of four species (Bouteloua aristidoides and Eragrostis lehmanniana [Poaceae], Tidestromia lanuginosa [Amaranthaceae], and Parkinsonia florida [Fabaceae]) at two locations on three dates (56 samples total). One sample per species was used to create a reference transcriptome via standard RNA‐seq. TagSeq performance was assessed by recovery of reference loci, specificity of tag alignments, and variation among samples.ResultsA high fraction of tags aligned to each reference and mapped uniquely. Expression patterns were quantifiable for tens of thousands of loci, which revealed consistent spatial differentiation in expression for all species.DiscussionTagSeq using de novo reference transcriptomes was an effective approach to quantifying gene expression in this study. Tags were highly locus specific and generated biologically informative profiles for four non‐model plant species.

Highlights

Gene expression studies that involve sampling many individuals or tissues can be powerful for identifying variation in transcriptional activity and function, as well as the structure of transcriptional networks and the genetic basis of gene expression variation (Wisecaver et al, 2017; Li et al, 2020)
Raw data for RNA-seq references and TagSeq gene expression were deposited at the NCBI Short Read Archive under BioProject #PRJNA599443
Metrics indicated that the most complete assembly was obtained for P. florida, with 78% BUSCO recovery, N50 of 895bp, and the largest fraction of contigs translating to known proteins (Table 1)

Summary

Introduction

Gene expression studies that involve sampling many individuals or tissues can be powerful for identifying variation in transcriptional activity and function (e.g. among populations, over time, in response to the environment or other treatments; Gould et al, 2018; Mead et al, 2019), as well as the structure of transcriptional networks and the genetic basis of gene expression variation (Wisecaver et al, 2017; Li et al, 2020) Such studies are of high interest for non-model species responding to natural environments, as well as for model species (Matz, 2018; Zaidem et al, 2019). A cost-effective approach is to target only a small region of each transcript for sequencing, identifying and quantifying its expression while avoiding sequencing across its full length Several versions of this approach have involved reading a short tag of sequence upstream of the polyA tail of mRNA. They find that TagSeq achieves higher accuracy than standard RNA-seq, presumably because sequencing effort is distributed more evenly to all transcripts when only the tag sequence is targeted

Objectives

Methods

Results

Conclusion