Genomic limitations to RNA sequencing expression profiling

The Plant Journal : for Cell and Molecular Biology
Cory D HirschCandice N Hirsch

Abstract

The field of genomics has grown rapidly with the advent of massively parallel sequencing technologies, allowing for novel biological insights with regards to genomic, transcriptomic, and epigenomic variation. One widely utilized application of high-throughput sequencing is transcriptional profiling using RNA sequencing (RNAseq). Understanding the limitations of a technology is critical for accurate biological interpretations, and clear interpretation of RNAseq data can be difficult in species with complex genomes. To understand the limitations of accurate profiling of expression levels we simulated RNAseq reads from annotated gene models in several plant species including Arabidopsis, brachypodium, maize, potato, rice, soybean, and tomato. The simulated reads were aligned using various parameters such as unique versus multiple read alignments. This allowed the identification of genes recalcitrant to RNAseq analyses by having over- and/or under-estimated expression levels. In maize, over 25% of genes deviated by more than 20% from the expected count values, suggesting the need for cautious interpretation of RNAseq data for certain genes. The reasons identified for deviation from expected expression varied between species due to ...Continue Reading

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Citations

Dec 26, 2015·BMC Plant Biology·Stephen PearceJorge Dubcovsky
Feb 12, 2017·Bioinformatics·Adam Price, Cynthia Gibas
Jul 7, 2018·The Plant Journal : for Cell and Molecular Biology·Oren TzfadiaAsaph Aharoni
Feb 23, 2020·The FEBS Journal·Alexander E Vinogradov, Olga V Anatskaya
May 28, 2019·Frontiers in Plant Science·Arun Kumaran Anguraj VadivelSangeeta Dhaubhadel
Jul 17, 2021·BMC Bioinformatics·Verônica R de Melo CostaRosario M Piro

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