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Transcriptome profiling of sorted endoreduplicated nuclei from tomato fruits: how the global shift in expression ascribed to DNA ploidy influences RNA ‐Seq data normalization and interpretation
Author(s) -
Pirrello Julien,
Deluche Cynthia,
Frangne Nathalie,
Gévaudant Frédéric,
Maza Elie,
Djari Anis,
Bourge Mickaël,
Renaudin JeanPierre,
Brown Spencer,
Bowler Chris,
Zouine Mohamed,
Chevalier Christian,
Gonzalez Nathalie
Publication year - 2018
Publication title -
the plant journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.058
H-Index - 269
eISSN - 1365-313X
pISSN - 0960-7412
DOI - 10.1111/tpj.13783
Subject(s) - endoreduplication , biology , ploidy , transcriptome , rna , rna seq , transcription (linguistics) , microbiology and biotechnology , genetics , gene expression , somatic cell , gene expression profiling , gene , linguistics , philosophy
Summary As part of normal development most eukaryotic organisms, ranging from insects and mammals to plants, display variations in nuclear ploidy levels resulting from somatic endopolyploidy. Endoreduplication is the major source of endopolyploidy in higher plants. Endoreduplication is a remarkable characteristic of the fleshy pericarp tissue of developing tomato fruits, where it establishes a highly integrated cellular system that acts as a morphogenetic factor supporting cell growth. However, the functional significance of endoreduplication is not fully understood. Although endoreduplication is thought to increase metabolic activity due to a global increase in transcription, the issue of gene‐specific ploidy‐regulated transcription remains open. To investigate the influence of endoreduplication on transcription in tomato fruit, we tested the feasibility of a RNA sequencing ( RNA ‐Seq) approach using total nuclear RNA extracted from purified populations of flow cytometry‐sorted nuclei based on their DNA content. Here we show that cell‐based approaches to the study of RNA ‐Seq profiles need to take into account the putative global shift in expression between samples for correct analysis and interpretation of the data. From ploidy‐specific expression profiles we found that the activity of cells inside the pericarp is related both to the ploidy level and their tissue location.