Comparative analysis of developmental transcriptome maps of arabidopsis thaliana and solanum lycopersicum

Aleksey A. Penin, Anna V. Klepikova, Artem S. Kasianov, Evgeny S. Gerasimov, Maria D. Logacheva

Research output: Contribution to journalArticlepeer-review

12 Citations (Scopus)

Abstract

The knowledge of gene functions in model organisms is the starting point for the analysis of gene function in non-model species, including economically important ones. Usually, the assignment of gene functions is based on sequence similarity. In plants, due to a highly intricate gene landscape, this approach has some limitations. It is often impossible to directly match gene sets from one plant species to another species based only on their sequences. Thus, it is necessary to use additional information to identify functionally similar genes. Expression patterns have great potential to serve as a source of such information. An important prerequisite for the comparative analysis of transcriptomes is the existence of high-resolution expression maps consisting of comparable samples. Here, we present a transcriptome atlas of tomato (Solanum lycopersicum) consisting of 30 samples of different organs and developmental stages. The samples were selected in a way that allowed for side-by-side comparison with the Arabidopsis thaliana transcriptome map. Newly obtained data are integrated in the TraVA database and are available online, together with tools for their analysis. In this paper, we demonstrate the potential of comparing transcriptome maps for inferring shifts in the expression of paralogous genes.

Original languageEnglish
Article number50
JournalGenes
Volume10
Issue number1
DOIs
Publication statusPublished - 1 Jan 2019

Keywords

  • RNA-seq
  • Solanum lycopersicum
  • Tomato
  • Transcriptome atlas

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