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Genes 2019, 10(1), 50; https://doi.org/10.3390/genes10010050

Comparative Analysis of Developmental Transcriptome Maps of Arabidopsis thaliana and Solanum lycopersicum

1
Institute for Information Transmission Problems of the Russian Academy of Sciences, Bolshoy Karetny per. 19, build. 1, Moscow 127051, Russia
2
Lomonosov Moscow State University, Leninskye Gory, Moscow 119992, Russia
3
Skolkovo Institute of Science and Technology, Center for Data-Intensive Biology and Biomedicine, Nobelya Ulitsa 3, Moscow 121205, Russia
4
Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina 3, Moscow 119991, Russia
These authors contributed equally to this work.
*
Author to whom correspondence should be addressed.
Received: 3 December 2018 / Revised: 31 December 2018 / Accepted: 4 January 2019 / Published: 15 January 2019
(This article belongs to the Special Issue Evolutionary Genetics of Gene Expression)
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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. View Full-Text
Keywords: tomato; Solanum lycopersicum; RNA-seq; transcriptome atlas tomato; Solanum lycopersicum; RNA-seq; transcriptome atlas
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Penin, A.A.; Klepikova, A.V.; Kasianov, A.S.; Gerasimov, E.S.; Logacheva, M.D. Comparative Analysis of Developmental Transcriptome Maps of Arabidopsis thaliana and Solanum lycopersicum. Genes 2019, 10, 50.

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