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

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.

Keywords: RNA-seq; Solanum lycopersicum; tomato; transcriptome atlas.

Figure 1

Hierarchical clustering of samples as represented by a clustering tree. Distance between samples is measured as 1 − Pearson r² correlation coefficient.

Figure 2

Estimation of the completeness of the expression map. (a) The number of expressed genes at different thresholds in three publicly available datasets and in our dataset; (b) the number of detected splice sites under different filters in three publicly available datasets and in our dataset.

Figure 3

Distribution of identity and expression distance for orthopairs, random pairs, interspecific pairs from ortho-triplets, and interspecific pairs from random triplets. (a) The distribution of expression distance; (b) the distribution of identity.

Figure 4

Expression patterns in ortho-triplet AT5G36930, Solyc09g092410, and Solyc09g007710. Identities are almost equal, while expression distances differ ~20-fold. Note that while Solyc09g007710, similar to AT5G36930, is expressed in leaves, Solyc09g092410 has a drastically different expression profile, with a maximum expression level in roots.