Nearby transposable elements impact plant stress gene regulatory networks: a meta-analysis in A. thaliana and S. lycopersicum

Table 1 Number of genes and TEs in the genomes of A. thaliana and S. lycopersicum. For well-defined TE superfamilies (TEFs) the number of TE-proximal genes and the number of TEs in the different genomic positionings with respect to their nearby protein-coding genes are given

	Genes	TE-proximal genes	UP	IN	DOWN	Gene-proximal TEs	Total TEs
A. thaliana	27,420	9540	10,099	2163	6997	14,420	31,189
S. lycopersicum	33,697	22,949	17,175	39,507	15,668	59,236	531,409

Genes is the total number of protein-coding genes annotated in the genome of the species. ‘TE-proximal genes’ is the total number of protein-coding genes adjacent to well-defined TEFs. Upstream (UP), intragenic (IN) and downstream (DOWN) refer to the relative positioning of TEs to adjacent genes, up to a maximum distance of 1 kb. ‘Gene-proximal TEs’ is the unique total number of TEs in well-defined TEFs adjacent to protein-coding genes, hence a combination of the upstream, intragenic and downstream positioning, where the same TE can be in different genomic locations for different genes. ‘Total TEs’ gives the total number of TEs annotated in the genome of the species

ISSN: 1471-2164