Evolutionary divergence and limits of conserved non-coding sequence detection in plant genomes

Abstract

The discovery of regulatory motifs embedded in upstream regions of plants is a particularly challenging bioinformatics task. Previous studies have shown that motifs in plants are short compared with those found in vertebrates. Furthermore, plant genomes have undergone several diversification mechanisms such as genome duplication events which impact the evolution of regulatory motifs. In this article, a systematic phylogenomic comparison of upstream regions is conducted to further identify features of the plant regulatory genomes, the component of genomes regulating gene expression, to enable future de novo discoveries. The findings highlight differences in upstream region properties between major plant groups and the effects of divergence times and duplication events. First, clear differences in upstream region evolution can be detected between monocots and dicots, thus suggesting that a separation of these groups should be made when searching for novel regulatory motifs, particularly since universal motifs such as the TATA box are rare. Second, investigating the decay rate of significantly aligned regions suggests that a divergence time of ∼100 mya sets a limit for reliable conserved non-coding sequence (CNS) detection. Insights presented here will set a framework to help identify embedded motifs of functional relevance by understanding the limits of bioinformatics detection for CNSs.

Bipartite Promoter Element Required for Auxin Response

“…Of all possible 5-mers contained within the 250 upstream bases, only four sequences were exactly conserved across all six genes examined here (AGACA, TCATG, TTCTC, TTTCT). This is consistent with a recent bioinformatic analysis showing rare conservation of plant promoter sequences across the monocot-dicot divide (Reineke et al, 2011). One of the 5-mers that was absolutely conserved was the A2-type of AuxRE variant (AGACA).…”

“…), soybean (Glycine max), and rice (Oryza sativa). This group spans more than 100 million years of evolutionary time (Reineke et al, 2011). Although blocks of extended shared sequence were still readily detectable in A. lyrata, this was not the case with any of the other promoters.…”

An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions

“…Plant CNSs have previously been identified on a genome-wide scale on the basis of the comparison of few or distant genomes (for example, maize versus rice [14][15][16] , Brachypodium distachyon versus rice 17 , A. thaliana versus Brassica oleracea 18,19 and sets of diverse angiosperms 20 ). This approach limits either the specificity provided by large divergence times or the sensitivity provided by the comparison of more closely related species 10,11,21 . Comparisons of paralogous noncoding regions flanking duplicated genes have also provided key insights into functional noncoding elements 16,22 , but intraspecies duplicated CNSs may often experience relaxed selective constraints.…”

Inference of Transcriptional Networks in Arabidopsis through Conserved Noncoding Sequence Analysis

“…Furthermore, taxon sampling is still limited for flowering plants with the exception of the Brassicaceae lineage. These factors make global alignment strategies for the detection of CNSs impractical for many of the currently available plant genomes (Reineke et al, 2011). An additional difficulty for phylogenetic footprinting in plants lays in the fact that it is not trivial to identify one-to-one orthology in plants, due to a wealth of paralogs (homologous genes created through a duplication event) in almost all plant lineages (Van Bel et al, 2012).…”