Comprehensive Genome-Wide Classification Reveals That Many Plant-Specific Transcription Factors Evolved in Streptophyte Algae

Abstract

Plant genomes encode many lineage-specific, unique transcription factors. Expansion of such gene families has been previously found to coincide with the evolution of morphological complexity, although comparative analyses have been hampered by severe sampling bias. Here, we make use of the recently increased availability of plant genomes. We have updated and expanded previous rule sets for domain-based classification of transcription associated proteins (TAPs), comprising transcription factors and transcriptional regulators. The genome-wide annotation of these protein families has been analyzed and made available via the novel TAPscan web interface. We find that many TAP families previously thought to be specific for land plants actually evolved in streptophyte (charophyte) algae; 26 out of 36 TAP family gains are inferred to have occurred in the common ancestor of the Streptophyta (uniting the land plants—Embryophyta—with their closest algal relatives). In contrast, expansions of TAP families were found to occur throughout streptophyte evolution. 17 out of 76 expansion events were found to be common to all land plants and thus probably evolved concomitant with the water-to-land-transition.

Comparative analyses of saprotrophy in Salisapilia sapeloensis and diverse plant pathogenic oomycetes reveal lifestyle-specific gene expression

“…Domain predictions using Interpro (Figure 7b) identified one Myb domain in the four Myb-related TF candidates, which is typical for Myb-related TFs [58,59]. Likewise, we confirmed the presence of the bZIP domain in the bZIP candidate, the NF-YB domain in the NF-YB candidate and one RWP-RK and Myb domain in the Nin-like candidate, typical for these TFs [59,60]. Interpro further predicted DNA binding sites in all seven candidates.…”

Ubiquitin ligase component LRS1 and transcription factor CrHy5 act as a light switch for photoprotection inChlamydomonas

“…To allow for sufficient read depth per experiment, only experiments with at least 10 6 mapped reads were kept. Transcription associated proteins required for prediction were pulled from https://plantcode.online.uni-marburg.de/tapscan/ (retrieved 10/19/2018) (Wilhelmsson et al, 2017). 975 experiments with 17731 transcripts were used to predict the regulatory interactions using genie3 (Huynh-Thu et al, 2010) with the transcription associated proteins as input genes, the random forest method (Breiman, 2001) with 1000 trees and the square root of the transcription associated proteins as input genes as regulators for each tree.…”

Identification of plant enhancers and their constituent elements by STARR-seq in tobacco leaves

“…Our approach bypasses the need for a species-specific protoplasting protocol by using transient expression of diverse STARR-seq libraries in tobacco leaves. As transcription factors are highly conserved among plant species 6,7 , the versatile tobacco system can serve as a proxy for many plant species, including crops.…”

“…Our approach bypasses the need for a species-specific protoplasting protocol by using transient expression of diverse STARR-seq libraries in tobacco leaves. As transcription factors are highly conserved among plant species 6,7 , the versatile tobacco system can serve as a proxy for many plant species, including crops.We used a green fluorescent protein (GFP) reporter gene under control of the Cauliflower mosaic virus 35S minimal promoter and the 35S core enhancer 8,9 (subdomains A1 and B1-3) to benchmark the assay.We systematically analyzed the position-and orientation-dependency of the enhancer (Fig. 1a).…”