Transcription associated proteins in plant development and evolution

Gene expression, the process in which DNA information is conveyed into a functional unit, is fundamental to cellular life. The extent to which gene expression can be regulated corresponds to a cells potential to modify its ability. One example is the progression through life stages of e.g. plants, going from seed to a tree, all achieved through different application of gene regulation upon the same identical DNA information. Transcriptional regulation is the process of regulating the initial step in gene expression, the transcribing of DNA into RNA. This is carried out by transcription associated proteins (TAPs). The work in this thesis aims to increase our knowledge of TAP involvement in plant development and to shed new light on TAP evolution in plants. By first providing an up-to-date method to screen for TAPs in plants (TAPscan), it was possible to screen a wide selection of plant genomes and transcriptomes. Using the data, ancestral states as well as gains, losses, expansion and contractions of TAPs, throughout the evolution of plants, could be calculated. The results suggest that many previously thought to be land plant specific TAPs actually predates the emergence of land plants. By analyzing RNA-sequence (RNA-seq) libraries of the dimorphic seed producing plant Aethionema arabicum (provided through the SeedAdapt consortium) it was possible to investigate TAP influence on seed development. In addition, a study evaluating the usefulness of a de novo assembly compared to a reference genome when identifying differentially expressed genes was conducted. The RNA-seq analysis, with TAP annotations, showed a clear distinction between the two seed morphs. The dehiscent (short term) seed being geared towards faster maturation and the indehiscent (long term) seed being geared towards dormancy was evident using both the de novo and reference approach