Abstract
BackgroundTranscription factors (TFs) are vital elements that regulate transcription and the spatio-temporal expression of genes, thereby ensuring the accurate development and functioning of an organism. The identification of TF-encoding genes in a liverwort, Marchantia polymorpha, offers insights into TF organization in the members of the most basal lineages of land plants (embryophytes). Therefore, a comparison of Marchantia TF genes with other land plants (monocots, dicots, bryophytes) and algae (chlorophytes, rhodophytes) provides the most comprehensive view of the rates of expansion or contraction of TF genes in plant evolution.ResultsIn this study, we report the identification of TF-encoding transcripts in M. polymorpha for the first time, as evidenced by deep RNA sequencing data. In total, 3,471 putative TF encoding transcripts, distributed in 80 families, were identified, representing 7.4% of the generated Marchantia gametophytic transcriptome dataset. Overall, TF basic functions and distribution across families appear to be conserved when compared to other plant species. However, it is of interest to observe the genesis of novel sequences in 24 TF families and the apparent termination of 2 TF families with the emergence of Marchantia. Out of 24 TF families, 6 are known to be associated with plant reproductive development processes. We also examined the expression pattern of these TF-encoding transcripts in six male and female developmental stages in vegetative and reproductive gametophytic tissues of Marchantia.ConclusionsThe analysis highlighted the importance of Marchantia, a model plant system, in an evolutionary context. The dataset generated here provides a scientific resource for TF gene discovery and other comparative evolutionary studies of land plants.
Highlights
Transcription factors (TFs) are vital elements that regulate transcription and the spatio-temporal expression of genes, thereby ensuring the accurate development and functioning of an organism
As the gene coding for Orphans in Arabidopsis has been found to be expressed in collective leaf structure, flowers, plant embryos, seed and shoots, playing a role in floral meristem determinacy and flower development [101], we suggest these transcripts are involved in reproductive transition determinacy in Marchantia. d) 11 transcripts coding for bHLH transcription factors (TFs) are found to be expressed in mature reproductive female (MF) reproductive stage in Marchantia. bHLH proteins are found both in plants and animals and are known to be involved in the regulation of a wide variety of essential growth and developmental processes [91]. bHLH TFs appear to be involved in carpel development and fruit dehiscence [102]
Liverworts as the sister of all land plants represent the basal lineage of land plants, providing a unique perspective on the regulatory origin of TFs and the genetic complexity of terrestrial plants
Summary
Transcription factors (TFs) are vital elements that regulate transcription and the spatio-temporal expression of genes, thereby ensuring the accurate development and functioning of an organism. Regulation of gene expression is central to all organisms [1] and is imperative for determining the morphology, functional competence, and development of a multicellular organism [2]. This regulation is tightly coordinated by a number of mechanisms, such as DNA methylation [3]; chromatin organization [4]; dimerization; and sequencespecific DNA binding, which is executed primarily by transcription factors (TFs). The genome of Arabidopsis thaliana includes 27,416 protein-coding genes (TAIR http://www.arabidopsis.org/), of which 6% (more than 1,700) encode TFs
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