related to improving plant biomass production, which is strongly affected by environmental conditions and has important ecological and economic implications. Studies
performed in angiosperm and gymnosperm woody plants suggest that the regulatory
network involved in stress responses and wood formation could be conserved.
1 Introduction
Trees represent nearly 80% of the plant biomass on Earth and have an important role
as carbon sinks. Plant biomass production is strongly affected by environmental
conditions, and its regulation is under complex and dynamic transcriptional control.
In this sense, secondary vascular growth represents a key adaptation and a major
carbon sink in woody plants. The regulation of gene expression plays a fundamental
role in numerous biological processes, and transcription factors (TFs) are key regulatory players that act mainly at the transcriptional level. TFs activate or repress the
expression of their target genes by binding to cis-regulatory elements to regulate
different signalling pathways. The difficulty to elucidate the transcriptional regulatory network that controls a particular biological process is correlated to the complex network of TFs and/or regulatory molecules, such as miRNAs, controlling the
expression of most genes (Hobert 2008; Hernández and Sanan-Mishra 2017).
The identification and organization of both TF families and their specific roles in
transcriptional regulation are necessary steps to understand the regulatory networks
associated with key processes in trees. TFs can be defined as proteins that generally
present a DNA-binding domain (DBD) that recognizes specific DNA sequences in
the promoters of target genes to regulate their expression. The classification of TFs
into gene families is generally based on their characteristic DBDs (Riechmann et al.
2000), and their size varies considerably among organisms (Wray et al. 2003). Most
of the existing knowledge about plant TFs was obtained from studies in Arabidopsis
thaliana, which contains 2,296 TF genes classified into 58 families (Jin et al. 2013).
This number is significantly larger than that found in Drosophila melanogaster
(708 TFs, Hammonds et al. 2013) or Caenorhabditis elegans (934 putative TFs,
Reece-Hoyes et al. 2005), which have genomes of a similar size (Riechmann et al.
2000). In addition, Arabidopsis shows a greater diversity of TF compared to these
two species and to other animals and fungi, suggesting that transcriptional regulation may be more complex and diversified in plants as a consequence of an adaptive response as a result of their lifestyles. Approximately 75% of the TF families in
common between plants and animals are more diversified in plants (Shiu et al. 2005).
To date, 320,370 TFs from 165 species of green plants, classified into 58 families,
have been identified. The average percentage of TFs in different taxonomic lineages of
green plants ranges from 1.2% in Chlorophyta to 5.1% in Eudicots of the genomes
encoding for putative TFs (Jin et al. 2017b), which often belong to large gene families,
such as WRKY, bZIP, MYB, AP2/EREBP and NAC (Shao et al. 2015). Despite the
differences in the genome size of green plants and in the total number of proteins
196
M. B. Pascual et al.
performed in angiosperm and gymnosperm woody plants suggest that the regulatory
network involved in stress responses and wood formation could be conserved.
1 Introduction
Trees represent nearly 80% of the plant biomass on Earth and have an important role
as carbon sinks. Plant biomass production is strongly affected by environmental
conditions, and its regulation is under complex and dynamic transcriptional control.
In this sense, secondary vascular growth represents a key adaptation and a major
carbon sink in woody plants. The regulation of gene expression plays a fundamental
role in numerous biological processes, and transcription factors (TFs) are key regulatory players that act mainly at the transcriptional level. TFs activate or repress the
expression of their target genes by binding to cis-regulatory elements to regulate
different signalling pathways. The difficulty to elucidate the transcriptional regulatory network that controls a particular biological process is correlated to the complex network of TFs and/or regulatory molecules, such as miRNAs, controlling the
expression of most genes (Hobert 2008; Hernández and Sanan-Mishra 2017).
The identification and organization of both TF families and their specific roles in
transcriptional regulation are necessary steps to understand the regulatory networks
associated with key processes in trees. TFs can be defined as proteins that generally
present a DNA-binding domain (DBD) that recognizes specific DNA sequences in
the promoters of target genes to regulate their expression. The classification of TFs
into gene families is generally based on their characteristic DBDs (Riechmann et al.
2000), and their size varies considerably among organisms (Wray et al. 2003). Most
of the existing knowledge about plant TFs was obtained from studies in Arabidopsis
thaliana, which contains 2,296 TF genes classified into 58 families (Jin et al. 2013).
This number is significantly larger than that found in Drosophila melanogaster
(708 TFs, Hammonds et al. 2013) or Caenorhabditis elegans (934 putative TFs,
Reece-Hoyes et al. 2005), which have genomes of a similar size (Riechmann et al.
2000). In addition, Arabidopsis shows a greater diversity of TF compared to these
two species and to other animals and fungi, suggesting that transcriptional regulation may be more complex and diversified in plants as a consequence of an adaptive response as a result of their lifestyles. Approximately 75% of the TF families in
common between plants and animals are more diversified in plants (Shiu et al. 2005).
To date, 320,370 TFs from 165 species of green plants, classified into 58 families,
have been identified. The average percentage of TFs in different taxonomic lineages of
green plants ranges from 1.2% in Chlorophyta to 5.1% in Eudicots of the genomes
encoding for putative TFs (Jin et al. 2017b), which often belong to large gene families,
such as WRKY, bZIP, MYB, AP2/EREBP and NAC (Shao et al. 2015). Despite the
differences in the genome size of green plants and in the total number of proteins
196
M. B. Pascual et al.