Genome wide characterization of barley NAC transcription factors enables the identification of grain-specific transcription factors exclusive for the Poaceae family of monocotyledonous plants

Abstract

The plant NAC transcription factors depict one of the largest plant transcription factor families. They regulate a wide range of different developmental processes and most probably played an important role in the evolutionary diversification of plants. This makes comparative studies of the NAC transcription factor family between individual species and genera highly relevant and such studies have in recent years been greatly facilitated by the increasing number of fully sequenced complex plant genomes. This study combines the characterization of the NAC transcription factors in the recently sequenced genome of the cereal crop barley with expression analysis and a comprehensive phylogenetic characterization of the NAC transcription factors in other monocotyledonous plant species. Our results provide evidence for the emergence of a NAC transcription factor subclade that is exclusively expressed in the grains of the Poaceae family of grasses. These notably comprise a number of cereal crops other than barley, such as wheat, rice, maize or millet, which are all cultivated for their starchy edible grains. Apparently, the grain specific subclade emerged from a well described subgroup of NAC transcription factors associated with the senescence process. A promoter exchange subsequently resulted in grain specific expression. We propose to designate this transcription factor subclade Grain-NACs and we discuss their involvement in programmed cell death as well as their potential role in the evolution of the Poaceae grain, which doubtlessly is of central importance for human nutrition.

Comparative Analysis of Transcriptome and sRNAs Expression Patterns in the Brachypodium distachyon—Magnaporthe oryzae Pathosystems

“…Interestingly, all PR genes shown in Table 5 were upregulated in leaves at 4 DPI, while leaf 2 DPI and root PR protein expression patterns did not overlap, with only two (PR-like and PR1-like) upregulated at 2 DPI, and three (two PR1-like and PR10) in the root datasets. Similarly, the strongest and most widespread upregulation in the other pathogen sensing/defense-related genes was observed at 4 DPI, with an upregulation of transcription factors belonging to MYB, WRKY and NAC families consistent with the upregulation observed in Bd after F. pseudograminearum infection [ 61 ], and the knowledge that these families regulate a variety of plant responses, including those to biotic stresses [ 63 , 64 , 65 ]. In line with the considerable overlap in Mo gene expression patterns between leaf 4 DPI and root datasets, the majority of genes found upregulated in Bd roots (80.9%) are also detected upregulated in leaves at 4 DPI, compared to 18% shared with the 2 DPI sample.…”

A novel NAC family transcription factor SPR suppresses seed storage protein synthesis in wheat

“…NAC is one of the largest TF families in higher plants and comprises more than 100 members in both monocot and dicot species (Murozuka et al ., 2018). In common wheat, NAC family TFs are involved in responses to abiotic and biotic stresses such as drought, salt tolerance and stripe rust (Feng et al ., 2014; Huang et al ., 2015; Mao et al ., 2014; Mao et al ., 2012; Tang et al ., 2012; Wang et al ., 2015; Xia et al ., 2010a,b; Xue et al ., 2006), as well as senescence, nutrient remobilization and grain‐filling duration (Alhabbar et al ., 2018b; Uauy et al ., 2006; Zhao et al ., 2015).…”

Evolutionary Divergence and Biased Expression of NAC Transcription Factors in Hexaploid Bread Wheat (Triticum aestivum L.)

“…Wheat is one of the typical poaceae plants; many studies have focused on the evolutionary analysis of NAC transcription factors in poaceae plants. NAC transcription factors were identified in barley [ 20 , 21 ]. The orthologous NAC transcription factors from Brachypodium , rice, Arabidopsis and barley showed sequence conservation and contain conserved functions through the analysis of HvNAC expression combined with functional verified NACs in other plants [ 20 ].…”

“…The orthologous NAC transcription factors from Brachypodium , rice, Arabidopsis and barley showed sequence conservation and contain conserved functions through the analysis of HvNAC expression combined with functional verified NACs in other plants [ 20 ]. To further understand the evolution of NAC transcription factors, a phylogenetic characterization of NAC transcription factors from barley and other monocotyledonous plant species was performed and a promoter exchange was found that resulted in grain specificity of NAC-d-9 subgroup [ 21 ]. The NAC transcription factors were identified in durum wheat and bread wheat [ 22 , 23 ], and the homologous NAC transcription factors were got, which showed similar expressed pattern through the expression analysis using RNA-seq data.…”