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A Bioinformatic Analysis of NAC Genes for Plant Cell Wall Development in Relation to Lignocellulosic Bioenergy Production

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Abstract

NAM, ATAF, and CUC2 (NAC) proteins are encoded by one of the largest plant-specific transcription factor gene families. The functions of many NAC proteins relate to different aspects of lignocellulosic biomass production, and a small group of NAC transcription factors has been characterized as master regulators of plant cell wall development. In the present study, a total of 1,232 NAC protein sequences from 11 different organisms were analyzed by sequence phylogeny based on protein DNA-binding domains. We included eight whole genomes (Arabidopsis, rice, poplar, grape, sorghum, soybean, moss (Physcomitrella patens), and spike moss (Selaginella moellendorffii)) and three not yet fully sequenced genomes (maize, switchgrass, and Medicago truncatula) in our analyses. Ninety-two potential PvNAC genes from switchgrass and 148 PtNAC genes from poplar were identified. The 1,232 NAC proteins were phylogenetically classified into eight subfamilies, each of which was further divided into subgroups according to their tree topology. The phylogenetic subgroups were then grouped into different clades each sharing conserved motif patterns in the C-terminal sequences, and those that may function in plant cell wall development were further identified through motif grouping and gene expression pattern analysis using publicly available microarray data. Our results provide a bioinformatic baseline for further functional analyses of candidate NAC genes for improving cell wall and environmental tolerance traits in the bioenergy crops switchgrass and poplar.

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Acknowledgments

This work was supported by grants to RAD and YX from the US Department of Energy Bioenergy Research Centers, through the Office of Biological and Environmental Research in the DOE Office of Science.

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Authors and Affiliations

  1. Plant Biology Division, Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA

    Hui Shen, Fang Chen & Richard A. Dixon

  2. Computational Systems Biology Lab, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA

    Yanbin Yin & Ying Xu

  3. Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA

    Yanbin Yin & Ying Xu

  4. Bioenergy Science Center (BESC), Oak Ridge, TN, USA

    Hui Shen, Yanbin Yin, Fang Chen, Ying Xu & Richard A. Dixon

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  1. Hui Shen
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  2. Yanbin Yin
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  3. Fang Chen
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  4. Ying Xu
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  5. Richard A. Dixon
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Correspondence to Ying Xu or Richard A. Dixon.

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Hui Shen and Yanbin Yin contributed equally to this study.

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Fig. S1

Intron-exon analysis of different NAC subfamilies. (a) to (h) show the intron-exon analysis for the NAC-a to NAC-h subfamilies, respectively. The available intron-exon structures are plotted on the phylogentic tree. Open box, exon; solid black box, exons that encode NAC AE domain regions; Line, intron; 0, 1 and 2, intron phase. (PDF 12349 kb)

Fig. S2

The motif clades and subgroups for the NAC-a subfamily. Subgroups are a-1 to a-9; motif clades are a-sc1 to a-sc20. Red/blue colored tree I.D. indicates NAC proteins from dicots and monocots, light blue PpNACs and green SmNACs. The bootstrap values of the branches are shown in black numbers. The MEME motifs are shown as different colored boxes; the solid red, pink, light blue, blue and yellow boxes at the N-terminal indicate the NAC domain region. (PDF 12349 kb)

Fig. S3

The motif clades and subgroups for the NAC-g subfamily. Subgroups are g-1 to g-9; motif clades are g-sc1 to g-sc11. Red/blue colored tree I.D. indicates NAC proteins from dicots and monocots, light blue PpNACs and green SmNACs. The bootstrap values of the branches are shown in black numbers. The MEME motifs are shown as different colored boxes; the solid red, pink, light blue, blue and yellow boxes at the N-terminal indicate the NAC domain region. (PDF 12349 kb)

Fig. S4

Sequence-specific MEME motifs for NAC-c (NST and VND) proteins. (a) MEME motif layout patterns identified in the NAC-c subfamily. (b-d) Logos and clade specific sequences for motifs C.M7, C.M6 and C.M9. (e) Logos and comparison of different clade -specific sequences for motif C.M10. Most of the NST proteins have the sequence specific C.M7 (c-sc8, c-sc9 and csc10), C.M6 (a-sc8, c-sc9 and c-sc10) and C.M9 (a-sc8, c-sc9 and c-sc10) motifs. (PDF 12349 kb)

Fig. S5

Sequence-specific MEME motifs for NAC-g (SND) proteins. (a) MEME motif layout patterns identified in the NAC-g subfamily. (b-e) Logos and comparison of different clade - specific sequences for motifs g.M7, g.M19, g.M25 and g.M47. (PDF 12349 kb)

Fig. S6

Tissue coexpression analysis of selected Arabidopsis NAC genes. All the ANACs identified in this study together with marker genes related to plant cell-wall development and biomass production were analyzed by the GENEVESTIGATOR program for tissue coexpression patterns. Hierarchical clustering was calculated by Pearson correlation. Red box, lignin biosynthetic gene pattern, with the dotted red box showing the pattern for monolignol synthetic genes. Blue box, the secondary cell-wall polysaccharide biosynthetic gene pattern. Green box, ANAC009, ANAC015, ANAC033, ANAC070 and ANAC094 co-expression pattern. Orange box: ANAC104/AtXND1, ANAC056 and NAC074 co-expression pattern. (PDF 12349 kb)

Table S1

The gene and phylogenetic tree IDs used in this study (XLS 187 kb)

Table S2

Subdomain and motif analyses for the 1,232 NAC proteins (XLS 507 kb)

Table S3

Functionally characterized NAC proteins and NAC subfamilies. (PDF 12349 kb)

Table S4

Comparison of the three phylogenetic classifications of NAC genes. (PDF 12349 kb)

Table S5

List of the Arabidopsis NAC genes selected for coexpression analysis (PDF 12349 kb)

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Shen, H., Yin, Y., Chen, F. et al. A Bioinformatic Analysis of NAC Genes for Plant Cell Wall Development in Relation to Lignocellulosic Bioenergy Production. Bioenerg. Res. 2, 217–232 (2009). https://doi.org/10.1007/s12155-009-9047-9

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