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. 2015 Aug 28;10(8):e0136993.
doi: 10.1371/journal.pone.0136993. eCollection 2015.

Genome-Wide Identification and Expression Analysis of the NAC Transcription Factor Family in Cassava

Wei Hu  1 , Yunxie Wei  1 , Zhiqiang Xia  1 , Yan Yan  1 , Xiaowan Hou  1 , Meiling Zou  1 , Cheng Lu  1 , Wenquan Wang  1 , Ming Peng  1
Affiliations
Free PMC article

Genome-Wide Identification and Expression Analysis of the NAC Transcription Factor Family in Cassava

Wei Hu et al. PLoS One. .
Free PMC article

Abstract

NAC [no apical meristem (NAM), Arabidopsis transcription activation factor [ATAF1/2] and cup-shaped cotyledon (CUC2)] proteins is one of the largest groups of plant specific transcription factors and plays a crucial role in plant growth, development, and adaption to the environment. Currently, no information is known about the NAC family in cassava. In this study, 96 NAC genes (MeNACs) were identified from the cassava genome. Phylogenetic analysis of the NACs from cassava and Arabidopsis showed that MeNAC proteins can be clustered into 16 subgroups. Gene structure analysis found that the number of introns of MeNAC genes varied from 0 to 5, with the majority of MeNAC genes containing two introns, indicating a small gene structure diversity of cassava NAC genes. Conserved motif analysis revealed that all of the identified MeNACs had the conserved NAC domain and/or NAM domain. Global expression analysis suggested that MeNAC genes exhibited different expression profiles in different tissues between wild subspecies and cultivated varieties, indicating their involvement in the functional diversity of different accessions. Transcriptome analysis demonstrated that MeNACs had a widely transcriptional response to drought stress and that they had differential expression profiles in different accessions, implying their contribution to drought stress resistance in cassava. Finally, the expression of twelve MeNAC genes was analyzed under osmotic, salt, cold, ABA, and H2O2 treatments, indicating that cassava NACs may represent convergence points of different signaling pathways. Taken together, this work found some excellent tissue-specific and abiotic stress-responsive candidate MeNAC genes, which would provide a solid foundation for functional investigation of the NAC family, crop improvement and improved understanding of signal transduction in plants. These data bring new insight on the complexity of the transcriptional control of MeNAC genes and support the hypothesis that NACs play an important role in plant growth, development, and adaption of environment.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Phylogenetic analysis of NAC proteins from cassava and Arabidopsis.
A total of 96 NACs from cassava and 105 NACs from Arabidopsis were used to construct the NJ tree with 1000 bootstrap based on the full length sequences of NACs. The NAC proteins are grouped into 16 distinct subgroups (TERN, NAC2, ONAC022, ANAC011, NAC1, SENU5, ATAF, AtNAC3, NAP, NAM, TIP, OSNAC8, OSNAC7, ANAC001, ONAC003 and ANAC063).“ANACs”are the NAC proteins from Arabidopsis. “MeNACs” indicate the NAC proteins from cassava.
Fig 2
Fig 2. The exon-intron structure of MeNAC genes according to the phylogenetic relationship.
The unrooted phylogenetic tree was constructed with 1000 bootstrap based on the full length sequences of MeNACs. Exon-intron structure analyses of MeNAC genes were performed by using the online tool GSDS. Lengths of exons and introns of each MeNAC gene were exhibited proportionally.
Fig 3
Fig 3. Conserved motifs of MeNAC proteins according to the phylogenetic relationship.
The conserved motifs in the MeNAC proteins were identified by MEME. Grey lines represent the non-conserved sequences, and each motif is indicated by a colored box numbered at the bottom. The length of motifs in each protein was exhibited proportionally.
Fig 4
Fig 4. Expression profiles of MeNAC genes in different tissues of two cassava accessions.
The transcript data generated from two replicates. The bar at the top of the heat map represents relative expression values.
Fig 5
Fig 5. Expression profiles of MeNAC genes in leaves and roots of three cassava accessions after drought treatment.
The transcript data generated from two replicates. The relative expression values were log2 transformed. The bar at the top of the heat map represents relative expression values.
Fig 6
Fig 6. Expression profiles of MeNAC genes in leaves under osmotic stress.
The relative expression levels of MeNAC genes in each treated time point were compared with that in each time point at normal conditions. NTC (no treatment control) at each time point was normalized as “1”. Data are means ± SE calculated from three biological replicates. Means denoted by the same letter do not significantly differ at P <0.05 as determined by Duncan’s multiple range test.
Fig 7
Fig 7. Expression profiles of MeNAC genes in leaves under salt stress.
The relative expression levels of MeNAC genes in each treated time point were compared with that in each time point at normal conditions. NTC (no treatment control) at each time point was normalized as “1”. Data are means ± SE calculated from three biological replicates. Means denoted by the same letter do not significantly differ at P <0.05 as determined by Duncan’s multiple range test.
Fig 8
Fig 8. Expression profiles of MeNAC genes in leaves under cold stress.
The relative expression levels of MeNAC genes in each treated time point were compared with that in each time point at normal conditions. NTC (no treatment control) at each time point was normalized as “1”. Data are means ± SE calculated from three biological replicates. Means denoted by the same letter do not significantly differ at P <0.05 as determined by Duncan’s multiple range test.
Fig 9
Fig 9. Expression profiles of MeNAC genes in leaves under ABA treatment.
The relative expression levels of MeNAC genes in each treated time point were compared with that in each time point at normal conditions. NTC (no treatment control) at each time point was normalized as “1”. Data are means ± SE calculated from three biological replicates. Means denoted by the same letter do not significantly differ at P <0.05 as determined by Duncan’s multiple range test.
Fig 10
Fig 10. Expression profiles of MeNAC genes in leaves under H2O2 treatment.
The relative expression levels of MeNAC genes in each treated time point were compared with that in each time point at normal conditions. NTC (no treatment control) at each time point was normalized as “1”. Data are means ± SE calculated from three biological replicates. Means denoted by the same letter do not significantly differ at P <0.05 as determined by Duncan’s multiple range test.
Fig 11
Fig 11. Expression profiles of MeNAC genes in leaves under various stresses, ABA and H2O2 treatments.
Log2 based values from three replicates of qRT-PCR data were used to create the heatmap. The scale represents the relative signal intensity values. Relative expression values for each gene after various treatments are provided in Figs 6–10 and S7 Table.
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This work was supported by the ‘973’ Program of the Ministry of Science and Technology of China (2010CB126600), the ‘863’ Program of the Ministry of Science and Technology of China (2012AA101204-2), the Natural Science Foundation of Hainan Province (314122, 20153048), the National Nonprofit Institute Research Grant of CATAS-ITBB (ITBB2015ZD04, ITBB2015ZY09), the Major Technology Project of Hainan (ZDZX2013023-1), the International Science & Technology Cooperation Program of China (2013DFA32020), and the International Science and Technology Cooperation Plan (2011DFB31690).

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