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Molecular evolution and expansion analysis of the NAC transcription factor in Zea mays.

Fan K, Wang M, Miao Y, Ni M, Bibi N, Yuan S, Li F, Wang X - PLoS ONE (2014)

Bottom Line: Different subfamily has different expansion rate, and NAC subfamily preference was found during the expansion in maize.Besides, the restriction of functional divergence was discovered after most of the gene duplication events.These results could provide novel insights into molecular evolution and expansion analysis of NAC family in maize, and advance the NAC researches in other plants, especially polyploid plants.

View Article: PubMed Central - PubMed

Affiliation: Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, P.R. China.

ABSTRACT
NAC (NAM, ATAF1, 2 and CUC2) family is a plant-specific transcription factor and it controls various plant developmental processes. In the current study, 124 NAC members were identified in Zea mays and were phylogenetically clustered into 13 distinct subfamilies. The whole genome duplication (WGD), especially an additional WGD event, may lead to expanding ZmNAC members. Different subfamily has different expansion rate, and NAC subfamily preference was found during the expansion in maize. Moreover, the duplication events might occur after the divergence of the lineages of Z. mays and S. italica, and segmental duplication seemed to be the dominant pattern for the gene duplication in maize. Furthermore, the expansion of ZmNAC members may be also related to gain and loss of introns. Besides, the restriction of functional divergence was discovered after most of the gene duplication events. These results could provide novel insights into molecular evolution and expansion analysis of NAC family in maize, and advance the NAC researches in other plants, especially polyploid plants.

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Phylogenetic relationships and putative conserved domain distributions of ZmNAC family.(A) The phylogenetic tree was generated using the Bayesian method based on the multiple alignments of ZmNAC protein sequences. The numbers in the clades are posterior probability values. The NAC subfamilies were indicated by different colors. (B) The conserved motifs were identified through MEME web server. Different motifs were represented by various colored boxes. The location of each motif can be estimated using the scale at the bottom.
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pone-0111837-g001: Phylogenetic relationships and putative conserved domain distributions of ZmNAC family.(A) The phylogenetic tree was generated using the Bayesian method based on the multiple alignments of ZmNAC protein sequences. The numbers in the clades are posterior probability values. The NAC subfamilies were indicated by different colors. (B) The conserved motifs were identified through MEME web server. Different motifs were represented by various colored boxes. The location of each motif can be estimated using the scale at the bottom.

Mentions: The phylogenetic analysis among the identified ZmNAC and ANAC proteins was processed by the PhyML and MrBayes tool. There were similar results with high support values from each method (Figure 1A, Figure S2). According to previous studies [8], [42], the ZmNAC family was divided into 13 subfamilies through the phylogenetic analysis. The member proportion was different in each ZmNAC subfamily (Figure 2A). The ONAC022 subfamily (17%) occupied the most members, followed by OsNAC7 subfamily (14%), ONAC003 subfamily (13%) and NAM subfamily (11%). The least was OsNAC8 and TIP subfamily (2%). Besides, ZmNAC sequences were submitted to OrthoMCL clustering. With the default stringency, 37 orthologous groups (OGs) were shown and they covered all the ZmNAC members in maize (Table S2). Each subfamily contained one or more OGs, and almost the different subfamilies had distinct OGs. The OG distributions were similar to the phylogenetic classifications of the NAC family in maize.


Molecular evolution and expansion analysis of the NAC transcription factor in Zea mays.

Fan K, Wang M, Miao Y, Ni M, Bibi N, Yuan S, Li F, Wang X - PLoS ONE (2014)

Phylogenetic relationships and putative conserved domain distributions of ZmNAC family.(A) The phylogenetic tree was generated using the Bayesian method based on the multiple alignments of ZmNAC protein sequences. The numbers in the clades are posterior probability values. The NAC subfamilies were indicated by different colors. (B) The conserved motifs were identified through MEME web server. Different motifs were represented by various colored boxes. The location of each motif can be estimated using the scale at the bottom.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4219692&req=5

pone-0111837-g001: Phylogenetic relationships and putative conserved domain distributions of ZmNAC family.(A) The phylogenetic tree was generated using the Bayesian method based on the multiple alignments of ZmNAC protein sequences. The numbers in the clades are posterior probability values. The NAC subfamilies were indicated by different colors. (B) The conserved motifs were identified through MEME web server. Different motifs were represented by various colored boxes. The location of each motif can be estimated using the scale at the bottom.
Mentions: The phylogenetic analysis among the identified ZmNAC and ANAC proteins was processed by the PhyML and MrBayes tool. There were similar results with high support values from each method (Figure 1A, Figure S2). According to previous studies [8], [42], the ZmNAC family was divided into 13 subfamilies through the phylogenetic analysis. The member proportion was different in each ZmNAC subfamily (Figure 2A). The ONAC022 subfamily (17%) occupied the most members, followed by OsNAC7 subfamily (14%), ONAC003 subfamily (13%) and NAM subfamily (11%). The least was OsNAC8 and TIP subfamily (2%). Besides, ZmNAC sequences were submitted to OrthoMCL clustering. With the default stringency, 37 orthologous groups (OGs) were shown and they covered all the ZmNAC members in maize (Table S2). Each subfamily contained one or more OGs, and almost the different subfamilies had distinct OGs. The OG distributions were similar to the phylogenetic classifications of the NAC family in maize.

Bottom Line: Different subfamily has different expansion rate, and NAC subfamily preference was found during the expansion in maize.Besides, the restriction of functional divergence was discovered after most of the gene duplication events.These results could provide novel insights into molecular evolution and expansion analysis of NAC family in maize, and advance the NAC researches in other plants, especially polyploid plants.

View Article: PubMed Central - PubMed

Affiliation: Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, P.R. China.

ABSTRACT
NAC (NAM, ATAF1, 2 and CUC2) family is a plant-specific transcription factor and it controls various plant developmental processes. In the current study, 124 NAC members were identified in Zea mays and were phylogenetically clustered into 13 distinct subfamilies. The whole genome duplication (WGD), especially an additional WGD event, may lead to expanding ZmNAC members. Different subfamily has different expansion rate, and NAC subfamily preference was found during the expansion in maize. Moreover, the duplication events might occur after the divergence of the lineages of Z. mays and S. italica, and segmental duplication seemed to be the dominant pattern for the gene duplication in maize. Furthermore, the expansion of ZmNAC members may be also related to gain and loss of introns. Besides, the restriction of functional divergence was discovered after most of the gene duplication events. These results could provide novel insights into molecular evolution and expansion analysis of NAC family in maize, and advance the NAC researches in other plants, especially polyploid plants.

Show MeSH