Comprehensive Analysis of NAC Domain Transcription Factor Gene Family in.Populus trichocarpa.Identification of NAC gene family in Populus.The NAC domain genes are plant specific TFs presented as one of the largest multigene families in Arabidopsis, rice, soybean, maize, grape and sorghum etc 3, 6, 8, 5.Hidden Markov Model HMM profile of the Pfam NAC domain PF0.NAC genes in Populus genome release 2.Initially, a total of 1.NAC genes were identified.In an attempt to demonstrate the reliability of the identified genes, keyword search with NAM against NCBI nucleotide database was performed, resulting in 1.NACs identified above.In comparison to the NAC gene family in Pln.TFDB http plntfdb.DPTF http dptf. Then, the discrepancy loci identified in our studies with the two databases mentioned above were further scrutinized to see if any misannotations were inferred.Among them, sixteen genes may represent putative pseudogenes or incorrect annotations, and manual reannotation was performed to correct and reannotate the putative NACs using online web server FGENESH http linux.In this endeavor, seven sequences encoding only truncated proteins were excluded from further analysis.In addition, we combined the newly released genome annotations with the results inferred by FGENESH to make the annotations more convincing.Finally, all the putative 1.NAC genes were further manually analyzed using Inter.Download Snd Bot Mu Online' title='Download Snd Bot Mu Online' />Pro.Scan program http www.ToolsInter. Pro. Webopedias list of Data File Formats and File Extensions makes it easy to look through thousands of extensions and file formats to find what you need.Official registrar of Turkish domain names such as.Ihqqptvp1kI/hqdefault.jpg' alt='Download Snd Bot Mu Online' title='Download Snd Bot Mu Online' />Scan to confirm the presence of NAM domain 6.In a recently published report, a total of 1.NAC genes were identified in Populus by a genome wide bioinformatics survey 5.In this study, we further revealed an expanded NAC family in Populus with totally 1. Ejemplo De Sistema De Control Manual Y Automatico Secuencial . We designated Populus NAC genes as PNAC following the nomenclature proposed in the previous study 6.The identified NAC genes in Populus encode proteins ranging from 1.MockIt_28012014205848.jpg' alt='Download Snd Bot Mu Online' title='Download Snd Bot Mu Online' />Remarkably, in most cases, two or more Populus NAC genes were found for every ortholog in Arabidopsis.The detailed information of NAC family genes in Populus, including accession numbers and similarities to their Arabidopsis orthologs as well as nucleotide and protein sequences was listed in Table 1 and Additional file 1.Table 1. NAC gene family in Populus.The NAC gene family in Populus is by far the largest one compared to the estimates for other plant species, which range from 1.Top VIdeos. Warning Invalid argument supplied for foreach in srvusersserverpilotappsjujaitalypublicindex.Arabidopsis 6, 1.The member of NAC genes in Populus is roughly 1.Arabidopsis, which is in consistency with the ratio of 1.Populus homologs for each Arabidopsis gene based on comparative genomics studies 5.In comparison to its closest woody perennial grape Vitis vinifera, which possesses only about 7.NAC genes 3, the NAC genes in Populus seems to be highly expanded 5.It can be speculated that the presence of more NAC genes in Populus genome may reflect the great needs for these genes to involve in the complicated transcriptional regulations in this woody perennial species.This expansion appears to be arisen from multiple gene duplication events, including a whole genome duplication event in the Populus lineage followed by multiple segmental and tandem duplication events 5.Phylogenetic analysis of NAC gene family in Populus, Arabidopsisand rice.To examine the phylogenetic relationship among the NAC domain proteins in Populus, Arabidopsis and rice, an unrooted tree was constructed from alignments of the full length NAC protein sequences Figure 1.The phylogenetic tree was constructed using MEGA 4.Neighbor Joining NJ, Minimal Evolution ME and Maximum Parsimony MP methods, respectively.The tree topologies produced by the three algorithms were largely comparable with only minor modifications at interior branches data not shown.Therefore, only the NJ phylogenetic tree was subject to further analysis in our study.Moreover, we constructed the phylogenetic tree with the conserved N terminal NAC domains A to E using the same algorithm, which was largely consistent to the phylogenetic analyses performed by the previous studies 5.Additional file 2.As indicated in Figure 1, the phylogenetic tree divided the NAC family proteins into 1.PNAC1. 09 was distinguished from other NAC members and formed an individual clade with a robust bootstrap value support 9.Figure 1 and Additional file 3.For simplicity, the subgroups were designated as alphabetical families NAC a to NAC r based on tree topologies.Although the bootstrap values were somewhat low due to the large number of sequences, which was also presented in previous studies 6.Populus, Arabidopsis and rice NAC proteins into distinct families Additional file 3.Moreover, we sought other evidences such as gene structure, motif compositions and expression patterns as described below to support the reliability of the subgroup classification.Figure 1. Joined phylogenetic tree of NAC domain containing proteins from.Populus,Arabidopsisand rice.The deduced full length amino acid sequences of 1.Populus, 1. 05 Arabidopsis and 1.NAC genes were aligned by Clustal X 1.MEGA 4. 0 by the Neighbor Joining NJ method with 1,0.Each NAC subfamily was indicated in a specific color.Members of NAC protein from Populus were denoted in red.In general, the NAC members demonstrated an interspersed distribution in majority of subfamilies, indicating that the expansion of NAC genes occurred before the divergence of Populus, Arabidopsis and rice.Noticeably, NAC genes with same functions showed a tendency to fall into one subgroup, similar to the previous reports 7, 8, 5.For instances, subfamily NAC a encompassed the NAC proteins involved in shoot organ boundary delimitation eg.CUC1, 2 2. 5, 2. NAC d possessed all the NAC proteins that function in shoot apical meristem SAM establishment, pattern formation in embryos and flowers eg.NAM 1. 1, stress responses eg.ATAF1, RD2. 6 and Os.NAC6 1. 8, 4. 7, 6.NAP 2. 9. This group also encompassed ANAC0.ANAC0. 55, which have been shown to be induced by abiotic stresses ABA, drought and salinity and to enhance tolerance to drought when ectopically over expressed 4.The membrane associated NAC proteins that mediate either cytokinin signaling during cell division or endoplasmic reticulum stress responses were clustered into the NAC i and NAC k subfamilies.The members in these two subgroups are distinct with other NACs in that they harbor a transmembrane TM motif with a predicted helix in the far C terminal region.In NAC k subfamily, there were only two well functionally characterized members namely NTM1 and NTM2.The well characterized genes in subfamily NAC f included FEZ, which was demonstrated to be associated with the orientation of cell division in root stem cells 3.Remarkably, subfamily NAC j did not include any Arabidopsis and rice NAC proteins but only members from Populus, suggesting that they may have been either lost in Arabidopsis and rice or acquired in the Populus lineages after divergence from the last common ancestor.We speculate that these subsets of genes may also have specialized roles with respect to the woody perennial habit in Populus.Phylogenetic analysis also revealed a subgroup NAC o that contained sequence representatives in Populus and Arabidopsis but not in rice, indicating that the NAC members in this subgroup were acquired or differentially retained in eudicots post divergence from monocots.In contrast, the subgroup NAC p was composed of 1.NAC proteins, but no Arabidopsis and Populus proteins, which suggests diversification and expansion of this subgroup after the monocot eudicot radiation.The NAC proteins associated with secondary wall formation in fiber and vascular vessel development were divided into three independent subfamilies.All NSTs NST1, NST2, NST3SND1 and VNDs VND1 VND7 were clustered into one subfamily NAC b, whereas SND2, SND3 and their counterparts were grouped into NAC q.The other well characterized NAC member XND1 in secondary wall formation was assigned to another different subfamily NAC e.All the six functional characterized NST3SND1 orthologs Pt.WND1. B to 6. B in Populus fell into subfamily NAC b 1.Although enormous evidences exemplified that all these NAC genes performed as key transcriptional switches in the secondary cell wall formation process, their exact functional roles diversified 5.The phylogenetic analysis conducted herein may provide a potential supporting for their functional diversities.
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