Comprehensive Analysis of NAC Domain Transcription Factor Gene Family in Populus trichocarpa

<p>Abstract</p> <p>Background</p> <p>NAC (<b>NAM, ATAF1/2 </b>and <b>CUC2</b>) domain proteins are plant-specific transcriptional factors known to play diverse roles in various plant developmental processes. NAC transcription factors comprise of a large gene family represented by more than 100 members in <it>Arabidopsis</it>, rice and soybean etc. Recently, a preliminary phylogenetic analysis was reported for NAC gene family from 11 plant species. However, no comprehensive study incorporating phylogeny, chromosomal location, gene structure, conserved motifs, and expression profiling analysis has been presented thus far for the model tree species <it>Populus</it>.</p> <p>Results</p> <p>In the present study, a comprehensive analysis of NAC gene family in <it>Populus </it>was performed. A total of 163 full-length NAC genes were identified in <it>Populus</it>, and they were phylogeneticly clustered into 18 distinct subfamilies. The gene structure and motif compositions were considerably conserved among the subfamilies. The distributions of 120 <it>Populus </it>NAC genes were non-random across the 19 linkage groups (LGs), and 87 genes (73%) were preferentially retained duplicates that located in both duplicated regions. The majority of NACs showed specific temporal and spatial expression patterns based on EST frequency and microarray data analyses. However, the expression patterns of a majority of duplicate genes were partially redundant, suggesting the occurrence of subfunctionalization during subsequent evolutionary process. Furthermore, quantitative real-time RT-PCR (RT-qPCR) was performed to confirm the tissue-specific expression patterns of 25 NAC genes.</p> <p>Conclusion</p> <p>Based on the genomic organizations, we can conclude that segmental duplications contribute significantly to the expansion of <it>Populus </it>NAC gene family. The comprehensive expression profiles analysis provides first insights into the functional divergence among members in NAC gene family. In addition, the high divergence rate of expression patterns after segmental duplications indicates that NAC genes in <it>Populus </it>are likewise to have been retained by substantial subfunctionalization. Taken together, our results presented here would be helpful in laying the foundation for functional characterization of NAC gene family and further gaining an understanding of the structure-function relationship between these family members.</p

Genome-Wide Identification, Evolutionary Expansion, and Expression Profile of Homeodomain-Leucine Zipper Gene Family in Poplar (Populus trichocarpa)

BACKGROUND: Homeodomain-leucine zipper (HD-ZIP) proteins are plant-specific transcriptional factors known to play crucial roles in plant development. Although sequence phylogeny analysis of Populus HD-ZIPs was carried out in a previous study, no systematic analysis incorporating genome organization, gene structure, and expression compendium has been conducted in model tree species Populus thus far. PRINCIPAL FINDINGS: In this study, a comprehensive analysis of Populus HD-ZIP gene family was performed. Sixty-three full-length HD-ZIP genes were found in Populus genome. These Populus HD-ZIP genes were phylogenetically clustered into four distinct subfamilies (HD-ZIP I-IV) and predominately distributed across 17 linkage groups (LG). Fifty genes from 25 Populus paralogous pairs were located in the duplicated blocks of Populus genome and then preferentially retained during the sequential evolutionary courses. Genomic organization analyses indicated that purifying selection has played a pivotal role in the retention and maintenance of Populus HD-ZIP gene family. Microarray analysis has shown that 21 Populus paralogous pairs have been differentially expressed across different tissues and under various stresses, with five paralogous pairs showing nearly identical expression patterns, 13 paralogous pairs being partially redundant and three paralogous pairs diversifying significantly. Quantitative real-time RT-PCR (qRT-PCR) analysis performed on 16 selected Populus HD-ZIP genes in different tissues and under both drought and salinity stresses confirms their tissue-specific and stress-inducible expression patterns. CONCLUSIONS: Genomic organizations indicated that segmental duplications contributed significantly to the expansion of Populus HD-ZIP gene family. Exon/intron organization and conserved motif composition of Populus HD-ZIPs are highly conservative in the same subfamily, suggesting the members in the same subfamilies may also have conservative functionalities. Microarray and qRT-PCR analyses showed that 89% (56 out of 63) of Populus HD-ZIPs were duplicate genes that might have been retained by substantial subfunctionalization. Taken together, these observations may lay the foundation for future functional analysis of Populus HD-ZIP genes to unravel their biological roles

Functional conservation and divergence of Miscanthus lutarioriparius GT43 gene family in xylan biosynthesis

Background: Xylan is the most abundant un-cellulosic polysaccharides of plant cell walls. Much progress in xylan biosynthesis has been gained in the model plant species Arabidopsis. Two homologous pairs Irregular Xylem 9 (IRX9)/9L and IRX14/14L from glycosyltransferase (GT) family 43 have been proved to play crucial roles in xylan backbone biosynthesis. However, xylan biosynthesis in grass such as Miscanthus remains poorly understood

Genome-Wide Analysis of Sorghum GT47 Family Reveals Functional Divergences of MUR3-Like Genes

Sorghum (Sorghum bicolor) is an important bioenergy crop. Its biomass mainly consists of the cellulosic and non-cellulosic polysaccharides, both which can be converted to biofuels. The biosynthesis of non-cellulosic polysaccharides involves several glycosyltransferases (GT) families including GT47. However, there was no systemic study on GT47 family in sorghum to date. Here, we identified 39 sorghum GT47 family members and showed the functional divergences of MURUS3 (MUR3) homologs. Sorghum GT47 proteins were phylogenetically clustered into four distinct subfamilies. Within each subfamily, gene structure was relatively conserved between the members. Ten gene pairs were identified from the 39 GT47 genes, of which two pairs might be originated from tandem duplication. 25.6% (10/39) of sorghum GT47 genes were homologous to Arabidopsis MUR3, a xyloglucan biosynthesis gene in primary cell walls. SbGT47_2, SbGT47_7, and SbGT47_8, three most homologous genes of MUR3, exhibited different tissue expression patterns and were selected for complementation into Arabidopsis mur3-3. Physiological and cell wall analyses showed that SbGT47_2 and SbGT47_7 may be two functional xyloglucan galactosyltransferases in sorghum. Further studies found that MUR3-like genes are widely present in the seed plants but not in the chlorophytic alga Chlamydomonas reinhardtii. Our results provide novel information for evolutionary analysis and functional dissection of sorghum GT47 family members

Derun dil

Safveti Ziya'nın Malumat'ta tefrika edilen Derun Dil adlı roman

Hybrid Field-Assisted Solid–Liquid–Solid Dispersive Extraction for the Determination of Organochlorine Pesticides in Tobacco with Gas Chromatography

A novel one-step sample preparation technique termed hybrid field-assisted solid–liquid–solid dispersive extraction (HF-SLSDE) was developed in this study. A simple glass system equipped with a condenser was designed as an extraction vessel. The HF-SLSDE technique was a three-phase dispersive extraction approach. Target analytes were extracted from the sample into the extraction solvent enhanced by the hybrid field. Meanwhile, the interfering components were adsorbed by dispersing sorbent. No cleanup step preceded chromatographic analysis. The efficiency of the HF-SLSDE approach was demonstrated in the determination of organochlorine pesticide (OCP) residues in tobacco with a gas chromatography-electron capture detector (GC-ECD). Various operation conditions were studied systematically. Low detection limits (0.3–1.6 μg/kg) and low quantification limits (1.0–4.5 μg/kg) were achieved under the optimized conditions. The recoveries of OCPs ranged from 70.2% to 118.2%, with relative standard deviations of <9.6%, except for the lowest fortification level. Because of the effect of the hybrid field, HF-SLSDE showed significant predominance compared with other extraction techniques. The dispersing sorbent with good cleanup ability used in this study was also found to be a microwave absorption medium, which could heat the nonpolar extraction solvent under microwave irradiation. Different microstructures of tobacco samples before and after extractions demonstrated the mechanism of HF-SLSDE was based on an explosion at the cell level. According to the results, HF-SLSDE was proved to be a simple and effective sample preparation method for the analysis of pesticide residues in solid samples and could potentially be extended to other nonpolar target analytes in a complex matrix