A simple and efficient method for isolating RNA from pine trees

Chang, Shujun; Puryear, Jeff; Cairney, John

doi:10.1007/bf02670468

Cited by 3,166 publications

(2,139 citation statements)

References 2 publications

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“…Alternatively, total RNA from cortex, old root and root tip were isolated by CTAB method [99] with minor modifications. RNA integrity was verified by 2% agar gel electrophoresis and SYBR Greenlstaining.…”

Section: Methodsmentioning

confidence: 99%

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

et al. 2010

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BackgroundNAC (NAM, ATAF1/2 and CUC2) 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 Arabidopsis, 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 Populus.ResultsIn the present study, a comprehensive analysis of NAC gene family in Populus was performed. A total of 163 full-length NAC genes were identified in Populus, 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 Populus 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.ConclusionBased on the genomic organizations, we can conclude that segmental duplications contribute significantly to the expansion of Populus 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 Populus 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.

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Section: Methodsmentioning

confidence: 99%

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

et al. 2010

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“…Total RNA extraction from the mycelium and ectomycorrhizae was carried out using the 'pine tree method' (Chang et al 1993). Genomic DNA was removed using a Turbo DNA-free™ reagent (Ambion, Austin, TX, USA), according to the manufacturer's instructions.…”

Section: Rna Isolation and Cdna Synthesismentioning

confidence: 99%

Understanding plant cell-wall remodelling during the symbiotic interaction between Tuber melanosporum and Corylus avellana using a carbohydrate microarray

Sillo

Fangel

Henrissat

et al. 2016

Planta

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“…To this 30 ml of 8 M guanidine hydrochloride was added, thoroughly mixed by shaking and centrifuged at 10,000 g for 15 min. The resultant supernatant was processed as described by Chang et al (1993). The quality of RNA was verified using a UV-Visible spectrophotometer (Shimadzu UV-1601).…”

Section: Seed Materialsmentioning

confidence: 99%

Differential expression analysis of transcripts related to oil metabolism in maturing seeds of Jatropha curcas L.

Chandran

Sankararamasubramanian

Kumar

et al. 2014

Physiol Mol Biol Plants

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Jatropha curcas has been widely studied at the molecular level due to its potential as an alternative source of fuel. Many of the reports till date on this plant have focussed mainly on genes contributing to the accumulation of oil in its seeds. A suppression subtractive hybridization strategy was employed to identify genes which are differentially expressed in the mid maturation stage of J. curcas seeds. Random expressed sequence tag sequencing of the cDNA subtraction library resulted in 385 contigs and 1,428 singletons, with 591 expressed sequence tags mapping for enzymes having catalytic roles in various metabolic pathways. Differences in transcript levels in early and mid-to-late maturation stages of seeds were also investigated using sequence information obtained from the cDNA subtraction library. Seven out of 12 transcripts having putative roles in central carbon metabolism were up regulated in early seed maturation stage while lipid metabolism related transcripts were detected at higher levels in the later stage of seed maturation. Interestingly, 4 of the transcripts revealed putative alternative splice variants that were specifically present or up regulated in the early or late maturation stage of the seeds. Transcript expression patterns from the current study using maturing seeds of J. curcas reveal a subtle balancing of oil accumulation and utilization, which may be influenced by their energy requirements.

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A simple and efficient method for isolating RNA from pine trees

Cited by 3,166 publications

References 2 publications

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

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

Understanding plant cell-wall remodelling during the symbiotic interaction between Tuber melanosporum and Corylus avellana using a carbohydrate microarray

Differential expression analysis of transcripts related to oil metabolism in maturing seeds of Jatropha curcas L.

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