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De novo sequencing, assembly, and analysis of the Taxodium‘Zhongshansa’ roots and shoots transcriptome in response to short-term waterlogging

Overview of attention for article published in BMC Plant Biology, July 2014
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1 tweeter

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Title
De novo sequencing, assembly, and analysis of the Taxodium‘Zhongshansa’ roots and shoots transcriptome in response to short-term waterlogging
Published in
BMC Plant Biology, July 2014
DOI 10.1186/s12870-014-0201-y
Pubmed ID
Authors

Baiyan Qi, Ying Yang, Yunlong Yin, Meng Xu, Huogen Li

Abstract

Background Taxodium is renowned for its strong tolerance to waterlogging stress, thus it has great ecological and economic potential.However, the scant genomic resources in genus Taxodium have greatly hindered further exploration of its underlying flood-tolerance mechanism.Taxodium `Zhongshansa¿ is an interspecies hybrid of T.distichum and T. mucronatum, and has been widely planted in southeastern China.To understand the genetic basis of its flood tolerance, we analyzed the transcriptomes of Taxodium `Zhongshansa¿ roots and shoots in response to short-term waterlogging.ResultsRNA-seq was used to analyze genome-wide transcriptome changes of Taxodium`Zhongshansa 406¿ clone root and shoot treated with 1 h of soil-waterlogging stress. After de novo assembly, 108,692 unigenes were achieved, and 70,260 (64.64%) of them were annotated. There were 2090 differentially expressed genes (DEGs) found in roots and 394 in shoots, with 174 shared by both of them, indicating that the aerial parts were also affected. Under waterlogging stress, the primary reaction of hypoxic-treated root was to activate the antioxidative defense system to prevent cells experiencing reactive oxygen species (ROS) poisoning. As respiration was inhibited and ATP decreased, another quick coping mechanism was repressing the energy-consuming biosynthetic processes through the whole plant. The glycolysis and fermentation pathway was activated to maintain ATP production in the hypoxic root. Constantly, the demand for carbohydrates increased, and carbohydrate metabolism were accumulated in the root as well as the shoot, possibly indicating that systemic communications between waterlogged and non-waterlogged tissues facilated survival. Amino acid metabolism was also greatly influenced, with down-regulation of genes involvedin serine degradation and up-regulation of aspartic acid degradation. Additionally, a non-symbiotic hemoglobin class 1 gene was up-regulated, which may also help the ATP production. Moreover, the gene expression pattern of 5 unigenes involving in the glycolysis pathway revealed by qRT-PCR confirmed the RNA-Seq data.ConclusionsWe conclude that ROS detoxification and energy maintenance were the primary coping mechanisms of `Zhongshansa¿in surviving oxygen deficiency, which may be responsible for its remarkable waterlogging tolerance. Our study not only provided the first large-scale assessment of genomic resources of Taxodium but also guidelines for probing the molecular mechanism underlying `Zhongshansa¿waterlogging tolerance.

Twitter Demographics

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Mendeley readers

The data shown below were compiled from readership statistics for 32 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 1 3%
Brazil 1 3%
Unknown 30 94%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 9 28%
Researcher 7 22%
Student > Postgraduate 4 13%
Student > Doctoral Student 3 9%
Student > Bachelor 1 3%
Other 2 6%
Unknown 6 19%
Readers by discipline Count As %
Agricultural and Biological Sciences 22 69%
Biochemistry, Genetics and Molecular Biology 2 6%
Immunology and Microbiology 1 3%
Chemistry 1 3%
Unknown 6 19%

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 25 July 2014.
All research outputs
#7,010,023
of 11,283,887 outputs
Outputs from BMC Plant Biology
#667
of 1,357 outputs
Outputs of similar age
#94,735
of 186,879 outputs
Outputs of similar age from BMC Plant Biology
#18
of 48 outputs
Altmetric has tracked 11,283,887 research outputs across all sources so far. This one is in the 23rd percentile – i.e., 23% of other outputs scored the same or lower than it.
So far Altmetric has tracked 1,357 research outputs from this source. They receive a mean Attention Score of 3.4. This one is in the 40th percentile – i.e., 40% of its peers scored the same or lower than it.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 186,879 tracked outputs that were published within six weeks on either side of this one in any source. This one is in the 38th percentile – i.e., 38% of its contemporaries scored the same or lower than it.
We're also able to compare this research output to 48 others from the same source and published within six weeks on either side of this one. This one has gotten more attention than average, scoring higher than 54% of its contemporaries.