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De novo transcriptome analysis of Medicago falcata reveals novel insights about the mechanisms underlying abiotic stress-responsive pathway

Overview of attention for article published in BMC Genomics, October 2015
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Title
De novo transcriptome analysis of Medicago falcata reveals novel insights about the mechanisms underlying abiotic stress-responsive pathway
Published in
BMC Genomics, October 2015
DOI 10.1186/s12864-015-2019-x
Pubmed ID
Authors

Zhenyan Miao, Wei Xu, Daofeng Li, Xiaona Hu, Jiaxing Liu, Rongxue Zhang, Zongyong Tong, Jiangli Dong, Zhen Su, Liwei Zhang, Min Sun, Wenjie Li, Zhenglin Du, Songnian Hu, Tao Wang

Abstract

The entire world is facing a deteriorating environment. Understanding the mechanisms underlying plant responses to external abiotic stresses is important for breeding stress-tolerant crops and herbages. Phytohormones play critical regulatory roles in plants in the response to external and internal cues to regulate growth and development. Medicago falcata is one of the stress-tolerant candidate leguminous species and is able to fix atmospheric nitrogen. This ability allows leguminous plants to grow in nitrogen deficient soils. We performed Illumina sequencing of cDNA prepared from abiotic stress treated M. falcata. Sequencedreads were assembled to provide a transcriptome resource. Transcripts were annotated using BLASTsearches against the NCBI non-redundant database and gene ontology definitions were assigned. Acomparison among the three abiotic stress treated samples was carried out. The expression of transcriptswas confirmed with qRT-PCR. We present an abiotic stress-responsive M. falcata transcriptome using next-generation sequencing data from samples grown under standard, dehydration, high salinity, and cold conditions. We combined reads from all samples and de novo assembled 98,515 transcripts to build the M. falcata gene index. A comprehensive analysis of the transcriptome revealed abiotic stress-responsive mechanisms underlying the metabolism and core signalling components of major phytohormones. We identified nod factor signalling pathways during early symbiotic nodulation that are modified by abiotic stresses. Additionally, a global comparison of homology between the M. falcata and M. truncatula transcriptomes, along with five other leguminous species, revealed a high level of global sequence conservation within the family. M. falcata is shown to be a model candidate for studying abiotic stress-responsive mechanisms in legumes. This global gene expression analysis provides new insights into the biochemical and molecular mechanisms involved in the acclimation to abiotic stresses. Our data provides many gene candidates that might be used for herbage and crop breeding. Additionally, FalcataBase ( http://bioinformatics.cau.edu.cn/falcata/ ) was built for storing these data.

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 49 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
India 2 4%
Chile 1 2%
Unknown 46 94%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 12 24%
Researcher 10 20%
Student > Doctoral Student 5 10%
Student > Postgraduate 3 6%
Student > Master 3 6%
Other 7 14%
Unknown 9 18%
Readers by discipline Count As %
Agricultural and Biological Sciences 23 47%
Biochemistry, Genetics and Molecular Biology 9 18%
Environmental Science 2 4%
Computer Science 1 2%
Physics and Astronomy 1 2%
Other 3 6%
Unknown 10 20%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 2. 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 02 July 2016.
All research outputs
#14,827,133
of 22,830,751 outputs
Outputs from BMC Genomics
#6,141
of 10,655 outputs
Outputs of similar age
#156,817
of 283,771 outputs
Outputs of similar age from BMC Genomics
#239
of 360 outputs
Altmetric has tracked 22,830,751 research outputs across all sources so far. This one is in the 32nd percentile – i.e., 32% of other outputs scored the same or lower than it.
So far Altmetric has tracked 10,655 research outputs from this source. They receive a mean Attention Score of 4.7. This one is in the 37th percentile – i.e., 37% 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 283,771 tracked outputs that were published within six weeks on either side of this one in any source. This one is in the 41st percentile – i.e., 41% of its contemporaries scored the same or lower than it.
We're also able to compare this research output to 360 others from the same source and published within six weeks on either side of this one. This one is in the 25th percentile – i.e., 25% of its contemporaries scored the same or lower than it.