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Global scale transcriptome analysis of Arabidopsis embryogenesis in vitro

Overview of attention for article published in BMC Genomics, April 2015
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Title
Global scale transcriptome analysis of Arabidopsis embryogenesis in vitro
Published in
BMC Genomics, April 2015
DOI 10.1186/s12864-015-1504-6
Pubmed ID
Authors

Anushka M Wickramasuriya, Jim M Dunwell

Abstract

Somatic embryogenesis (SE) in plants is a process by which embryos are generated directly from somatic cells, rather than from the fused products of male and female gametes. Despite the detailed expression analysis of several somatic-to-embryonic marker genes, a comprehensive understanding of SE at a molecular level is still lacking. The present study was designed to generate high resolution transcriptome datasets for early SE providing the way for future research to understand the underlying molecular mechanisms that regulate this process. We sequenced Arabidopsis thaliana somatic embryos collected from three distinct developmental time-points (5, 10 and 15 d after in vitro culture) using the Illumina HiSeq 2000 platform. This study yielded a total of 426,001,826 sequence reads mapped to 26,520 genes in the A. thaliana reference genome. Analysis of embryonic cultures after 5 and 10 d showed differential expression of 1,195 genes; these included 778 genes that were more highly expressed after 5 d as compared to 10 d. Moreover, 1,718 genes were differentially expressed in embryonic cultures between 10 and 15 d. Our data also showed at least eight different expression patterns during early SE; the majority of genes are transcriptionally more active in embryos after 5 d. Comparison of transcriptomes derived from somatic embryos and leaf tissues revealed that at least 4,951 genes are transcriptionally more active in embryos than in the leaf; increased expression of genes involved in DNA cytosine methylation and histone deacetylation were noted in embryogenic tissues. In silico expression analysis based on microarray data found that approximately 5% of these genes are transcriptionally more active in somatic embryos than in actively dividing callus and non-dividing leaf tissues. Moreover, this identified 49 genes expressed at a higher level in somatic embryos than in other tissues. This included several genes with unknown function, as well as others related to oxidative and osmotic stress, and auxin signalling. The transcriptome information provided here will form the foundation for future research on genetic and epigenetic control of plant embryogenesis at a molecular level. In follow-up studies, these data could be used to construct a regulatory network for SE; the genes more highly expressed in somatic embryos than in vegetative tissues can be considered as potential candidates to validate these networks.

Twitter Demographics

The data shown below were collected from the profiles of 3 tweeters who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 102 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Germany 1 <1%
Unknown 101 99%

Demographic breakdown

Readers by professional status Count As %
Researcher 25 25%
Student > Ph. D. Student 22 22%
Student > Master 14 14%
Student > Doctoral Student 10 10%
Student > Bachelor 5 5%
Other 9 9%
Unknown 17 17%
Readers by discipline Count As %
Agricultural and Biological Sciences 56 55%
Biochemistry, Genetics and Molecular Biology 21 21%
Engineering 2 2%
Earth and Planetary Sciences 1 <1%
Unknown 22 22%

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 21 January 2016.
All research outputs
#12,660,018
of 19,211,930 outputs
Outputs from BMC Genomics
#6,055
of 9,730 outputs
Outputs of similar age
#138,192
of 244,041 outputs
Outputs of similar age from BMC Genomics
#1
of 1 outputs
Altmetric has tracked 19,211,930 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 9,730 research outputs from this source. They receive a mean Attention Score of 4.5. This one is in the 30th percentile – i.e., 30% of its peers scored the same or lower than it.
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