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Transcriptome characterization of three wild Chinese Vitis uncovers a large number of distinct disease related genes

Overview of attention for article published in BMC Genomics, March 2015
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Title
Transcriptome characterization of three wild Chinese Vitis uncovers a large number of distinct disease related genes
Published in
BMC Genomics, March 2015
DOI 10.1186/s12864-015-1442-3
Pubmed ID
Authors

Chen Jiao, Min Gao, Xiping Wang, Zhangjun Fei

Abstract

Grape is one of the most valuable fruit crops and can serve for both fresh consumption and wine production. Grape cultivars have been selected and evolved to produce high-quality fruits during their domestication over thousands of years. However, current widely planted grape cultivars suffer extensive loss to many diseases while most wild species show resistance to various pathogens. Therefore, a comprehensive evaluation of wild grapes would contribute to the improvement of disease resistance in grape breeding programs. We performed deep transcriptome sequencing of three Chinese wild grapes using the Illumina strand-specific RNA-Seq technology. High quality transcriptomes were assembled de novo and more than 93% transcripts were shared with the reference PN40024 genome. Over 1,600 distinct transcripts, which were absent or highly divergent from sequences in the reference PN40024 genome, were identified in each of the three wild grapes, among which more than 1,000 were potential protein-coding genes. Gene Ontology (GO) and pathway annotations of these distinct genes showed those involved in defense responses and plant secondary metabolisms were highly enriched. More than 87,000 single nucleotide polymorphisms (SNPs) and 2,000 small insertions or deletions (indels) were identified between each genotype and PN40024, and approximately 20% of the SNPs caused nonsynonymous mutations. Finally, we discovered 100 to 200 highly confident cis-natural antisense transcript (cis-NAT) pairs in each genotype. These transcripts were significantly enriched with genes involved in secondary metabolisms and plant responses to abiotic stresses. The three de novo assembled transcriptomes provide a comprehensive sequence resource for molecular genetic research in grape. The newly discovered genes from wild Vitis, as well as SNPs and small indels we identified, may facilitate future studies on the molecular mechanisms related to valuable traits possessed by these wild Vitis and contribute to the grape breeding programs. Furthermore, we identified hundreds of cis-NAT pairs which showed their potential regulatory roles in secondary metabolism and abiotic stress responses.

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 43 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
New Zealand 1 2%
United States 1 2%
Uruguay 1 2%
Brazil 1 2%
Unknown 39 91%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 7 16%
Researcher 6 14%
Professor > Associate Professor 6 14%
Student > Master 6 14%
Professor 3 7%
Other 10 23%
Unknown 5 12%
Readers by discipline Count As %
Agricultural and Biological Sciences 31 72%
Biochemistry, Genetics and Molecular Biology 3 7%
Computer Science 1 2%
Engineering 1 2%
Unknown 7 16%
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 24 April 2015.
All research outputs
#14,219,838
of 22,796,179 outputs
Outputs from BMC Genomics
#5,699
of 10,648 outputs
Outputs of similar age
#138,799
of 262,851 outputs
Outputs of similar age from BMC Genomics
#156
of 282 outputs
Altmetric has tracked 22,796,179 research outputs across all sources so far. This one is in the 35th percentile – i.e., 35% of other outputs scored the same or lower than it.
So far Altmetric has tracked 10,648 research outputs from this source. They receive a mean Attention Score of 4.7. This one is in the 42nd percentile – i.e., 42% 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 262,851 tracked outputs that were published within six weeks on either side of this one in any source. This one is in the 44th percentile – i.e., 44% of its contemporaries scored the same or lower than it.
We're also able to compare this research output to 282 others from the same source and published within six weeks on either side of this one. This one is in the 39th percentile – i.e., 39% of its contemporaries scored the same or lower than it.