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Defining the full tomato NB-LRR resistance gene repertoire using genomic and cDNA RenSeq

Overview of attention for article published in BMC Plant Biology, May 2014
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About this Attention Score

  • Above-average Attention Score compared to outputs of the same age (51st percentile)
  • Good Attention Score compared to outputs of the same age and source (65th percentile)

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Title
Defining the full tomato NB-LRR resistance gene repertoire using genomic and cDNA RenSeq
Published in
BMC Plant Biology, May 2014
DOI 10.1186/1471-2229-14-120
Pubmed ID
Authors

Giuseppe Andolfo, Florian Jupe, Kamil Witek, Graham J Etherington, Maria R Ercolano, Jonathan D G Jones

Abstract

The availability of draft crop plant genomes allows the prediction of the full complement of genes that encode NB-LRR resistance gene homologs, enabling a more targeted breeding for disease resistance. Recently, we developed the RenSeq method to reannotate the full NB-LRR gene complement in potato and to identify novel sequences that were not picked up by the automated gene prediction software. Here, we established RenSeq on the reference genome of tomato (Solanum lycopersicum) Heinz 1706, using 260 previously identified NB-LRR genes in an updated Solanaceae RenSeq bait library.Result: Using 250-bp MiSeq reads after RenSeq on genomic DNA of Heinz 1706, we identified 105 novel NB-LRR sequences. Reannotation included the splitting of gene models, combination of partial genes to a longer sequence and closing of assembly gaps. Within the draft S. pimpinellifolium LA1589 genome, RenSeq enabled the annotation of 355 NB-LRR genes. The majority of these are however fragmented, with 5[prime]- and 3[prime]-end located on the edges of separate contigs. Phylogenetic analyses show a high conservation of all NB-LRR classes between Heinz 1706, LA1589 and the potato clone DM, suggesting that all sub-families were already present in the last common ancestor. A phylogenetic comparison to the Arabidopsis thaliana NB-LRR complement verifies the high conservation of the more ancient CCRPW8-type NB-LRRs. Use of RenSeq on cDNA from uninfected and late blight-infected tomato leaves allows the avoidance of sequence analysis of non-expressed paralogues.

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 233 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 4 2%
Cuba 1 <1%
Australia 1 <1%
Norway 1 <1%
United Kingdom 1 <1%
Israel 1 <1%
Slovenia 1 <1%
Canada 1 <1%
Unknown 222 95%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 63 27%
Researcher 60 26%
Student > Master 16 7%
Student > Bachelor 16 7%
Professor 11 5%
Other 36 15%
Unknown 31 13%
Readers by discipline Count As %
Agricultural and Biological Sciences 146 63%
Biochemistry, Genetics and Molecular Biology 40 17%
Computer Science 3 1%
Environmental Science 1 <1%
Arts and Humanities 1 <1%
Other 7 3%
Unknown 35 15%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 3. 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 17 January 2015.
All research outputs
#13,176,295
of 22,756,196 outputs
Outputs from BMC Plant Biology
#916
of 3,235 outputs
Outputs of similar age
#109,428
of 227,398 outputs
Outputs of similar age from BMC Plant Biology
#16
of 49 outputs
Altmetric has tracked 22,756,196 research outputs across all sources so far. This one is in the 41st percentile – i.e., 41% of other outputs scored the same or lower than it.
So far Altmetric has tracked 3,235 research outputs from this source. They receive a mean Attention Score of 3.0. This one has gotten more attention than average, scoring higher than 70% of its peers.
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 227,398 tracked outputs that were published within six weeks on either side of this one in any source. This one has gotten more attention than average, scoring higher than 51% of its contemporaries.
We're also able to compare this research output to 49 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 65% of its contemporaries.