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Mining microsatellite markers from public expressed sequence tags databases for the study of threatened plants

Overview of attention for article published in BMC Genomics, October 2015
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Title
Mining microsatellite markers from public expressed sequence tags databases for the study of threatened plants
Published in
BMC Genomics, October 2015
DOI 10.1186/s12864-015-2031-1
Pubmed ID
Authors

Lua Lopez, Rodolfo Barreiro, Markus Fischer, Marcus A. Koch

Abstract

Simple Sequence Repeats (SSRs) are widely used in population genetic studies but their classical development is costly and time-consuming. The ever-increasing available DNA datasets generated by high-throughput techniques offer an inexpensive alternative for SSRs discovery. Expressed Sequence Tags (ESTs) have been widely used as SSR source for plants of economic relevance but their application to non-model species is still modest. Here, we explored the use of publicly available ESTs (GenBank at the National Center for Biotechnology Information-NCBI) for SSRs development in non-model plants, focusing on genera listed by the International Union for the Conservation of Nature (IUCN). We also search two model genera with fully annotated genomes for EST-SSRs, Arabidopsis and Oryza, and used them as controls for genome distribution analyses. Overall, we downloaded 16 031 555 sequences for 258 plant genera which were mined for SSRsand their primers with the help of QDD1. Genome distribution analyses in Oryza and Arabidopsis were done by blasting the sequences with SSR against the Oryza sativa and Arabidopsis thaliana reference genomes implemented in the Basal Local Alignment Tool (BLAST) of the NCBI website. Finally, we performed an empirical test to determine the performance of our EST-SSRs in a few individuals from four species of two eudicot genera, Trifolium and Centaurea. We explored a total of 14 498 726 EST sequences from the dbEST database (NCBI) in 257 plant genera from the IUCN Red List. We identify a very large number (17 102) of ready-to-test EST-SSRs in most plant genera (193) at no cost. Overall, dinucleotide and trinucleotide repeats were the prevalent types but the abundance of the various types of repeat differed between taxonomic groups. Control genomes revealed that trinucleotide repeats were mostly located in coding regions while dinucleotide repeats were largely associated with untranslated regions. Our results from the empirical test revealed considerable amplification success and transferability between congenerics. The present work represents the first large-scale study developing SSRs by utilizing publicly accessible EST databases in threatened plants. Here we provide a very large number of ready-to-test EST-SSR (17 102) for 193 genera. The cross-species transferability suggests that the number of possible target species would be large. Since trinucleotide repeats are abundant and mainly linked to exons they might be useful in evolutionary and conservation studies. Altogether, our study highly supports the use of EST databases as an extremely affordable and fast alternative for SSR developing in threatened plants.

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Mendeley readers

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The data shown below were compiled from readership statistics for 54 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Malaysia 1 2%
Unknown 53 98%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 15 28%
Researcher 10 19%
Student > Bachelor 7 13%
Student > Master 3 6%
Student > Doctoral Student 2 4%
Other 5 9%
Unknown 12 22%
Readers by discipline Count As %
Agricultural and Biological Sciences 25 46%
Biochemistry, Genetics and Molecular Biology 11 20%
Environmental Science 1 2%
Social Sciences 1 2%
Neuroscience 1 2%
Other 0 0%
Unknown 15 28%
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 04 February 2016.
All research outputs
#16,688,690
of 25,528,120 outputs
Outputs from BMC Genomics
#6,552
of 11,275 outputs
Outputs of similar age
#163,502
of 291,675 outputs
Outputs of similar age from BMC Genomics
#243
of 375 outputs
Altmetric has tracked 25,528,120 research outputs across all sources so far. This one is in the 34th percentile – i.e., 34% of other outputs scored the same or lower than it.
So far Altmetric has tracked 11,275 research outputs from this source. They receive a mean Attention Score of 4.8. This one is in the 41st percentile – i.e., 41% 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 291,675 tracked outputs that were published within six weeks on either side of this one in any source. This one is in the 43rd percentile – i.e., 43% of its contemporaries scored the same or lower than it.
We're also able to compare this research output to 375 others from the same source and published within six weeks on either side of this one. This one is in the 34th percentile – i.e., 34% of its contemporaries scored the same or lower than it.