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Comparative in silico analysis of SSRs in coding regions of high confidence predicted genes in Norway spruce (Picea abies) and Loblolly pine (Pinus taeda)

Overview of attention for article published in BMC Genomic Data, December 2015
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Title
Comparative in silico analysis of SSRs in coding regions of high confidence predicted genes in Norway spruce (Picea abies) and Loblolly pine (Pinus taeda)
Published in
BMC Genomic Data, December 2015
DOI 10.1186/s12863-015-0304-y
Pubmed ID
Authors

Sonali Sachin Ranade, Yao-Cheng Lin, Yves Van de Peer, María Rosario García-Gil

Abstract

Microsatellites or simple sequence repeats (SSRs) are DNA sequences consisting of 1-6 bp tandem repeat motifs present in the genome. SSRs are considered to be one of the most powerful tools in genetic studies. We carried out a comparative study of perfect SSR loci belonging to class I (≥20) and class II (≥12 and <20 bp) types located in coding regions of high confidence genes in Picea abies and Pinus taeda. SSRLocator was used to retrieve SSRs from the full length CDS of predicted genes in both species. Trimers were the most abundant motifs in class I followed by hexamers in Picea abies, while trimers and hexamers were equally abundant in Pinus taeda class I SSRs. Hexamers were most frequent within class II SSRs followed by trimers, in both species. Although the frequency of genes containing SSRs was slightly higher in Pinus taeda, SSR counts per Mbp for class I was similar in both species (P-value = 0.22); while for class II SSRs, it was significantly higher in Picea abies (P-value = 0.00009). AT-rich motifs were higher in abundance than the GC-rich motifs, within class II SSRs in both the species (P-values = 10(-9) and 0). With reference to class I SSRs, AT-rich and GC-rich motifs were detected with equal frequency in Pinus taeda (P-value = 0.24); while in Picea abies, GC-rich motifs were detected with higher frequency than the AT-rich motifs (P-value = 0.0005). Our study gives a comparative overview of the genome SSRs composition based on high confidence genes in the two recently sequenced and economically important conifers and, also provides information on functional molecular markers that can be applied in genetic studies in Pinus and Picea species.

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 9 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 9 100%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 2 22%
Researcher 2 22%
Student > Master 2 22%
Professor 1 11%
Student > Bachelor 1 11%
Other 0 0%
Unknown 1 11%
Readers by discipline Count As %
Agricultural and Biological Sciences 5 56%
Nursing and Health Professions 1 11%
Medicine and Dentistry 1 11%
Unknown 2 22%
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 27 December 2015.
All research outputs
#16,721,208
of 25,373,627 outputs
Outputs from BMC Genomic Data
#606
of 1,204 outputs
Outputs of similar age
#229,239
of 397,000 outputs
Outputs of similar age from BMC Genomic Data
#16
of 43 outputs
Altmetric has tracked 25,373,627 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 1,204 research outputs from this source. They receive a mean Attention Score of 4.3. This one is in the 45th percentile – i.e., 45% of its peers scored the same or lower than it.
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We're also able to compare this research output to 43 others from the same source and published within six weeks on either side of this one. This one is in the 48th percentile – i.e., 48% of its contemporaries scored the same or lower than it.