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X Demographics
Mendeley readers
Attention Score in Context
| Title |
Natural Allelic Variations in Highly Polyploidy Saccharum Complex
|
|---|---|
| Published in |
Frontiers in Plant Science, June 2016
|
| DOI | 10.3389/fpls.2016.00804 |
| Pubmed ID | |
| Authors |
Jian Song, Xiping Yang, Marcio F. R. Resende, Leandro G. Neves, James Todd, Jisen Zhang, Jack C. Comstock, Jianping Wang |
| Abstract |
Sugarcane (Saccharum spp.) is an important sugar and biofuel crop with high polyploid and complex genomes. The Saccharum complex, comprised of Saccharum genus and a few related genera, are important genetic resources for sugarcane breeding. A large amount of natural variation exists within the Saccharum complex. Though understanding their allelic variation has been challenging, it is critical to dissect allelic structure and to identify the alleles controlling important traits in sugarcane. To characterize natural variations in Saccharum complex, a target enrichment sequencing approach was used to assay 12 representative germplasm accessions. In total, 55,946 highly efficient probes were designed based on the sorghum genome and sugarcane unigene set targeting a total of 6 Mb of the sugarcane genome. A pipeline specifically tailored for polyploid sequence variants and genotype calling was established. BWA-mem and sorghum genome approved to be an acceptable aligner and reference for sugarcane target enrichment sequence analysis, respectively. Genetic variations including 1,166,066 non-redundant SNPs, 150,421 InDels, 919 gene copy number variations, and 1,257 gene presence/absence variations were detected. SNPs from three different callers (Samtools, Freebayes, and GATK) were compared and the validation rates were nearly 90%. Based on the SNP loci of each accession and their ploidy levels, 999,258 single dosage SNPs were identified and most loci were estimated as largely homozygotes. An average of 34,397 haplotype blocks for each accession was inferred. The highest divergence time among the Saccharum spp. was estimated as 1.2 million years ago (MYA). Saccharum spp. diverged from Erianthus and Sorghum approximately 5 and 6 MYA, respectively. The target enrichment sequencing approach provided an effective way to discover and catalog natural allelic variation in highly polyploid or heterozygous genomes. |
X Demographics
The data shown below were collected from the profiles of 2 X users who shared this research output. Click here to find out more about how the information was compiled.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Switzerland | 1 | 50% |
| Unknown | 1 | 50% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Scientists | 1 | 50% |
| Members of the public | 1 | 50% |
Mendeley readers
The data shown below were compiled from readership statistics for 70 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Brazil | 4 | 6% |
| Spain | 1 | 1% |
| Unknown | 65 | 93% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Researcher | 14 | 20% |
| Student > Master | 14 | 20% |
| Student > Ph. D. Student | 9 | 13% |
| Student > Doctoral Student | 7 | 10% |
| Student > Bachelor | 6 | 9% |
| Other | 10 | 14% |
| Unknown | 10 | 14% |
| Readers by discipline | Count | As % |
|---|---|---|
| Agricultural and Biological Sciences | 35 | 50% |
| Biochemistry, Genetics and Molecular Biology | 20 | 29% |
| Economics, Econometrics and Finance | 1 | 1% |
| Neuroscience | 1 | 1% |
| Unknown | 13 | 19% |
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 08 June 2016.
All research outputs
#17,807,987
of 22,876,619 outputs
Outputs from Frontiers in Plant Science
#12,078
of 20,268 outputs
Outputs of similar age
#241,461
of 340,472 outputs
Outputs of similar age from Frontiers in Plant Science
#260
of 524 outputs
Altmetric has tracked 22,876,619 research outputs across all sources so far. This one is in the 19th percentile – i.e., 19% of other outputs scored the same or lower than it.
So far Altmetric has tracked 20,268 research outputs from this source. They receive a mean Attention Score of 4.0. This one is in the 31st percentile – i.e., 31% of its peers scored the same or lower than it.
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We're also able to compare this research output to 524 others from the same source and published within six weeks on either side of this one. This one is in the 41st percentile – i.e., 41% of its contemporaries scored the same or lower than it.