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Mining sequence variations in representative polyploid sugarcane germplasm accessions

Overview of attention for article published in BMC Genomics, August 2017
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Title
Mining sequence variations in representative polyploid sugarcane germplasm accessions
Published in
BMC Genomics, August 2017
DOI 10.1186/s12864-017-3980-3
Pubmed ID
Authors

Xiping Yang, Jian Song, Qian You, Dev R. Paudel, Jisen Zhang, Jianping Wang

Abstract

Sugarcane (Saccharum spp.) is one of the most important economic crops because of its high sugar production and biofuel potential. Due to the high polyploid level and complex genome of sugarcane, it has been a huge challenge to investigate genomic sequence variations, which are critical for identifying alleles contributing to important agronomic traits. In order to mine the genetic variations in sugarcane, genotyping by sequencing (GBS), was used to genotype 14 representative Saccharum complex accessions. GBS is a method to generate a large number of markers, enabled by next generation sequencing (NGS) and the genome complexity reduction using restriction enzymes. To use GBS for high throughput genotyping highly polyploid sugarcane, the GBS analysis pipelines in 14 Saccharum complex accessions were established by evaluating different alignment methods, sequence variants callers, and sequence depth for single nucleotide polymorphism (SNP) filtering. By using the established pipeline, a total of 76,251 non-redundant SNPs, 5642 InDels, 6380 presence/absence variants (PAVs), and 826 copy number variations (CNVs) were detected among the 14 accessions. In addition, non-reference based universal network enabled analysis kit and Stacks de novo called 34,353 and 109,043 SNPs, respectively. In the 14 accessions, the percentages of single dose SNPs ranged from 38.3% to 62.3% with an average of 49.6%, much more than the portions of multiple dosage SNPs. Concordantly called SNPs were used to evaluate the phylogenetic relationship among the 14 accessions. The results showed that the divergence time between the Erianthus genus and the Saccharum genus was more than 10 million years ago (MYA). The Saccharum species separated from their common ancestors ranging from 0.19 to 1.65 MYA. The GBS pipelines including the reference sequences, alignment methods, sequence variant callers, and sequence depth were recommended and discussed for the Saccharum complex and other related species. A large number of sequence variations were discovered in the Saccharum complex, including SNPs, InDels, PAVs, and CNVs. Genome-wide SNPs were further used to illustrate sequence features of polyploid species and demonstrated the divergence of different species in the Saccharum complex. The results of this study showed that GBS was an effective NGS-based method to discover genomic sequence variations in highly polyploid and heterozygous species.

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 64 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 64 100%

Demographic breakdown

Readers by professional status Count As %
Researcher 16 25%
Student > Ph. D. Student 12 19%
Student > Master 10 16%
Student > Bachelor 6 9%
Student > Doctoral Student 4 6%
Other 5 8%
Unknown 11 17%
Readers by discipline Count As %
Agricultural and Biological Sciences 37 58%
Biochemistry, Genetics and Molecular Biology 10 16%
Nursing and Health Professions 2 3%
Environmental Science 1 2%
Business, Management and Accounting 1 2%
Other 4 6%
Unknown 9 14%
Attention Score in Context

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 11 August 2017.
All research outputs
#16,099,609
of 23,881,329 outputs
Outputs from BMC Genomics
#6,842
of 10,793 outputs
Outputs of similar age
#202,967
of 319,748 outputs
Outputs of similar age from BMC Genomics
#136
of 224 outputs
Altmetric has tracked 23,881,329 research outputs across all sources so far. This one is in the 22nd percentile – i.e., 22% of other outputs scored the same or lower than it.
So far Altmetric has tracked 10,793 research outputs from this source. They receive a mean Attention Score of 4.8. This one is in the 27th percentile – i.e., 27% of its peers scored the same or lower than it.
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We're also able to compare this research output to 224 others from the same source and published within six weeks on either side of this one. This one is in the 33rd percentile – i.e., 33% of its contemporaries scored the same or lower than it.