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Identification of recombination events in outbred species with next-generation sequencing data

Overview of attention for article published in BMC Genomics, May 2018
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Title
Identification of recombination events in outbred species with next-generation sequencing data
Published in
BMC Genomics, May 2018
DOI 10.1186/s12864-018-4791-x
Pubmed ID
Authors

Shentong Tao, Jiyan Wu, Dan Yao, Yuhua Chen, Wenguo Yang, Chunfa Tong

Abstract

Meiotic recombination events include crossovers and non-crossovers or gene conversions. Although the rate of crossovers is often used for genetic mapping, the gene conversion events are not well studied especially in outbred species, which could produce distorted markers and thus affect the precision of genetic maps. We proposed a strategy for identifying gene conversion events in Populus with the next-generation sequencing (NGS) data from the two parents and their progeny in an F1 hybrid population. The strategy first involved phasing the heterozygous SNPs of the parents to obtain the parental haplotype blocks by NGS analytical tools, permitting to identify the parental gene conversion events with progeny genotypes. By incorporating available genetic linkage maps, longer haplotype blocks each corresponding to a chromosome can be created, not only allowing to detect crossover events but also possibly to locate a crossover in a small region. Our analysis revealed that gene conversions are more abundant than crossovers in Populus, with a higher probability to generate distorted markers in the regions involved than in the other regions on genome. The analytical procedures were implemented with Perl scripts as a freely available package, findGCO at https://github.com/tongchf/findGCO . The novel strategy and the new developed Perl package permit to identify gene conversion events with the next-generation sequencing technology in a hybrid population of outbred species. The new method revealed that in a genetic mapping population some distorted genetic markers are possibly due to the gene conversion events.

Twitter Demographics

The data shown below were collected from the profiles of 2 tweeters who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 19 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 19 100%

Demographic breakdown

Readers by professional status Count As %
Researcher 6 32%
Student > Ph. D. Student 4 21%
Student > Postgraduate 2 11%
Student > Master 1 5%
Student > Bachelor 1 5%
Other 0 0%
Unknown 5 26%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 7 37%
Agricultural and Biological Sciences 6 32%
Environmental Science 1 5%
Unknown 5 26%

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 30 May 2018.
All research outputs
#10,378,624
of 13,010,971 outputs
Outputs from BMC Genomics
#5,912
of 7,653 outputs
Outputs of similar age
#203,300
of 271,344 outputs
Outputs of similar age from BMC Genomics
#13
of 21 outputs
Altmetric has tracked 13,010,971 research outputs across all sources so far. This one is in the 11th percentile – i.e., 11% of other outputs scored the same or lower than it.
So far Altmetric has tracked 7,653 research outputs from this source. They receive a mean Attention Score of 4.3. This one is in the 12th percentile – i.e., 12% of its peers scored the same or lower than it.
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We're also able to compare this research output to 21 others from the same source and published within six weeks on either side of this one. This one is in the 19th percentile – i.e., 19% of its contemporaries scored the same or lower than it.