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Genome evolutionary dynamics followed by diversifying selection explains the complexity of the Sesamum indicum genome

Overview of attention for article published in BMC Genomics, March 2017
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Title
Genome evolutionary dynamics followed by diversifying selection explains the complexity of the Sesamum indicum genome
Published in
BMC Genomics, March 2017
DOI 10.1186/s12864-017-3599-4
Pubmed ID
Authors

Jingyin Yu, Linhai Wang, Hui Guo, Boshou Liao, Graham King, Xiurong Zhang

Abstract

Whole genome duplication (WGD) and tandem duplication (TD) provide two critical sources of raw genetic material for genome complexity and evolutionary novelty. Little is known about the complexity of the Sesamum indicum genome after it diverged from a common ancestor with the paleodiploid Vitis vinifera and further experienced WGD and TD events. Here, we analyzed the functional divergence of different classes of inter- and intra-genome gene pairs from ancestral events to uncover multiple-layers of evolutionary dynamics acting during the process of forming the modern S. indicum genome. Comprehensive inter-genome analyses revealed that 60% and 70% of syntenic orthologous gene pairs were retained among the two subgenomes in S. indicum compared to V. vinifera, although there was no evidence of significant differences under selection pressure. For the intra-genomic analyses, 5,932 duplicated gene pairs experienced fractionation, with the remaining 1,236 duplicated gene pairs having undergone functional divergence under diversifying selection. Analysis of the TD events indicated that 2,945 paralogous gene pairs, from 1,089 tandem arrays of 2-16 genes, experienced functional divergence under diversifying selection. Sequence diversification of different classes of gene pairs revealed that most of TD events occurred after the WGD event, with others following the ancestral gene order indicating ancient TD events at some time prior to the WGD event. Our comparison-of-function analyses for different classes of gene pairs indicated that the WGD and TD evolutionary events were both responsible for introducing genes that enabled exploration of novel and complementary functionalities, whilst maintaining individual plant ruggedness. In this study, we first investigated functional divergence of different classes of gene pairs to characterize the dynamic processes associated with each evolutionary event in S. indicum. The data demonstrated massive and distinct functional divergence among different classes of gene pairs, and provided a genome-scale view of gene function diversification explaining the complexity of the S. indicum genome. We hope this provides a biological model to study the mechanism of plant species formation, particularly in the context of the evolutionary history of flowering plants, and offers novel insights for the study of angiosperm genomes.

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Geographical breakdown

Country Count As %
Unknown 20 100%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 5 25%
Researcher 5 25%
Student > Doctoral Student 1 5%
Student > Master 1 5%
Student > Bachelor 1 5%
Other 2 10%
Unknown 5 25%
Readers by discipline Count As %
Agricultural and Biological Sciences 8 40%
Biochemistry, Genetics and Molecular Biology 4 20%
Pharmacology, Toxicology and Pharmaceutical Science 1 5%
Unknown 7 35%
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 28 March 2017.
All research outputs
#15,451,618
of 22,961,203 outputs
Outputs from BMC Genomics
#6,717
of 10,686 outputs
Outputs of similar age
#194,525
of 309,205 outputs
Outputs of similar age from BMC Genomics
#127
of 200 outputs
Altmetric has tracked 22,961,203 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 10,686 research outputs from this source. They receive a mean Attention Score of 4.7. This one is in the 28th percentile – i.e., 28% of its peers scored the same or lower than it.
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We're also able to compare this research output to 200 others from the same source and published within six weeks on either side of this one. This one is in the 32nd percentile – i.e., 32% of its contemporaries scored the same or lower than it.