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Relationships of Gag-pol Diversity between Ty3/Gypsy and Retroviridae LTR retroelements and the three kings hypothesis

Overview of attention for article published in BMC Evolutionary Biology, January 2008
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Title
Relationships of Gag-pol Diversity between Ty3/Gypsy and Retroviridae LTR retroelements and the three kings hypothesis
Published in
BMC Evolutionary Biology, January 2008
DOI 10.1186/1471-2148-8-276
Pubmed ID
Authors

Carlos Llorens, Mario A Fares, Andres Moya

Abstract

The origin of vertebrate retroviruses (Retroviridae) is yet to be thoroughly investigated, but due to their similarity and identical gag-pol (and env) genome structure, it is accepted that they evolve from Ty3/Gypsy LTR retroelements the retrotransposons and retroviruses of plants, fungi and animals. These 2 groups of LTR retroelements code for 3 proteins rarely studied due to the high variability - gag polyprotein, protease and GPY/F module. In relation to 3 previously proposed Retroviridae classes I, II and II, investigation of the above proteins conclusively uncovers important insights regarding the ancient history of Ty3/Gypsy and Retroviridae LTR retroelements. We performed a comprehensive study of 120 non-redundant Ty3/Gypsy and Retroviridae LTR retroelements. Phylogenetic reconstruction inferred based on the concatenated analysis of the gag and pol polyproteins shows a robust phylogenetic signal regarding the clustering of OTUs. Evaluation of gag and pol polyproteins separately yields discordant information. While pol signal supports the traditional perspective (2 monophyletic groups), gag polyprotein describes an alternative scenario where each Retroviridae class can be distantly related with one or more Ty3/Gypsy lineages. We investigated more in depth this evidence through comparative analyses performed based on the gag polyprotein, the protease and the GPY/F module. Our results indicate that contrary to the traditional monophyletic view of the origin of vertebrate retroviruses, the Retroviridae class I is a molecular fossil, preserving features that were probably predominant among Ty3/Gypsy ancestors predating the split of plants, fungi and animals. In contrast, classes II and III maintain other phenotypes that emerged more recently during Ty3/Gypsy evolution. The 3 Retroviridae classes I, II and III exhibit phenotypic differences that delineate a network never before reported between Ty3/Gypsy and Retroviridae LTR retroelements. This new scenario reveals how the diversity of vertebrate retroviruses is polyphyletically recurrent into the Ty3/Gypsy evolution, i.e. older than previously thought. The simplest hypothesis to explain this finding is that classes I, II and III trace back to at least 3 Ty3/Gypsy ancestors that emerged at different evolutionary times prior to protostomes-deuterostomes divergence. We have called this "the three kings hypothesis" concerning the origin of vertebrate retroviruses.

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Mendeley readers

The data shown below were compiled from readership statistics for 75 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Brazil 3 4%
Italy 2 3%
France 2 3%
Spain 1 1%
United Kingdom 1 1%
Germany 1 1%
Japan 1 1%
United States 1 1%
Netherlands 1 1%
Other 2 3%
Unknown 60 80%

Demographic breakdown

Readers by professional status Count As %
Researcher 22 29%
Student > Ph. D. Student 19 25%
Student > Bachelor 8 11%
Professor 5 7%
Student > Master 5 7%
Other 16 21%
Readers by discipline Count As %
Agricultural and Biological Sciences 50 67%
Biochemistry, Genetics and Molecular Biology 14 19%
Unspecified 4 5%
Medicine and Dentistry 3 4%
Computer Science 2 3%
Other 2 3%

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 21 June 2016.
All research outputs
#4,158,077
of 7,926,939 outputs
Outputs from BMC Evolutionary Biology
#1,431
of 1,927 outputs
Outputs of similar age
#83,145
of 175,630 outputs
Outputs of similar age from BMC Evolutionary Biology
#48
of 69 outputs
Altmetric has tracked 7,926,939 research outputs across all sources so far. This one is in the 27th percentile – i.e., 27% of other outputs scored the same or lower than it.
So far Altmetric has tracked 1,927 research outputs from this source. They typically receive more attention than average, with a mean Attention Score of 9.0. This one is in the 16th percentile – i.e., 16% of its peers scored the same or lower than it.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 175,630 tracked outputs that were published within six weeks on either side of this one in any source. This one is in the 40th percentile – i.e., 40% of its contemporaries scored the same or lower than it.
We're also able to compare this research output to 69 others from the same source and published within six weeks on either side of this one. This one is in the 21st percentile – i.e., 21% of its contemporaries scored the same or lower than it.