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Rhodopsin gene copies in Japanese eel originated in a teleost-specific genome duplication

Overview of attention for article published in Zoological Letters, October 2017
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Title
Rhodopsin gene copies in Japanese eel originated in a teleost-specific genome duplication
Published in
Zoological Letters, October 2017
DOI 10.1186/s40851-017-0079-2
Pubmed ID
Authors

Yoji Nakamura, Motoshige Yasuike, Miyuki Mekuchi, Yuki Iwasaki, Nobuhiko Ojima, Atushi Fujiwara, Seinen Chow, Kenji Saitoh

Abstract

Gene duplication is considered important to increasing the genetic diversity in animals. In fish, visual pigment genes are often independently duplicated, and the evolutionary significance of such duplications has long been of interest. Eels have two rhodopsin genes (rho), one of which (freshwater type, fw-rho) functions in freshwater and the other (deep-sea type, ds-rho) in marine environments. Hence, switching of rho expression in retinal cells is tightly linked with eels' unique life cycle, in which they migrate from rivers or lakes to the sea. These rho genes are apparently paralogous, but the timing of their duplication is unclear due to the deep-branching phylogeny. The aim of the present study is to elucidate the evolutionary origin of the two rho copies in eels using comparative genomics methods. In the present study, we sequenced the genome of Japanese eel Anguilla japonica and reconstructed two regions containing rho by de novo assembly. We found a single corresponding region in a non-teleostean primitive ray-finned fish (spotted gar) and two regions in a primitive teleost (Asian arowana). The order of ds-rho and the neighboring genes was highly conserved among the three species. With respect to fw-rho, which was lost in Asian arowana, the neighboring genes were also syntenic between Japanese eel and Asian arowana. In particular, the pattern of gene losses in ds-rho and fw-rho regions was the same as that in Asian arowana, and no discrepancy was found in any of the teleost genomes examined. Phylogenetic analysis supports mutual monophyly of these two teleostean synteny groups, which correspond to the ds-rho and fw-rho regions. Syntenic and phylogenetic analyses suggest that the duplication of rhodopsin gene in Japanese eel predated the divergence of eel (Elopomorpha) and arowana (Osteoglossomorpha). Thus, based on the principle of parsimony, it is most likely that the rhodopsin paralogs were generated through a whole genome duplication in the ancestor of teleosts, and have remained till the present in eels with distinct functional roles. Our result indicates, for the first time, that teleost-specific genome duplication may have contributed to a gene innovation involved in eel-specific migratory life cycle.

Twitter Demographics

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Mendeley readers

The data shown below were compiled from readership statistics for 31 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 31 100%

Demographic breakdown

Readers by professional status Count As %
Student > Master 8 26%
Researcher 5 16%
Student > Ph. D. Student 5 16%
Student > Doctoral Student 4 13%
Professor > Associate Professor 3 10%
Other 2 6%
Unknown 4 13%
Readers by discipline Count As %
Agricultural and Biological Sciences 13 42%
Biochemistry, Genetics and Molecular Biology 8 26%
Neuroscience 2 6%
Economics, Econometrics and Finance 1 3%
Computer Science 1 3%
Other 0 0%
Unknown 6 19%

Attention Score in Context

This research output has an Altmetric Attention Score of 3. 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 13 November 2017.
All research outputs
#13,336,323
of 23,006,268 outputs
Outputs from Zoological Letters
#115
of 169 outputs
Outputs of similar age
#159,894
of 326,542 outputs
Outputs of similar age from Zoological Letters
#4
of 5 outputs
Altmetric has tracked 23,006,268 research outputs across all sources so far. This one is in the 41st percentile – i.e., 41% of other outputs scored the same or lower than it.
So far Altmetric has tracked 169 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 13.7. This one is in the 30th percentile – i.e., 30% 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 326,542 tracked outputs that were published within six weeks on either side of this one in any source. This one has gotten more attention than average, scoring higher than 50% of its contemporaries.
We're also able to compare this research output to 5 others from the same source and published within six weeks on either side of this one.