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Draft genome of Dugesia japonica provides insights into conserved regulatory elements of the brain restriction gene nou-darake in planarians

Overview of attention for article published in Zoological Letters, August 2018
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About this Attention Score

  • In the top 25% of all research outputs scored by Altmetric
  • Among the highest-scoring outputs from this source (#43 of 123)
  • Good Attention Score compared to outputs of the same age (72nd percentile)

Mentioned by

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11 tweeters

Citations

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19 Dimensions

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47 Mendeley
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Title
Draft genome of Dugesia japonica provides insights into conserved regulatory elements of the brain restriction gene nou-darake in planarians
Published in
Zoological Letters, August 2018
DOI 10.1186/s40851-018-0102-2
Pubmed ID
Authors

Yang An, Akane Kawaguchi, Chen Zhao, Atsushi Toyoda, Ali Sharifi-Zarchi, Seyed Ahmad Mousavi, Reza Bagherzadeh, Takeshi Inoue, Hajime Ogino, Asao Fujiyama, Hamidreza Chitsaz, Hossein Baharvand, Kiyokazu Agata

Abstract

Planarians are non-parasitic Platyhelminthes (flatworms) famous for their regeneration ability and for having a well-organized brain. Dugesia japonica is a typical planarian species that is widely distributed in the East Asia. Extensive cellular and molecular experimental methods have been developed to identify the functions of thousands of genes in this species, making this planarian a good experimental model for regeneration biology and neurobiology. However, no genome-level information is available for D. japonica, and few gene regulatory networks have been identified thus far. To obtain whole-genome information on this species and to study its gene regulatory networks, we extracted genomic DNA from 200 planarians derived from a laboratory-bred asexual clonal strain, and sequenced 476 Gb of data by second-generation sequencing. Kmer frequency graphing and fosmid sequence analysis indicated a complex genome that would be difficult to assemble using second-generation sequencing short reads. To address this challenge, we developed a new assembly strategy and improved the de novo genome assembly, producing a 1.56 Gb genome sequence (DjGenome ver1.0, including 202,925 scaffolds and N50 length 27,741 bp) that covers 99.4% of all 19,543 genes in the assembled transcriptome, although the genome is fragmented as 80% of the genome consists of repeated sequences (genomic frequency ≥ 2). By genome comparison between two planarian genera, we identified conserved non-coding elements (CNEs), which are indicative of gene regulatory elements. Transgenic experiments using Xenopus laevis indicated that one of the CNEs in the Djndk gene may be a regulatory element, suggesting that the regulation of the ndk gene and the brain formation mechanism may be conserved between vertebrates and invertebrates. This draft genome and CNE analysis will contribute to resolving gene regulatory networks in planarians. The genome database is available at: http://www.planarian.jp.

Twitter Demographics

The data shown below were collected from the profiles of 11 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 47 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 47 100%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 7 15%
Researcher 6 13%
Student > Doctoral Student 4 9%
Professor > Associate Professor 4 9%
Student > Bachelor 3 6%
Other 11 23%
Unknown 12 26%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 16 34%
Agricultural and Biological Sciences 8 17%
Neuroscience 2 4%
Immunology and Microbiology 2 4%
Computer Science 2 4%
Other 3 6%
Unknown 14 30%

Attention Score in Context

This research output has an Altmetric Attention Score of 7. 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 19 December 2018.
All research outputs
#2,562,574
of 14,056,657 outputs
Outputs from Zoological Letters
#43
of 123 outputs
Outputs of similar age
#73,137
of 271,658 outputs
Outputs of similar age from Zoological Letters
#1
of 1 outputs
Altmetric has tracked 14,056,657 research outputs across all sources so far. Compared to these this one has done well and is in the 81st percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 123 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 11.2. This one has gotten more attention than average, scoring higher than 64% of its peers.
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 271,658 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 72% of its contemporaries.
We're also able to compare this research output to 1 others from the same source and published within six weeks on either side of this one. This one has scored higher than all of them