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Transcriptome sequencing based annotation and homologous evidence based scaffolding of Anguilla japonica draft genome

Overview of attention for article published in BMC Genomics, January 2016
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Title
Transcriptome sequencing based annotation and homologous evidence based scaffolding of Anguilla japonica draft genome
Published in
BMC Genomics, January 2016
DOI 10.1186/s12864-015-2306-6
Pubmed ID
Authors

Yu-Chen Liu, Sheng-Da Hsu, Chih-Hung Chou, Wei-Yun Huang, Yu-Hung Chen, Chia-Yu Liu, Guan-Jay Lyu, Shao-Zhen Huang, Sergey Aganezov, Max A. Alekseyev, Chung-Der Hsiao, Hsien-Da Huang

Abstract

Anguilla japonica (Japanese eel) is currently one of the most important research subjects in eastern Asia aquaculture. Enigmatic life cycle of the organism makes study of artificial reproduction extremely limited. Henceforth genomic and transcriptomic resources of eels are urgently needed to help solving the problems surrounding this organism across multiple fields. We hereby provide a reconstructed transcriptome from deep sequencing of juvenile (glass eels) whole body samples. The provided expressed sequence tags were used to annotate the currently available draft genome sequence. Homologous information derived from the annotation result was applied to improve the group of scaffolds into available linkage groups. With the transcriptome sequence data combined with publicly available expressed sequence tags evidences, 18,121 genes were structurally and functionally annotated on the draft genome. Among them, 3,921 genes were located in the 19 linkage groups. 137 scaffolds covering 13 million bases were grouped into the linkage groups in additional to the original partial linkage groups, increasing the linkage group coverage from 13 to 14 %. This annotation provide information of the coding regions of the genes supported by transcriptome based evidence. The derived homologous evidences pave the way for phylogenetic analysis of important genetic traits and the improvement of the genome assembly.

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The data shown below were collected from the profiles of 3 X users who shared this research output. Click here to find out more about how the information was compiled.
Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 34 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 1 3%
Unknown 33 97%

Demographic breakdown

Readers by professional status Count As %
Researcher 9 26%
Student > Master 6 18%
Professor > Associate Professor 4 12%
Professor 3 9%
Student > Ph. D. Student 3 9%
Other 5 15%
Unknown 4 12%
Readers by discipline Count As %
Agricultural and Biological Sciences 12 35%
Biochemistry, Genetics and Molecular Biology 7 21%
Computer Science 2 6%
Engineering 2 6%
Environmental Science 1 3%
Other 5 15%
Unknown 5 15%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 2. 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 29 January 2016.
All research outputs
#13,964,379
of 22,842,950 outputs
Outputs from BMC Genomics
#5,350
of 10,655 outputs
Outputs of similar age
#200,280
of 394,940 outputs
Outputs of similar age from BMC Genomics
#133
of 243 outputs
Altmetric has tracked 22,842,950 research outputs across all sources so far. This one is in the 37th percentile – i.e., 37% of other outputs scored the same or lower than it.
So far Altmetric has tracked 10,655 research outputs from this source. They receive a mean Attention Score of 4.7. This one is in the 46th percentile – i.e., 46% 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 394,940 tracked outputs that were published within six weeks on either side of this one in any source. This one is in the 48th percentile – i.e., 48% of its contemporaries scored the same or lower than it.
We're also able to compare this research output to 243 others from the same source and published within six weeks on either side of this one. This one is in the 38th percentile – i.e., 38% of its contemporaries scored the same or lower than it.