Evidence map›Paper›PMID 26818233›Full record

ArticleBMC genomics2016

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

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 and 2 more

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Article in BMC genomics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

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Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed.

  1. Article
  2. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

12 authors.

Yu-Chen LiuInstitute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu, 300, Taiwan, ROC.
Sheng-Da HsuInstitute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu, 300, Taiwan, ROC.
Chih-Hung ChouInstitute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu, 300, Taiwan, ROC.
Wei-Yun HuangInstitute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu, 300, Taiwan, ROC.
Yu-Hung ChenInstitute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu, 300, Taiwan, ROC.
Chia-Yu LiuInstitute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu, 300, Taiwan, ROC.
Guan-Jay LyuInstitute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu, 300, Taiwan, ROC.
Shao-Zhen HuangInstitute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu, 300, Taiwan, ROC.
Sergey AganezovComputational Biology Institute & Department of Mathematics, George Washington University, Washington, DC, USA.
Max A AlekseyevComputational Biology Institute & Department of Mathematics, George Washington University, Washington, DC, USA.
Chung-Der HsiaoDepartment of Bioscience Technology, Chung Yuan Christian University, Chung-Li, Taiwan, ROC. cdhsiao@cycu.edu.tw.
Hsien-Da HuangInstitute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu, 300, Taiwan, ROC. bryan@mail.nctu.edu.tw.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundAnguilla 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.

resultsWith 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%.

conclusionsThis 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.

Indexed as

GenomeAnguillaAnimalsChromosome MappingFishesGenetic LinkageHigh-Throughput Nucleotide SequencingPhylogenyPolymorphism, Single NucleotideReceptors, Cytoplasmic and NuclearSequence Analysis, RNATranscription FactorsReceptors, Cytoplasmic and NuclearTranscription Factors

Identifiers

PMID26818233
PMCPMC4895481

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.