title: Transcriptome sequencing based annotation and homologous evidence based scaffolding of Anguilla japonica draft genome.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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%.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu, 300, Taiwan, ROC.
authors.forename: Yu-Chen
authors.initials: YC
authors.lastname: Liu
authors.affiliation: Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu, 300, Taiwan, ROC.
authors.forename: Sheng-Da
authors.initials: SD
authors.lastname: Hsu
authors.affiliation: Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu, 300, Taiwan, ROC.
authors.forename: Chih-Hung
authors.initials: CH
authors.lastname: Chou
authors.affiliation: Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu, 300, Taiwan, ROC.
authors.forename: Wei-Yun
authors.initials: WY
authors.lastname: Huang
authors.affiliation: Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu, 300, Taiwan, ROC.
authors.forename: Yu-Hung
authors.initials: YH
authors.lastname: Chen
authors.affiliation: Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu, 300, Taiwan, ROC.
authors.forename: Chia-Yu
authors.initials: CY
authors.lastname: Liu
authors.affiliation: Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu, 300, Taiwan, ROC.
authors.forename: Guan-Jay
authors.initials: GJ
authors.lastname: Lyu
authors.affiliation: Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu, 300, Taiwan, ROC.
authors.forename: Shao-Zhen
authors.initials: SZ
authors.lastname: Huang
authors.affiliation: Computational Biology Institute & Department of Mathematics, George Washington University, Washington, DC, USA.|Department of Higher Mathematics, ITMO University, St. Petersburg, Russia.
authors.forename: Sergey
authors.initials: S
authors.lastname: Aganezov
authors.affiliation: Computational Biology Institute & Department of Mathematics, George Washington University, Washington, DC, USA.
authors.forename: Max A
authors.initials: MA
authors.lastname: Alekseyev
authors.affiliation: Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li, Taiwan, ROC. cdhsiao@cycu.edu.tw.
authors.forename: Chung-Der
authors.initials: CD
authors.lastname: Hsiao
authors.affiliation: Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu, 300, Taiwan, ROC. bryan@mail.nctu.edu.tw.|Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu, 300, Taiwan, ROC. bryan@mail.nctu.edu.tw.|Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan. bryan@mail.nctu.edu.tw.
authors.forename: Hsien-Da
authors.initials: HD
authors.lastname: Huang
mesh_terms: D000811:Anguilla / Q000235:genetics*; D000818:Animals; D002874:Chromosome Mapping; D005399:Fishes / Q000235:genetics; D008040:Genetic Linkage; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D018160:Receptors, Cytoplasmic and Nuclear / Q000145:classification / Q000235:genetics; D017423:Sequence Analysis, RNA; D014157:Transcription Factors / Q000145:classification / Q000235:genetics
chemical_list: D018160:Receptors, Cytoplasmic and Nuclear; D014157:Transcription Factors
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