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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.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-015-2306-6) contains supplementary material, which is available to authorized users.

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