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

BMC Genomics
Yu-Chen LiuHsien-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 transcr...Continue Reading

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Citations

Oct 19, 2016·Molecular Ecology Resources·Scott A PaveyLouis Bernatchez
Jan 19, 2018·Fish Physiology and Biochemistry·Quanquan CaoShaowu Yin
Apr 29, 2019·BMC Plant Biology·L F SamayoaA Butrón

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Datasets Mentioned

BETA
SRX115953

Methods Mentioned

BETA
454 deep sequencing
RNA-seq
environmental stress

Software Mentioned

Port
CAP3
BLASTX
Swiss
RepeatScout
MAKER
SNAP
Toolkit
Illumina
Trans

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