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Transcriptome sequencing based annotation and homologous evidence based scaffolding of Anguilla japonica draft genome
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 neede...
Autores principales: | , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4895481/ https://www.ncbi.nlm.nih.gov/pubmed/26818233 http://dx.doi.org/10.1186/s12864-015-2306-6 |
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author | Liu, Yu-Chen Hsu, Sheng-Da Chou, Chih-Hung Huang, Wei-Yun Chen, Yu-Hung Liu, Chia-Yu Lyu, Guan-Jay Huang, Shao-Zhen Aganezov, Sergey Alekseyev, Max A. Hsiao, Chung-Der Huang, Hsien-Da |
author_facet | Liu, Yu-Chen Hsu, Sheng-Da Chou, Chih-Hung Huang, Wei-Yun Chen, Yu-Hung Liu, Chia-Yu Lyu, Guan-Jay Huang, Shao-Zhen Aganezov, Sergey Alekseyev, Max A. Hsiao, Chung-Der Huang, Hsien-Da |
author_sort | Liu, Yu-Chen |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-4895481 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-48954812016-06-10 Transcriptome sequencing based annotation and homologous evidence based scaffolding of Anguilla japonica draft genome Liu, Yu-Chen Hsu, Sheng-Da Chou, Chih-Hung Huang, Wei-Yun Chen, Yu-Hung Liu, Chia-Yu Lyu, Guan-Jay Huang, Shao-Zhen Aganezov, Sergey Alekseyev, Max A. Hsiao, Chung-Der Huang, Hsien-Da BMC Genomics Proceedings 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. BioMed Central 2016-01-11 /pmc/articles/PMC4895481/ /pubmed/26818233 http://dx.doi.org/10.1186/s12864-015-2306-6 Text en © Liu et al. 2015 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Proceedings Liu, Yu-Chen Hsu, Sheng-Da Chou, Chih-Hung Huang, Wei-Yun Chen, Yu-Hung Liu, Chia-Yu Lyu, Guan-Jay Huang, Shao-Zhen Aganezov, Sergey Alekseyev, Max A. Hsiao, Chung-Der Huang, Hsien-Da Transcriptome sequencing based annotation and homologous evidence based scaffolding of Anguilla japonica draft genome |
title | Transcriptome sequencing based annotation and homologous evidence based scaffolding of Anguilla japonica draft genome |
title_full | Transcriptome sequencing based annotation and homologous evidence based scaffolding of Anguilla japonica draft genome |
title_fullStr | Transcriptome sequencing based annotation and homologous evidence based scaffolding of Anguilla japonica draft genome |
title_full_unstemmed | Transcriptome sequencing based annotation and homologous evidence based scaffolding of Anguilla japonica draft genome |
title_short | Transcriptome sequencing based annotation and homologous evidence based scaffolding of Anguilla japonica draft genome |
title_sort | transcriptome sequencing based annotation and homologous evidence based scaffolding of anguilla japonica draft genome |
topic | Proceedings |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4895481/ https://www.ncbi.nlm.nih.gov/pubmed/26818233 http://dx.doi.org/10.1186/s12864-015-2306-6 |
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