The aquatic animals’ transcriptome resource for comparative functional analysis
Abstract Background Aquatic animals have great economic and ecological importance. Among them, non-model organisms have been studied regarding eco-toxicity, stress biology, and environmental adaptation. Due to recent advances in next-generation sequencing techniques, large amounts of RNA-seq data fo...
| Main Authors: | , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2018-05-01
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| Series: | BMC Genomics |
| Online Access: | http://link.springer.com/article/10.1186/s12864-018-4463-x |
| _version_ | 1818034813465001984 |
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| author | Chih-Hung Chou Hsi-Yuan Huang Wei-Chih Huang Sheng-Da Hsu Chung-Der Hsiao Chia-Yu Liu Yu-Hung Chen Yu-Chen Liu Wei-Yun Huang Meng-Lin Lee Yi-Chang Chen Hsien-Da Huang |
| author_facet | Chih-Hung Chou Hsi-Yuan Huang Wei-Chih Huang Sheng-Da Hsu Chung-Der Hsiao Chia-Yu Liu Yu-Hung Chen Yu-Chen Liu Wei-Yun Huang Meng-Lin Lee Yi-Chang Chen Hsien-Da Huang |
| author_sort | Chih-Hung Chou |
| collection | DOAJ |
| description | Abstract Background Aquatic animals have great economic and ecological importance. Among them, non-model organisms have been studied regarding eco-toxicity, stress biology, and environmental adaptation. Due to recent advances in next-generation sequencing techniques, large amounts of RNA-seq data for aquatic animals are publicly available. However, currently there is no comprehensive resource exist for the analysis, unification, and integration of these datasets. This study utilizes computational approaches to build a new resource of transcriptomic maps for aquatic animals. This aquatic animal transcriptome map database dbATM provides de novo assembly of transcriptome, gene annotation and comparative analysis of more than twenty aquatic organisms without draft genome. Results To improve the assembly quality, three computational tools (Trinity, Oases and SOAPdenovo-Trans) were employed to enhance individual transcriptome assembly, and CAP3 and CD-HIT-EST software were then used to merge these three assembled transcriptomes. In addition, functional annotation analysis provides valuable clues to gene characteristics, including full-length transcript coding regions, conserved domains, gene ontology and KEGG pathways. Furthermore, all aquatic animal genes are essential for comparative genomics tasks such as constructing homologous gene groups and blast databases and phylogenetic analysis. Conclusion In conclusion, we establish a resource for non model organism aquatic animals, which is great economic and ecological importance and provide transcriptomic information including functional annotation and comparative transcriptome analysis. The database is now publically accessible through the URL http://dbATM.mbc.nctu.edu.tw/. |
| first_indexed | 2024-12-10T06:45:07Z |
| format | Article |
| id | doaj.art-58e2ed9717a54b719cb4575a889aa215 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-10T06:45:07Z |
| publishDate | 2018-05-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-58e2ed9717a54b719cb4575a889aa2152022-12-22T01:58:41ZengBMCBMC Genomics1471-21642018-05-0119S216117010.1186/s12864-018-4463-xThe aquatic animals’ transcriptome resource for comparative functional analysisChih-Hung Chou0Hsi-Yuan Huang1Wei-Chih Huang2Sheng-Da Hsu3Chung-Der Hsiao4Chia-Yu Liu5Yu-Hung Chen6Yu-Chen Liu7Wei-Yun Huang8Meng-Lin Lee9Yi-Chang Chen10Hsien-Da Huang11Institute of Bioinformatics and Systems Biology, National Chiao Tung UniversityInstitute of Bioinformatics and Systems Biology, National Chiao Tung UniversityInstitute of Bioinformatics and Systems Biology, National Chiao Tung UniversityInstitute of Bioinformatics and Systems Biology, National Chiao Tung UniversityDepartment of Bioscience Technology, Chung Yuan Christian UniversityInstitute of Bioinformatics and Systems Biology, National Chiao Tung UniversityInstitute of Bioinformatics and Systems Biology, National Chiao Tung UniversityInstitute of Bioinformatics and Systems Biology, National Chiao Tung UniversityDepartment of Biological Science and Technology, National Chiao Tung UniversityDepartment of Biological Science and Technology, National Chiao Tung UniversityInstitute of Molecular Medicine and Bioengineering, National Chiao Tung UniversityInstitute of Bioinformatics and Systems Biology, National Chiao Tung UniversityAbstract Background Aquatic animals have great economic and ecological importance. Among them, non-model organisms have been studied regarding eco-toxicity, stress biology, and environmental adaptation. Due to recent advances in next-generation sequencing techniques, large amounts of RNA-seq data for aquatic animals are publicly available. However, currently there is no comprehensive resource exist for the analysis, unification, and integration of these datasets. This study utilizes computational approaches to build a new resource of transcriptomic maps for aquatic animals. This aquatic animal transcriptome map database dbATM provides de novo assembly of transcriptome, gene annotation and comparative analysis of more than twenty aquatic organisms without draft genome. Results To improve the assembly quality, three computational tools (Trinity, Oases and SOAPdenovo-Trans) were employed to enhance individual transcriptome assembly, and CAP3 and CD-HIT-EST software were then used to merge these three assembled transcriptomes. In addition, functional annotation analysis provides valuable clues to gene characteristics, including full-length transcript coding regions, conserved domains, gene ontology and KEGG pathways. Furthermore, all aquatic animal genes are essential for comparative genomics tasks such as constructing homologous gene groups and blast databases and phylogenetic analysis. Conclusion In conclusion, we establish a resource for non model organism aquatic animals, which is great economic and ecological importance and provide transcriptomic information including functional annotation and comparative transcriptome analysis. The database is now publically accessible through the URL http://dbATM.mbc.nctu.edu.tw/.http://link.springer.com/article/10.1186/s12864-018-4463-x |
| spellingShingle | Chih-Hung Chou Hsi-Yuan Huang Wei-Chih Huang Sheng-Da Hsu Chung-Der Hsiao Chia-Yu Liu Yu-Hung Chen Yu-Chen Liu Wei-Yun Huang Meng-Lin Lee Yi-Chang Chen Hsien-Da Huang The aquatic animals’ transcriptome resource for comparative functional analysis BMC Genomics |
| title | The aquatic animals’ transcriptome resource for comparative functional analysis |
| title_full | The aquatic animals’ transcriptome resource for comparative functional analysis |
| title_fullStr | The aquatic animals’ transcriptome resource for comparative functional analysis |
| title_full_unstemmed | The aquatic animals’ transcriptome resource for comparative functional analysis |
| title_short | The aquatic animals’ transcriptome resource for comparative functional analysis |
| title_sort | aquatic animals transcriptome resource for comparative functional analysis |
| url | http://link.springer.com/article/10.1186/s12864-018-4463-x |
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