碩士 / 國立交通大學 / 生物資訊及系統生物研究所 / 103 / Neocaridina denticulata, known as black cherry shrimps, has been as test subjects in Taiwan for water toxicity texting experiments for its tribute tendency to response to a variety of chronic or acute toxicity. However, both the genomic and transcriptomic information of such an organism is limited. To further improve the current experiment design and elucidate the mechanism of Neocaridina denticulata’s response to pollutants, we reconstructed the transcriptome through high throughput sequencing. From the sequencing of mRNA from whole body tissues of Neocaridina denticulata, 6.7 gigabases of reads were generated. The reads were then assembled through three mainstream tools: Oases, SOAPdenovo-trans and Trinity, into 68,457 unigenes, with an average length of 1,606 bp and a N50 of 3,694 bp. The unigenes were annotated through sequence alignment search, 42.0% of them were found in NCBI non-redundant protein databases. Gene descriptions, protein conserved domains, and gene ontology terms of these unigenes are also provided. Functional categorization reveals unigenes and pathways related to hydrolase activity, oxidoreductase activity, peroxidase activity and nitrogen compound metabolic process, all of them were found and proven related to toxicity. This is the first report of reconstructed transcriptome of Neocaridina denticulata through next generation sequencing technology and assists further on gene discovery and molecular mechanisms in Neocaridina denticulata’s response to toxicity for future pollution indicators related searches or other experiment design.
| Identifer | oai:union.ndltd.org:TW/103NCTU5112144 |
| Date | January 2015 |
| Creators | Lu, Kuan-Chieh, 呂冠杰 |
| Contributors | Huang, Hsien-Da, 黃憲達 |
| Source Sets | National Digital Library of Theses and Dissertations in Taiwan |
| Language | zh-TW |
| Detected Language | English |
| Type | 學位論文 ; thesis |
| Format | 40 |
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