多齒新米蝦的轉錄體及其功能性分析資料庫之建置

Abstract

多齒新米蝦或俗稱的黑殼蝦，是台灣常見的水質指標物種，已用在許多水質毒性實驗中，提供各種在急性毒與慢性毒水質中的生物反應指標。若能從基因體角度去研究此生物的功能性及反應機制，必能對相關研究作出貢獻。然而對於非模式生物而言，現有的資源不管是基因體或是轉錄體的資訊都十分有限，為了更多優化現有的水質試驗設計並闡明多齒新米蝦在汙染物中的反應機制，透過高通量定序技術重建轉錄體序列成為一件首先需要完成的要事。 從黑殼蝦全體組織中抽得全mRNA產生定序深度6.7GB的Reads量。這些Reads接著分別三個轉錄體拼接工具Oases, SOAPdenovo-trans 和 Trinity拼接後重組成68,457個unigenes，有良好的平均長度（1,606bp）和N50長度長度（3,694bp）。接著將這些序列align到NCBI non-redundant蛋白質資料庫，共有42.0%的比例被搜尋到，提供這些unigenes的Gene descriptions, protein conserved domains, 還有GO terms。功能性分類顯示hydrolase activity, oxidoreductase activity, peroxidase activity 及 nitrogen compound metabolic process相關的unigenes 及pathways，可以提供更完整的資訊以供後續研究及實驗設計參考。這是第一個重建多齒新米蝦轉錄體的研究報告，並使用次世代定序技術挖掘出該物種基因發現及分子機制的可能性，進一步供未來的相關研究及實驗設計。

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.