Development of Genetic Markers for the Management of Genetic Resources in Taiwan Cuttlefishes(I)

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Project title

Code/計畫編號

MOST107-2313-B019-004

Translated Name/計畫中文名

臺灣烏賊的遺傳資源管理與分子標記開發

Project Coordinator/計畫主持人

Te-Hua Hsu

Funding Organization/主管機關

National Science and Technology Council

Department/Unit

The Center of Excellence for the Ocean,National Taiwan Ocean University

Website

https://www.grb.gov.tw/search/planDetail?id=12673112

Year

2018

Start date/計畫起

01-08-2018

Expected Completion/計畫迄

31-07-2019

Bugetid/研究經費

900千元

ResearchField/研究領域

漁業

The cuttlefish is commercially important fisheries worldwide. However, in the recent years, the cuttlefish is threatened in Taiwan. The annual capture production has dramatically decreased in the past 15 years. In this project, the wild cuttlefish and its eggs will be introduced and cultured in the flow-through aquaculture systems. The long-term captive culture of cuttlefish will also be studied. Additionally, we will develop a cuttlefish strain (5 generations) as experimental animals. Accurate species composition and genetic diversity for stock assessments are necessary. We will develop a species identification method (mtDNA and LAMP) and to study population genetics for cuttlefishes. We develop the universal (cross-species) microsatellites for cuttlefish by transcriptome sequencing. Four cuttlefish (Sepia esculenta, Sepia pharaonis, Sepia lycidas and Sepiella japonica), one squid (Sepioteuthis lessoniana) and one Octopus (Octopus vulgaris) were used. Transcriptome sequencing on the Illumina NextSeq 500 sequencing platform generated a total of 2.77-3.37 Gb of raw data. De novo assembly yielded a total of 57,192-76,153 unigenes. The transcriptome of Sepia esculenta was used as the reference, and 1900 universal microsatellites were found among three Sepia species. These microsatellites are containing at least 100 bp flanking sequences could be further designed primers. Additionally, there are 566 microsatellites shared among four Sepiida species, and 220 microsatellites among five Decapodiformes species, four microsatellites among six Neocoleoidea species. It means the possible universal microsatellites not only present among the cuttlefish but also share with the squid. This rapid cross-species microsatellite development strategy will facilitate genetic diversity studies. 烏賊是世界重要的商業漁業之一。然而在過去15年，台灣烏賊的年捕獲量急劇下降，烏賊資源出現匱乏的徵兆。透過建立烏賊繁養殖及種苗生產放流技術，將可做為未來持續放流之對象。本研究將調查、收集及蓄養野生烏賊，並生產受精卵與種苗進行放流與遺傳管理，另外將其開發成實驗動物。此外，由於準確的物種組成和遺傳多樣性是評估烏賊資源的重要資訊，因此我們將開發一個烏賊快速鑑種方法（mtDNA及LAMP），並研究烏賊的族群遺傳。另外，由於目前缺乏烏賊的分子標記，因此我們透過轉錄組定序來開發烏賊屬通用（跨物種）的微衛星標記。其中包括四種烏賊（金烏賊、虎斑烏賊、唇瓣烏賊、日本無針烏賊），一種鎖管（萊氏擬烏賊）和一種章魚（真鞘）。轉錄組測序使用Illumina NextSeq 500，得到總共2.77-3.37 Gb的原始數據。重測序組裝後共得到57,192-76,153個unigenes。用金烏賊的轉錄組作為參考序列，在三種烏賊屬（Genus Sepia）物種中發現了1900個通用微衛星標記。這些微衛星標記包含至少100 bp的側翼序列可以進一步用來設計引子對。此外，擴大至四個烏賊目物種中則共有566個微衛星標記，五個十足目物種中有220個微衛星標記，六個新鞘亞綱物種中有4個微衛星標記。這顯示可能的通用微衛星標記不僅存在於烏賊屬中，甚至可擴大至與鎖管共享。此快速的跨物種微衛星發展策略將加速遺傳多樣性的研究。

Keyword(s)

分子標記
微衛星標記
轉錄組
遺傳多樣性
烏賊
Molecular marker
microsatellite
Transcriptome
Genetic diversity
Sepia

DSpace CRIS

Development of Genetic Markers for the Management of Genetic Resources in Taiwan Cuttlefishes(I)

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