BioChip J. (2012) 6(4): 325-334 DOI 10.1007/s13206-012-6404-0 Abstract Countless species occur in the marine microalgal domain. Some are used as health func- tional foods or medical products but many species are harmful such as those that cause the red tide. There- fore, it is necessary to conduct prompt and accurate identification of microalgal species. As it is quite difficult to accurately distinguish all species in terms of morphology, we performed DNA barcoding analy- sis using molecular markers for more accurate and rapid screening. DNA barcoding analysis, i.e., DNA chip technology, is a powerful method for studies on microalgal taxonomy and biodiversity. We used the mitochondrial cytochrome c oxidase subunit I (mtCOI) as a barcoding gene to identify microalgal species. In this study, the diversity and phylogenetic differences among different microalgae were analyzed. Additio- nally, a microalgal species-specific probe was screen- ed by 21-23 bp and the result was printed on silylated slide for use in a robotic microarrayer. As a result, we performed a DNA chip assay for each of 25 microalgal species and determined that the COI barcode gene was suitable as a marker gene, as it could identify various microalgae from the Korean South Sea by species. Keywords: Microalgae, DNA barcoding, Mitochond- rial cytochrome c oxidase subunit I, DNA chip assay, Marker gene Introduction Marine microalgae are primary producers and useful biological resources, as they provide the food base for bio-organisms used for culturing, pharmaceutical products, and biological fertilizers. However, rapid proliferation of some marine microalgae may cause tremendous harm to the marine ecosystem and fish- ery resources. The rapid proliferation of some marine microalgae creates red tides, which leads to death of many organisms and causes harmful algal blooms by discharging toxic substances into the sea. Therefore, early identification of marine microalgal species should be prioritized to take a speedy response against these red tides 1,2 . Ways to identify species using morphological charac- ters include general biological appearance, specific structure, internal morphology, and embryological dif- ferences. Additionally, characters such as the physio- logy characters of metabolism and excretion, behavio- ral characters such as courtship displays, and ecologi- cal characters such as habitats, food, seasonal variation, and biogeological distribution characters 3,4 are used to identify species. Many methods are available to classify life using Original Research Development of DNA chip for verification of 25 microalgae collected from southern coastal region in Korea Gunsup Lee 1 , So Yun Park 2 , Seungshic Yum 1 , Seonock Woo 1 , Youn-Ho Lee 3 , Seung Yong Hwang 4 , Heung-Sik Park 5 , Sang Hyun Moh 6 , Sukchan Lee 7 & Taek-Kyun Lee 1 Received: 21 July 2012 / Accepted: 13 August 2012 / Published online: 20 December 2012 � The Korean BioChip Society and Springer 2012 1 South Sea Environment Research Department, Korea Institute of Ocean Science and Technology, Geoje 656-830, Korea 2 Medical Research Center of Neural Dysfunction, Gyeonsang National University, Jinju 660-751, Korea 3 Marine Living Resources Research Department, Korea Institute of Ocean Science and Technology, Ansan, Gyeonggi-do 425-600, Korea 4 Department of Biochemistry, Hanyang University & GenoCheck Co. Ltd., Sangnok-gu, Ansan, Gyeonggi-do 426-791, Korea 5 Korea South Pacific Ocean Research Center, Korea Institute of Ocean Science and Technology, Ansan, Gyeonggi-do 425-600, Korea 6 Bio-FD&C., Ltd, Anti-aging Research Institute, 57 Eunbong-ro, Namdong-gu, Incheon 405-849, Korea 7 Department of Genetic Engineering, Sungkyunkwan University, 300 Chunchun-dong, Jangan-gu, Suwon 440-746, Korea Correspondence and requests for materials should be addressed to T.-K. Lee ( tklee@kiost.ac)