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제안 방법
- SSU has proven to be useful for the study of intra and inter-specific genetic variation in Dinophyceae. Here, we sequenced SSU to investigate phylogenetic relationships, and the evolutionary process by undertaking a detailed examination of the mixotrophic C. polykrikoides to establish its association with related species. We also obtained other sequences through GenBank search to form a combined data set.
- micans in close relationship to Gymnodiniales (bootstrap >90% in NJ and parsimony analyses, Fig 5a). To better illustrate the relationships within this group, we performed a branch and bound search on a broad data set consisting of P. balticum, P. trietinum, and P. minimum retrieved from the GenBank database. The resulting phylogenetic tTee was shown in Fig.
- Amplification product obtained with the primers NS1 (forward) and NS2 (reverse) for Nannochloropsis salina EUS-001. 100 bp DNA ladder was used as molecular size marker in this study.
대상 데이터
- Cochlodinium polykrikoides was collected from red tide waters in Korea, 2004. A total of 24 species were provided from Korea Marine Microalgae Culture, Pukyong University in Busan.
- 5c [13] as a subprogram NEIGHBOR. PHYLIP was used dinoflagellates such as Protoperidinium thulesense AB261522, Noctiluca scintillans DQ388461, Gyrodinium aureolum D-97z Dinopkysis acuminate AJ506972, D. fortii AB073118, D. norvegica AY260470, Prorocentrum lima AB189780, P. minimum AJ415520, P. triestinum AB183673, Gambierdiscus toxicus DQ388463, Alexnadrium tamarense AJ415510, A. ostenfeldii AJ535384, Coolia monotis AJ415509z Ostreopsis ovata AF244939, Ceratium furca AJ276699, C. fusus AF022153, Gonyalulax polygramma AJ833631, Gymnodiniwm mikimotoi AF022195, Karena brevis AF352822, Pfiesteria shumwaye AF080093, P. piscicida AY033488, Gymnodinium fuscum AF022194, G. galatheanum AF272049, Gyrodinium spirals AB120001, Scrippsiella trochoidea AJ415515, Takayanui pulchellum AY800130, Akashiwo sanguinea AJ415513. This search for parsimony analysis was repeated several times from different random starting points using the stepwise addition option to make certain the most parsimonious tree was found.
이론/모형
- Sequence data were aligned using the multiple alignment program Clustal W [51] and determined by parsimony and distances methods incorporated in PHYLIP (Phylogeny Inference Package) ver. 3.5c [13] as a subprogram NEIGHBOR. PHYLIP was used dinoflagellates such as Protoperidinium thulesense AB261522, Noctiluca scintillans DQ388461, Gyrodinium aureolum D-97z Dinopkysis acuminate AJ506972, D.
- Distance matrix was analyzed by subprogram NEIGHBOR in PHYLIP with algorithms based on Saitou and Nefs NJ method [41], All nucleotide substituions were equally wighted and unordered alignment gaps were treated as missing information. Reliability of the tree was constructed using subprogram CONSENSE in PHYLIP after pairwise sequence distances were estimated by Kimura's two-parameter method, which attempts to correct observed dissimilarities for multiple substitutions in sequences evolving with a transition bias.
- Phylogram was constructed by inferring from nucleotide sequences of partial SSU region. The tree was obtained using subprogram NEIHGBOR in PHYLIP with the option of Kimura's two-parameter method. The tree was rooted using Microcystis aeruginosa FC-070.
- Phylogram was constructed by inferring from nucleotide sequences of partial SSU resion. The tree was obtained using subprogram NEIGBOR in PHYLIP with the option of Kimura's two-parameter. The topology represents the consensus tree from a heuristic search yielding two equally most parsimonious.
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