Genetic diversity of Pseudo-nitzschia pungens (Bacillariophyceae) in Borneo, Malaysia

Pseudo-nitzschia pungens is a chain forming cosmopolitan marine pennate diatom. It is known to produce the neurotoxin, domoic acid (DA) which is responsible for amnesic shellfish poisoning (ASP). In this study, clonal cultures of P. pungens were established from Sabah and Sarawak. To examine the genetic diversity of P. pungens, the ITS region of rDNA was amplified. Nucleotide sequences obtained were used in secondary structure modeling based on homologous modeling and free energy minimization. The ITS sequences of P. pungens showed common structure of ITS1 and ITS2 transcripts. Universal motifs were found in the ITS2 transcript with pyrimidine-pyrimidine (U-U) mismatch and AAA motif between Helix II-III and UGGU motif in the Helix III. Unambiguous orthologous structural sequence alignment was subsequently used in genetic population analyses. Seven haplotypes were found in the Borneon populations. Kuching haplotype is exclusive from the six haplotypes found in Kudat population. The Kuching and Kudat strains formed two distinctive groups inferred by the Profile Neigboring Joining (PNJ) tree. High FST value (>0.69) suggested no gene flow among the populations of P. pungens in Sabah and Sarawak.