Molecular identification of red tide-causing microalga Heterosigma akashiwo strains based on their chloroplast DNA sequences

ABSTRACT:   In order to establish genetic signatures for intraspecific identification, parts of the genes rbcL , rbcS and psbA and their intergenic spacer (IGS) regions were amplified by polymerase chain reaction (PCR) from the chloroplast genomes of Heterosigma akashiwo strains isolated from Japan. A transfer RNA-Leu gene trnL and a hypothetical gene cfxQ , which is related to ribulose bisphosphate carboxylase/oxygenase expression, were found in the upstream region of the rbcL gene and in the rbcS-psbA IGS region, respectively. All the gene-coding regions and the IGS regions between rbcL and rbcS showed the same sequences among the strains tested. In contrast, the rbcL upstream regions and the rbcS-cfxQ IGS regions showed some differences such as nucleotide substitutions, duplications and inversions between NIES-5 and the other strains. Based on these sequence data, five genetic signatures were established and their simple and rapid detection by means of strain-specific PCR primers and PCR-restriction fragment length polymorphism techniques was examined. The results suggested the usefulness of these genetic signatures and techniques for the discrimination of H. akashiwo populations.