New inter-species phylogenetic markers for Nannochloropsis. (A) Comparison of the sensitivity and specificity among candidate regions/markers for inter-species phylogenetic reconstruction. The regions/markers derived from genic and intergenic sequences of pt and mt of the seven strains were listed on the X axe. The % nucleotide difference of each region/markers was calculated as the index for sensitivity. The average bootstrap values of all branches in the sequence-specific phylogenetic trees (maximum parsimony; MP) were shown as the index for specificity. *: presently used markers. Arrow: candidate phylogenetic markers that provided higher sensitivity than ITS2. (B) Phylogeny of Nannochloropsis strains reconstructed from the presently used and our proposed sequence markers. Phylograms were derived using MP analysis. *: reference trees based on the concatenated sequences of all pt/mt protein-coding genes. **: presently used markers. Blank box: presently used markers whose phylogenetic reconstructions are not consistent with the reference trees. CCMP537 was assigned as the root for each of the trees.