Classifying amoebae is difficult due to limited morphological characters that can be used to distinguish them. Biodiversity within amoeboid organisms still remains poorly studied. DNA sequences such as small subunit ribosomal RNA and Cox1 genes are almost exactly the same between Cochliopodium minus & C. pentatrifurcatum. However, they have a very different structure of the scales. Cochliopodium scales have been believed to be species-specific and features of scale morphology has been used for unambiguous identification of morphospecies within the genus. In this study, we investigated transcriptome data in order to compare the two species and find genetic evidence of the observed scale morphology difference from the gene expression data. Gene expression analysis show that C. pentatrifurcatum and C. minus express some genes differentially. Genes such as collagen alpha, multidrug resistance-associated protein 1 and polyubiquitin might explain the observed morphological differences.
