A Simplistic Bioinformatics Approach to Clade Identification in Chlorella‐like Green Algae

Abstract

Using the 18S (partial), ITS1 (Internal Transcribed Spacer 1), 5.8S, ITS2 (Internal Transcribed Spacer 2) regions of the genomic SSU (small subunit) DNA, we are able to use basic bioinformatics tools to create an effective phylogenetic tree. Sanger sequencing produces a 1.2–1.5 kb region for each individual species that is annotated into four elements, (partial 18S, ITS1, 5.8S, and ITS2) and is formatted for stand‐alone MAFFT v6.903b (Multiple Alignment using Fast Fourier Transform). The multiple alignment is then carried out on each element and concatenated to remove the potential overlap between the elements. Stand‐alone PhyML v3.0 (Phylogenetic estimation using Maximum Likelihood) is then used on the multiple alignment data, and a tree can be viewed using FigTree v1.3.1 (a phylogenetic tree editor and viewer program). The results of this method gives well‐defined clades that are now being used in genera and even species level determination. Using our simplistic method is an effective way to engaging the problem of green algae identification.