Phylogenetic inference is an important approach that allows the recovery of the evolutionary history and the origin of the Chlorellaceae species. Despite the species potential for biofuel feedstock production, their high phenotypic plasticity and similar morphological structures among the species have muddled the taxonomy and identification of the Chlorellaceae species. This study aimed to decipher Chlorellaceae DNA barcode marker heterogeneity by examining the sequence divergence and genomic properties of 18S rRNA, ITS (ITS1-5.8S rRNA-ITS2-28S rRNA), and rbcL from 655 orthologous sequences of 64 species across 31 genera in the Chlorellaceae family. The study assessed the distinct evolutionary properties of the DNA markers that may have caused the discordance between individual trees in the phylogenetic inference using the Robinson-Foulds distance and the Shimodaira-Hasegawa test. Our findings suggest that using the supermatrix approach improves the congruency between trees by reducing.....

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The objective of the study was to develop a supermatrix framework by incorporating the unique evolutionary signals of each gene that can improve phylogenetic inferences. The aim was to address the issue of the supermatrix approach, which potentially disregards individual gene properties. The study involved two main experiments: i) Experiment 1 focused on the effect of evolutionary signals across housekeeping genes on phylogeny inference using Chlorellaceae species. ii) Experiment 2 involved the development of a bioinformatics framework using the supermatrix approach. The framework incorporates unique properties of each gene in phylogenetic tree construction, such as sequence heterogeneity, sequence informative sites, taxonomic conflicts at the kingdom level, and tree distance between the gene tree and species tree. The genes were concatenated, based on their similar gene properties, into a supermatrix for phylogeny inference. Generated phylogenetic tree was compared with tree-of-life, .....

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