Phylogenetic Study Of Chlorophyta Based On Chloroplast Genome

Phylogenetic relationships within the green algal phylum Chlorophyta have proven difficult to resolve.The core Chlorophyta include Chlorophyceae,Ulvophyceae,Trebouxiophyceae,Pedinophyceae and Chlorodendrophyceae,but the relationships among these classes remain disputed and the monophyly of Ulvophyceae and Trebouxiophyceae are highly controversial.We analyzed a dataset of 101 green algae and 73 protein-coding genes sampled from complete and partial chloroplast genomes,including six newly sequenced ulvophyte genomes(Blidingia minima NIES-1837,Ulothrix zonata NIES-537,Halochlorococcum sp.NIES-1838,Scotinosphaera sp.NIES-154,Caulerpa brownii and Cephaleuros sp.HZ-2017),and conducted phylogenomic analyses with strong phylogenetic signals and heterogeneous models.We have found that high GC-heterogeneity sites contain strong conflict signals.Homogeneous model is too simplistic and not realistic for this dataset,leading to erroneous topologies.We applied the Tree Cerrtainty(TC)score to quantify the level of incongruence between phylogenetic trees in chloroplast genomic datasets,and show that the conflicting phylogenetic trees of core Chlorophyta stem from the most GC-heterogeneous sites.With removing the most GC-heterogeneous sites,our phylogenomic analyses support monophyly of the Chlorophyceae and Trebouxiophyceae,but the Ulvophyceae is resolved as polyphyletic.Our analytical framework provides an efficient approach to recover the optimal phylogenetic relationships by minimizing conflicting signals,and improve the accuracy of phylogenetic inference at ancient divergences.