Organelle and transcriptomic genomes of a freshwater brown alga and further insights on the phylogenetic relationship of red secondary plastid-derived lineages

Freshwater brown algae have been acknowledged as the least diverse of all groups of freshwater algae. Morphological and molecular investigation were conducted on a freshwater brown alga collected in this study. Morphological characterization and phylogenetic tree based on the rbcL gene confirmed its attribution to Heribaudiella fluviatilis. The complete organelle genomes of H. fluviatilis were determined and assembled from high-throughput sequencing. A circular tetrad structure of 128,880 bp was identified for the chloroplast, and the mitochondrial genome was assembled as a circle with 43,657 bp in length. This study provides the first and only record of organelle genomic information of the freshwater Phaeophyceae, which are important for understanding the endosymbiosis theories. Concatenated (Bayesian inference, maximum likelihood under MFP and GHOST models) and coalescent methods were used to construct the phylogenetic relationship among secondary plastid-bearing lineages based on organelle genomes. Obvious conflicts were observed in grouping relationships of chloroplast and mitochondrial genomes, even among different evolutionary models and tree-constructing methods. The transcriptome of H. fluviatilis was sequenced and used to construct the phylogenetic relationship among secondary plastid-bearing lineages. The phylogenetic relationships in nuclear and mitochondrial genomes were consistent in grouping CHSR taxa (cryptophytes, haptophytes, stramenopiles and rhizarians) in an independent branch. The phylogenetic relationship constructed from nuclear transcriptomes was highly reliable by owning robust supporting values on each node and was consistent with the serial endosymbiosis theory on evolution of red secondary plastid-derived lineages.