Plastid genome structure and phylogenomics of the freshwater red algal order Batrachospermales (Rhodophyta)

For the freshwater red algal order Batrachospermales, the number of plastid genomes available is relatively small compared to the number of genera. Fully assembled plastid genomes can provide insights into plastid evolution and crucial data for phylogenetic reconstruction. In the present study, 18 plastid genomes were generated for a total of 40 plastid genomes from 38 species representing 18 of the 23 genera. The greatly expanded dataset allowed for comparison of the plastid genome structural characteristics with the other orders in the Nemaliophycidae and inference of the phylogenetic relationships of the genera within the order. Results showed the plastid genomes had either one or two RNA operons, and this variation could be intrageneric. All plastid genomes had the chlB gene with an intron like all Nemaliophycidae but lacked the apcF gene present in all Nemaliophycidae. The loss of the pbsA gene was variable in the Batrachospermales and the Nemaliophycidae. Phylogenetic analysis using a 126-gene concatenated dataset produced a fully supported Batrachospermales. In addition, generally high support for the relationships among the genera resulted in the most robust phylogeny to date. Nevertheless, the phylogeny also highlighted that potentially more data will be needed to resolve the relationship among sections of Nothocladus and other related genera. Overall, the Batrachospermalean genera were split into two well-supported lineages, which had been noted in other studies using plastid and mitochondrial genomes. However, we lack a combination of characters to distinguish these two lineages, as the morphological characters to describe taxa are shared between them.