Iha C., Grassa C.J., Lyra G.M., Davis C.C., Verbruggen H. & Oliveira M.C.
Organellar genomics: a useful tool for clarifying evolutionary relationships and understanding molecular evolution in Gracilariaceae (Gracilariales, Rhodophyta)
Journal of Phycology: submitted


Gracilariaceae is a worldwide distributed family that includes numerous economically important species. We applied high-throughput sequencing (HTS) to assemble and annotate organellar genomes (mitochondria and chloroplast) from eight species of Gracilariaceae. We used these data, combined with published genomes, to infer phylogenies and compare the genome architecture of these species representing the main lineages in Gracilariaceae. Our phylogenetic analyses demonstrate similar evolutionary histories between the chloroplast and mitochondrial genomes. However, chloroplast phylogeny was better resolved with full support. Previous members of Hydropuntia are not monophyletic in any of our organellar phylogenetic trees. Additionally, the mitochondrial and chloroplast genomes are highly conserved in gene synteny, which were previously observed in organellar genomes in Gracilariaceae and Florideophyceae. For both genomes, variation mainly occurred in regions where insertions of plasmid-derived sequences (PDSs) were found. All PDSs were similar to known red algae extrachromosomal plasmids, except a bacterial leuC/leuD operon found in Gracilaria tenuistipitata and G. chilensis. In mitochondrial genomes, the PDS insertions were in two regions where the transcription direction changes; between cob and trnL genes, and trnA and trnN genes. PDS insertions in chloroplast genome were in different positions but generally found between psdD and rrs genes. Plasmids have been recognized as mobile elements and their origin remain unclear. Gracilariaceae may be a good model system to study this phenomenon due to the frequent presence of plasmid sequence insertion in organellar genomes. Complete organellar genomes are attractive approach for evolutionary studies for Gracilariaceae, even for Rhodophyta.

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