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To understand the evolution of  Ulva  chloroplast genomes at intraspecific and interspecific levels, in this study, three complete chloroplast genomes of  Ulva compressa  Linnaeus were sequenced and compared with the available  Ulva  cpDNA data. Our comparative analyses unveiled many noticeable findings. First, genome size variations of  Ulva  cpDNAs at intraspecific and interspecific levels were mainly caused by differences in gain or loss of group I/II introns, integration of foreign DNA fragments, and content of non-coding intergenic spacer regions. Second, chloroplast genomes of  U. compressa  shared the same 100 conserved genes as other  Ulva  cpDNA, whereas  Ulva flexuosa  appears to be the only  Ulva  species with the  minD  gene retained in its cpDNA. Third, five types of group I introns, most of which carry a LAGLIDADG or GIY-YIG homing endonuclease, and three of group II introns, usually encoding a reverse transcriptase/maturase, were detected at 26 insertion sites of 14 host genes in the 23  Ulva  chloroplast genomes, and many intron insertion-sites have been found for the first time in Chlorophyta. Fourth, one degenerate group II intron previously ignored has been detected in the  infA  genes of all  Ulva  species, but not in the closest neighbor,  Pseudoneochloris marina , and the other chlorophycean taxa, indicating that it should be the result of an independent invasion event that occurred in a common ancestor of  Ulva  species. Finally, the seven  U. compressa  cpDNAs represented a novel gene order which was different from that of other  Ulva  cpDNAs. The structure of  Ulva  chloroplast genomes is not conserved, but remarkably plastic, due to multiple rearrangement events.

Chloroplast Genomes of the Green-Tide Forming Alga Ulva compressa: Comparative Chloroplast Genomics in the Genus Ulva (Ulvophyceae, Chlorophyta)