AUTHOR=Liu Feng , Melton James T. 

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

JOURNAL=Frontiers in Marine Science

VOLUME=8

YEAR=2021

URL=https://www.frontiersin.org/journals/marine-science/articles/10.3389/fmars.2021.668542

DOI=10.3389/fmars.2021.668542

ISSN=2296-7745

ABSTRACT=<p>To understand the evolution of <italic>Ulva</italic> chloroplast genomes at intraspecific and interspecific levels, in this study, three complete chloroplast genomes of <italic>Ulva compressa</italic> Linnaeus were sequenced and compared with the available <italic>Ulva</italic> cpDNA data. Our comparative analyses unveiled many noticeable findings. First, genome size variations of <italic>Ulva</italic> 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 <italic>U. compressa</italic> shared the same 100 conserved genes as other <italic>Ulva</italic> cpDNA, whereas <italic>Ulva flexuosa</italic> appears to be the only <italic>Ulva</italic> species with the <italic>minD</italic> 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 <italic>Ulva</italic> 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 <italic>infA</italic> genes of all <italic>Ulva</italic> species, but not in the closest neighbor, <italic>Pseudoneochloris marina</italic>, and the other chlorophycean taxa, indicating that it should be the result of an independent invasion event that occurred in a common ancestor of <italic>Ulva</italic> species. Finally, the seven <italic>U. compressa</italic> cpDNAs represented a novel gene order which was different from that of other <italic>Ulva</italic> cpDNAs. The structure of <italic>Ulva</italic> chloroplast genomes is not conserved, but remarkably plastic, due to multiple rearrangement events.</p>