| Summary: | <i>Acaryochloris</i> is a marine cyanobacterium that synthesizes chlorophyll <i>d</i>, a unique chlorophyll that absorbs far-red lights. <i>Acaryochloris</i> is also characterized by the loss of phycobiliprotein (PBP), a photosynthetic antenna specific to cyanobacteria; however, only the type-strain <i>A. marina</i> MBIC11017 retains PBP, suggesting that PBP-related genes were reacquired through horizontal gene transfer (HGT). <i>Acaryochloris</i> is thought to have adapted to various environments through its huge genome size and the genes acquired through HGT; however, genomic information on <i>Acaryochloris</i> is limited. In this study, we report the complete genome sequence of <i>A.</i> <i>marina</i> MBIC10699, which was isolated from the same area of ocean as <i>A. marina</i> MBIC11017 as a PBP-less strain. The genome of <i>A.</i><i>marina</i> MBIC10699 consists of a 6.4 Mb chromosome and four large plasmids totaling about 7.6 Mb, and the phylogenic analysis shows that <i>A.</i><i>marina</i> MBIC10699 is the most closely related to <i>A. marina</i> MBIC11017 among the <i>Acaryochloris</i> species reported so far. Compared with <i>A. marina</i> MBIC11017, the chromosomal genes are highly conserved between them, while the genes encoded in the plasmids are significantly diverse. Comparing these genomes provides clues as to how the genes for PBPs were reacquired and what changes occurred in the genes for photosystems during evolution.
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