title: Reconstructing the complex evolutionary history of mobile plasmids in red algal genomes.
abstract: The integration of foreign DNA into algal and plant plastid genomes is a rare event, with only a few known examples of horizontal gene transfer (HGT). Plasmids, which are well-studied drivers of HGT in prokaryotes, have been reported previously in red algae (Rhodophyta). However, the distribution of these mobile DNA elements and their sites of integration into the plastid (ptDNA), mitochondrial (mtDNA), and nuclear genomes of Rhodophyta remain unknown. Here we reconstructed the complex evolutionary history of plasmid-derived DNAs in red algae. Comparative analysis of 21 rhodophyte ptDNAs, including new genome data for 5 species, turned up 22 plasmid-derived open reading frames (ORFs) that showed syntenic and copy number variation among species, but were conserved within different individuals in three lineages. Several plasmid-derived homologs were found not only in ptDNA but also in mtDNA and in the nuclear genome of green plants, stramenopiles, and rhizarians. Phylogenetic and plasmid-derived ORF analyses showed that the majority of plasmid DNAs originated within red algae, whereas others were derived from cyanobacteria, other bacteria, and viruses. Our results elucidate the evolution of plasmid DNAs in red algae and suggest that they spread as parasitic genetic elements. This hypothesis is consistent with their sporadic distribution within Rhodophyta.
authors.affiliation: Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea.
authors.forename: JunMo
authors.initials: J
authors.lastname: Lee
authors.affiliation: Marine Biodiversity Institute of Korea, Seocheon, 325-902, Korea.
authors.forename: Kyeong Mi
authors.initials: KM
authors.lastname: Kim
authors.affiliation: Marine Ecosystem Research Division, Korea Institute of Ocean Science &Technology, Ansan, 15627, Korea.
authors.forename: Eun Chan
authors.initials: EC
authors.lastname: Yang
authors.affiliation: Herbarium, University of California at Berkeley, 1001 Valley Life Sciences Building 2465, Berkeley, California, 94720-2465, USA.
authors.forename: Kathy Ann
authors.initials: KA
authors.lastname: Miller
authors.affiliation: Department of Biology, Chungnam National University, Daejeon, 34134, Korea.
authors.forename: Sung Min
authors.initials: SM
authors.lastname: Boo
authors.affiliation: Department of Ecology, Evolution and Natural Resources and Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ 08901, USA.
authors.forename: Debashish
authors.initials: D
authors.lastname: Bhattacharya
authors.affiliation: Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea.
authors.forename: Hwan Su
authors.initials: HS
authors.lastname: Yoon
mesh_terms: D056915:DNA Copy Number Variations; D004272:DNA, Mitochondrial / Q000235:genetics*; D018744:DNA, Plant / Q000235:genetics*; D019143:Evolution, Molecular; D063990:Gene Ontology; D022761:Gene Transfer, Horizontal; D054627:Genome, Plastid; D058977:Molecular Sequence Annotation; D016366:Open Reading Frames; D010802:Phylogeny; D010957:Plasmids / Q000737:chemistry / Q000378:metabolism*; D018087:Plastids / Q000235:genetics; D000461:Rhodophyta / Q000145:classification / Q000235:genetics*
chemical_list: D004272:DNA, Mitochondrial; D018744:DNA, Plant