title: The Plastid Genome of Polytoma uvella Is the Largest Known among Colorless Algae and Plants and Reflects Contrasting Evolutionary Paths to Nonphotosynthetic Lifestyles.
abstract: The loss of photosynthesis is frequently associated with parasitic or pathogenic lifestyles, but it also can occur in free-living, plastid-bearing lineages. A common consequence of becoming nonphotosynthetic is the reduction in size and gene content of the plastid genome. In exceptional circumstances, it can even result in the complete loss of the plastid DNA (ptDNA) and its associated gene expression system, as reported recently in several lineages, including the nonphotosynthetic green algal genus Polytomella Closely related to Polytomella is the polyphyletic genus Polytoma, the members of which lost photosynthesis independently of Polytomella Species from both genera are free-living organisms that contain nonphotosynthetic plastids, but unlike Polytomella, Polytoma members have retained a genome in their colorless plastid. Here, we present the plastid genome of Polytoma uvella: to our knowledge, the first report of ptDNA from a nonphotosynthetic chlamydomonadalean alga. The P. uvella ptDNA contains 25 protein-coding genes, most of which are related to gene expression and none are connected to photosynthesis. However, despite its reduced coding capacity, the P. uvella ptDNA is inflated with short repeats and is tens of kilobases larger than the ptDNAs of its closest known photosynthetic relatives, Chlamydomonas leiostraca and Chlamydomonas applanata In fact, at approximately 230 kb, the ptDNA of P. uvella represents the largest plastid genome currently reported from a nonphotosynthetic alga or plant. Overall, the P. uvella and Polytomella plastid genomes reveal two very different evolutionary paths following the loss of photosynthesis: expansion and complete deletion, respectively. We hypothesize that recombination-based DNA-repair mechanisms are at least partially responsible for the different evolutionary outcomes observed in such closely related nonphotosynthetic algae.
authors.affiliation: Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada E3B 5A3 (F.F.-M., A.M.N., A.R.-P.).|Consejo Nacional de Ciencia y Tecnología-Universidad Autónoma Metropolitana, Vicentina, Mexico City 0934, Mexico (F.F.-M.).|Biology Department, University of Western Ontario, London, Ontario, Canada N6A 5B7 (D.R.S.); and.|Integrated Microbiology Program, Canadian Institute for Advanced Research, Toronto, Ontario, Canada M5G 1Z8 (A.R.-P.).
authors.forename: Francisco
authors.identifier: 0000-0003-0037-5091
authors.initials: F
authors.lastname: Figueroa-Martinez
authors.affiliation: Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada E3B 5A3 (F.F.-M., A.M.N., A.R.-P.).|Consejo Nacional de Ciencia y Tecnología-Universidad Autónoma Metropolitana, Vicentina, Mexico City 0934, Mexico (F.F.-M.).|Biology Department, University of Western Ontario, London, Ontario, Canada N6A 5B7 (D.R.S.); and.|Integrated Microbiology Program, Canadian Institute for Advanced Research, Toronto, Ontario, Canada M5G 1Z8 (A.R.-P.).
authors.forename: Aurora M
authors.identifier: 0000-0002-7517-2419
authors.initials: AM
authors.lastname: Nedelcu
authors.affiliation: Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada E3B 5A3 (F.F.-M., A.M.N., A.R.-P.); dsmit242@uwo.ca areyes@unb.ca.|Consejo Nacional de Ciencia y Tecnología-Universidad Autónoma Metropolitana, Vicentina, Mexico City 0934, Mexico (F.F.-M.); dsmit242@uwo.ca areyes@unb.ca.|Biology Department, University of Western Ontario, London, Ontario, Canada N6A 5B7 (D.R.S.); and dsmit242@uwo.ca areyes@unb.ca.|Integrated Microbiology Program, Canadian Institute for Advanced Research, Toronto, Ontario, Canada M5G 1Z8 (A.R.-P.) dsmit242@uwo.ca areyes@unb.ca.
authors.forename: David R
authors.identifier: 0000-0001-9560-5210
authors.initials: DR
authors.lastname: Smith
authors.affiliation: Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada E3B 5A3 (F.F.-M., A.M.N., A.R.-P.); dsmit242@uwo.ca areyes@unb.ca.|Consejo Nacional de Ciencia y Tecnología-Universidad Autónoma Metropolitana, Vicentina, Mexico City 0934, Mexico (F.F.-M.); dsmit242@uwo.ca areyes@unb.ca.|Biology Department, University of Western Ontario, London, Ontario, Canada N6A 5B7 (D.R.S.); and dsmit242@uwo.ca areyes@unb.ca.|Integrated Microbiology Program, Canadian Institute for Advanced Research, Toronto, Ontario, Canada M5G 1Z8 (A.R.-P.) dsmit242@uwo.ca areyes@unb.ca.
authors.forename: Adrian
authors.identifier: 0000-0002-0413-6162
authors.initials: A
authors.lastname: Reyes-Prieto
mesh_terms: D020856:AT Rich Sequence / Q000235:genetics; D001483:Base Sequence; D005075:Biological Evolution; D000460:Chlorophyta / Q000235:genetics*; D017124:Conserved Sequence / Q000235:genetics; D018742:DNA, Chloroplast / Q000235:genetics; D054627:Genome, Plastid; D016013:Likelihood Functions; D010788:Photosynthesis / Q000235:genetics*; D010802:Phylogeny
chemical_list: D018742:DNA, Chloroplast