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Chloroplast Genome Evolution

Chloroplast Genome Evolution. Level 3 Molecular Evolution and Bioinformatics Jim Provan. References. Douglas SE (1998) “Plastid evolution: origins, diversity, trends” Current Opinion in Genetics and Development 8 : 655-661

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Chloroplast Genome Evolution

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  1. Chloroplast Genome Evolution Level 3 Molecular Evolution and Bioinformatics Jim Provan

  2. References Douglas SE (1998) “Plastid evolution: origins, diversity, trends” Current Opinion in Genetics and Development 8: 655-661 Sugiura M (1995) “The chloroplast genome” Essays in Biochemistry 30: 49-57 Gray MW (1993) “Origin and evolution of organelle genomes” Current Opinion in Genetics and Development 3: 884-890

  3. The chloroplast • Carries out photosynthesis • Contains own genome • Believed to be of endosymbiotic origin • Phylogenetically related to cyanobacteria

  4. Rhodophytes Chlorophytes Glaucocystophytes Algal lineages Primary (Double membrane) Secondary (Three or more membranes) Cryptophytes Heterokonts Haptophytes Dinoflagellates Apicomplexans Euglenoids Chlorarachniophytes

  5. Odontella Pylaiella Guillardia Emiliania Porphyra Marchantia Klebsormidium 100 Chlorella Cyanophora Glaucocystis Pseudanabaena PCC 7409 Pseudanabaena PCC 6903 Phormidium Pseudanabaena PCC 7367 SSU rRNA Monophyly of primary plastids - chloroplast evidence • Phylogeny of SSU rRNA based on good sample of both cyanobacteria and plastids • Also supported by: • tufA • atpB • rpoC1 • psbA

  6. Cyanidioschyzon Cyanidium Gracilariopsis Chondrus 98% Porphyra Triticum Marchantia Prototheca Tetraselmis m. Tetraselmis s. Monophyly of primary plastids - mitochondrial and nuclear evidence • Tree based on five mitochondrial genes shows strong support for monophyly • Nuclear genes: • -tubulin - inconclusive • rRNAs - poorly resolved • RPB1 - rejects • TPI / EF-1 - weak support • GAPDH / actin - better support

  7. Glaucocystis nostochinearum Cyanophora paradoxa Cyanophora paradoxa Gloeochaete wittrockiana Euglena gracilis Astasia longa Chlorarachnion spp. Chlorarachnion reptans Chlorarachnion spp. Glycine max Zea mays Marchantia polymorpha Closterium ehrenbergii Chara spp. Chlorella ellipsoidea Chlorella vulgaris Skeletonema costatum Pylaiella littoratis Heterosigma akashiwo Cyanidium caldarum Galdiera sulphuraria Guillardia theta Rhodomonas salina Ochrosphaera neapolitana Emiliana huxleyi Pavlova cf. salina Porphyridium aerugineum Glaucosphaera vacuolata Palmaria palmata Antithamnion sp. Chondrus crispus Secondary plastids • Plastid SSU rDNA tree shows that euglenophytes and chloroarachiophytes associate with green algae and that heterokonts, cryptophytes and haptophytes associate with red algae • Studies on nucleomorphs also confirm ancestry of cryptophytes and chloroarachniophytes

  8. The chloroplast genome • Sequenced chloroplast genomes range from 70kb - 201kb • Variation in length mainly due to presence of inverted repeat (IR) • Generally 100-250 genes: • Gene expression • Photosynthesis • Metabolism

  9. Pinus Nicotiana Porphyra The inverted repeat (IR) • Ranges from 5bk to 76kb in length • IR contains rRNA genes plus others: • None in brown algae (5kb) • 10 in tobacco (25kb) • 40 in geranium (76kb) • Present in: • Land plants (exc. legumes) • Chlorophytes • Chromophytes • Partial in conifers

  10. Synechocystis 3573 kbp ~3000 genes Porphyra chloroplast 201 kbp ~250 genes Chloroplast genome evolution • Rapid and massive reduction in number of genes: • Transferred to nucleus • Lost • 80-90% of plastid proteins are encoded in nucleus • Great overlap in gene content suggests that last common ancestor of cpDNA had ~300 genes

  11. Zea (75) 1 (0) Oryza (75) 5 (2) 4 (0) Nicotiana (76) 12 (0) 7 (5) Pinus (69) 1 (0) 129 (34) Marchantia (84) 34 (9) Euglena (58) 14 (14) 1 (0) Porphyra (200) Ancestral plastid (235) 20 (1) 77 (0) Odontella (124) 99 (3) Cyanophora (136) Gene loss in chloroplast evolution • 45 genes present in all genomes • Unique losses (68) outnumbered by parallel losses (122) • Confirms that ancestral plastid genome was already highly reduced from that of cyanobacteria

  12. Chloroplast gene content Group 1 Gene expression Photosynthesis Metabolism Rhodophytes s. l. Glaucocystophytes Group 2 Gene expression Photosynthesis Metabolism Chlorophytes s. l Group 3 Gene expression Photosynthesis Metabolism Non-photosynthtic Chlorophytes (e.g. Epifagus) and apicomplexans Group 4 Gene expression Photosynthesis Metabolism Yet to be discovered (cf. Hydrogenosomes in mitochondria)

  13. Land Plants Algae Photosyn. Epifagus Euglena Others Porphyra Chloroplast genes (excluding ycf) Total 101-107 40 82 113-166 181 Gene expression rRNA tRNA r-protein Other 4 30-32 2-21 5-6 4 17 15 2 3 27 21 4 3 28-36 21-44 6-9 3 35 47 18 Photosynthesis RuBisCo/thylakoid ndh 29-30 11 - - 26 - 31-48 -/10 53 - 1-5 2 1 7-14 25 Metabolism/misc. 18-21 6 149+ -/1/3 - Introns

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