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: Sugiura M (1995) “The chloroplast genome” Essays in Biochemistry 30: Gray MW (1993) “Origin and evolution of organelle genomes” Current Opinion in Genetics and Development 3:

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

Algal lineages Rhodophytes ChlorophytesGlaucocystophytes CryptophytesHeterokontsHaptophytesDinoflagellatesApicomplexansEuglenoidsChlorarachniophytes Primary (Double membrane) Secondary (Three or more membranes)

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 Odontella Pylaiella Guillardia Emiliania Porphyra Marchantia Klebsormidium Chlorella Cyanophora Glaucocystis 100 Pseudanabaena PCC 7409 Pseudanabaena PCC 6903 Phormidium Pseudanabaena PCC 7367 SSU rRNA

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 Cyanidioschyzon Cyanidium Gracilariopsis Chondrus Porphyra Triticum Marchantia Prototheca Tetraselmis m. Tetraselmis s. 98%

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 Glaucocystis nostochinearum Cyanophora paradoxa Gloeochaete wittrockiana Euglena gracilis Astasia longa Chlorarachnion spp. Chlorarachnion reptans 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

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

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 Pinus Nicotiana Porphyra

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 Synechocystis 3573 kbp ~3000 genes Porphyra chloroplast 201 kbp ~250 genes

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 Zea (75) Oryza (75) Nicotiana (76) Pinus (69) Marchantia (84) Euglena (58) Porphyra (200) Odontella (124) Cyanophora (136) 1 (0) 5 (2) 12 (0) 4 (0) 1 (0) 7 (5) 34 (9) 129 (34) 20 (1) 1 (0) 77 (0) 99 (3) Ancestralplastid (  235) 14 (14)

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

Chloroplast genes (excluding ycf) Total Gene expression rRNA rRNA tRNA tRNA r-protein r-protein Other Other Photosynthesis RuBisCo/thylakoid RuBisCo/thylakoid ndh ndh Metabolism/misc. Introns Land Plants Algae Photosyn.EpifagusEuglenaOthersPorphyra / /1/