Chloroplast Genome 5r6bm

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 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

The chloroplast

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

Algal lineages Primary

(Double membrane)

Rhodophytes

Secondary

(Three or more membranes)

Chlorophytes

Glaucocystophytes

Cryptophytes

Dinoflagellates

Euglenoids

Heterokonts

Apicomplexans

Chlorarachniophytes

Haptophytes

Monophyly of primary plastids chloroplast evidence

Guillardia

Odontella Pylaiella

Emiliania Porphyra Marchantia 100

Klebsormidium Chlorella

Cyanophora Glaucocystis Pseudanabaena PCC 7409 Pseudanabaena PCC 6903 Phormidium Pseudanabaena PCC 7367

SSU rRNA

Phylogeny of SSU rRNA based on good sample of both cyanobacteria and plastids Also ed by: tufA atpB rpoC1 psbA

Monophyly of primary plastids mitochondrial and nuclear evidence Cyanidioschyzon Cyanidium Gracilariopsis Chondrus 98%

Porphyra Triticum Marchantia Prototheca Tetraselmis m. Tetraselmis s.

Tree based on five mitochondrial genes shows strong for monophyly Nuclear genes: -tubulin - inconclusive rRNAs - poorly resolved RPB1 - rejects TPI / EF-1 - weak GAPDH / actin - better

Secondary plastids 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

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

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

The inverted repeat (IR) Pinus

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)

Nicotiana

Present in: Porphyra

Land plants (exc. legumes) Chlorophytes Chromophytes Partial in conifers

Chloroplast genome evolution

Synechocystis 3573 kbp ~3000 genes

Porphyra chloroplast 201 kbp ~250 genes

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 DNA had ~300 genes

Gene loss in chloroplast evolution Zea (75)

1 (0)

Oryza (75)

5 (2) 4 (0) 12 (0)

7 (5) 1 (0)

129 (34)

Pinus (69)

Marchantia (84)

34 (9)

14 (14)

Ancestral plastid (235)

Nicotiana (76)

1 (0) 20 (1) 99 (3)

77 (0)

Euglena (58)

Porphyra (200) Odontella (124)

Cyanophora (136)

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

Chloroplast gene content Group 1

Group 2

Gene expression Photosynthesis Metabolism

Gene expression Photosynthesis Metabolism

Rhodophytes s. l. Glaucocystophytes

Chlorophytes s. l

Group 3

Group 4

Gene expression Photosynthesis Metabolism

Gene expression Photosynthesis Metabolism

Non-photosynthtic Chlorophytes (e.g. Epifagus) and apicomplexans

Yet to be discovered (cf. Hydrogenosomes in mitochondria)

Chloroplast genes (excluding ycf) Land Plants

Epifagus

Euglena

Others

Porphyra

101-107

40

82

113-166

181

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

29-30 11

-

26 -

31-48 -/10

53 -

1-5

2

1

7-14

25

18-21

6

149+

-/1/3

-

Photosyn.

Total Gene expression rRNA tRNA r-protein Other Photosynthesis RuBisCo/thylakoid

ndh

Metabolism/misc. Introns

Algae