Post on 27-Nov-2015
description
Chloroplast Genome Chloroplast Genome EvolutionEvolution
Level 3 Molecular Evolution and Level 3 Molecular Evolution and BioinformaticsBioinformatics
Jim ProvanJim Provan
ReferencesReferences
Douglas SE (1998) “Plastid evolution: origins, Douglas SE (1998) “Plastid evolution: origins, diversity, trends” diversity, trends” Current Opinion in Genetics Current Opinion in Genetics and Development and Development 88: 655-661: 655-661
Sugiura M (1995) “The chloroplast genome” Sugiura M (1995) “The chloroplast genome” Essays in Biochemistry Essays in Biochemistry 3030: 49-57: 49-57
Gray MW (1993) “Origin and evolution of Gray MW (1993) “Origin and evolution of organelle genomes” organelle genomes” Current Opinion in Current Opinion in Genetics and Development Genetics and Development 33: 884-890: 884-890
The chloroplastThe chloroplast
Carries out Carries out photosynthesisphotosynthesisContains own genomeContains own genomeBelieved to be of Believed to be of endosymbiotic originendosymbiotic originPhylogenetically related Phylogenetically related to cyanobacteriato cyanobacteria
Algal lineagesAlgal lineages
RhodophytesRhodophytes ChlorophytesChlorophytes GlaucocystophytesGlaucocystophytes
CryptophytesCryptophytes
HeterokontsHeterokonts
HaptophytesHaptophytes
DinoflagellatesDinoflagellates
ApicomplexansApicomplexans
EuglenoidsEuglenoids
ChlorarachniophytesChlorarachniophytes
PrimaryPrimary(Double (Double membrane)membrane)
SecondarySecondary(Three or more (Three or more membranes)membranes)
Monophyly of primary plastids - Monophyly of primary plastids - chloroplast evidencechloroplast evidence
Phylogeny of SSU Phylogeny of SSU rRNA based on good rRNA based on good sample of both sample of both cyanobacteria and cyanobacteria and plastidsplastids
Also supported by:Also supported by:tuftufAA
atpBatpB
rporpoC1C1
psbpsbAA
OdontellaOdontellaPylaiellaPylaiella
GuillardiaGuillardiaEmilianiaEmiliania
PorphyraPorphyraMarchantiaMarchantia
KlebsormidiumKlebsormidiumChlorellaChlorella
CyanophoraCyanophoraGlaucocystisGlaucocystis
100100
Pseudanabaena PCC 7409Pseudanabaena PCC 7409Pseudanabaena PCC 6903Pseudanabaena PCC 6903PhormidiumPhormidium
Pseudanabaena PCC 7367Pseudanabaena PCC 7367
SSU rRNASSU rRNA
Monophyly of primary plastids - Monophyly of primary plastids - mitochondrial and nuclear mitochondrial and nuclear
evidenceevidence
Tree based on five Tree based on five mitochondrial genes mitochondrial genes shows strong support shows strong support for monophylyfor monophylyNuclear genes:Nuclear genes:
-tubulin - inconclusive-tubulin - inconclusiverRNAs - poorly resolvedrRNAs - poorly resolvedRPB1 - rejectsRPB1 - rejectsTPI / EF-1TPI / EF-1 - weak - weak supportsupportGAPDH / actin - better GAPDH / actin - better supportsupport
CyanidioschyzonCyanidioschyzon
CyanidiumCyanidium
GracilariopsisGracilariopsis
ChondrusChondrus
PorphyraPorphyra
TriticumTriticum
MarchantiaMarchantia
ProtothecaPrototheca
Tetraselmis m.Tetraselmis m.
Tetraselmis s.Tetraselmis s.
98%98%
Secondary plastidsSecondary plastids
Plastid SSU rDNA tree Plastid SSU rDNA tree shows that euglenophytes shows that euglenophytes and chloroarachiophytes and chloroarachiophytes associate with green associate with green algae and that algae and that heterokonts, cryptophytes heterokonts, cryptophytes and haptophytes and haptophytes associate with red algaeassociate with red algaeStudies on nucleomorphs Studies on nucleomorphs also confirm ancestry of also confirm ancestry of cryptophytes and cryptophytes and chloroarachniophyteschloroarachniophytes
Glaucocystis nostochinearumGlaucocystis nostochinearumCyanophora paradoxaCyanophora paradoxaCyanophora paradoxaCyanophora paradoxa
Gloeochaete wittrockianaGloeochaete wittrockianaEuglena gracilisEuglena gracilis
Astasia longaAstasia longaChlorarachnion Chlorarachnion spp.spp.
Chlorarachnion Chlorarachnion spp.spp.Chlorarachnion reptansChlorarachnion reptans
Glycine maxGlycine maxZea maysZea mays
Marchantia polymorphaMarchantia polymorphaClosterium ehrenbergiiClosterium ehrenbergii
Chara Chara spp.spp.Chlorella ellipsoideaChlorella ellipsoidea
Chlorella vulgarisChlorella vulgarisSkeletonema costatumSkeletonema costatum
Pylaiella littoratisPylaiella littoratisHeterosigma akashiwoHeterosigma akashiwoCyanidium caldarumCyanidium caldarum
Galdiera sulphurariaGaldiera sulphurariaGuillardia thetaGuillardia thetaRhodomonas salinaRhodomonas salina
Ochrosphaera neapolitanaOchrosphaera neapolitanaEmiliana huxleyiEmiliana huxleyiPavlova Pavlova cf. cf. salinasalina
Porphyridium aerugineumPorphyridium aerugineumGlaucosphaera vacuolataGlaucosphaera vacuolata
Palmaria palmataPalmaria palmataAntithamnion Antithamnion sp.sp.Chondrus crispusChondrus crispus
The chloroplast genomeThe chloroplast genome
Sequenced chloroplast Sequenced chloroplast genomes range from genomes range from 70kb - 201kb70kb - 201kb
Variation in length Variation in length mainly due to presence mainly due to presence of inverted repeat (IR)of inverted repeat (IR)
Generally 100-250 Generally 100-250 genes:genes:
Gene expressionGene expression
PhotosynthesisPhotosynthesis
MetabolismMetabolism
The inverted repeat (IR)The inverted repeat (IR)
Ranges from 5bk to 76kb in Ranges from 5bk to 76kb in lengthlength
IR contains rRNA genes IR contains rRNA genes plus others:plus others:
None in brown algae (5kb)None in brown algae (5kb)
10 in tobacco (25kb)10 in tobacco (25kb)
40 in geranium (76kb)40 in geranium (76kb)
Present in:Present in:Land plants (exc. legumes)Land plants (exc. legumes)
ChlorophytesChlorophytes
ChromophytesChromophytes
Partial in conifersPartial in conifers
PinusPinus
NicotianaNicotiana
PorphyraPorphyra
Chloroplast genome evolutionChloroplast genome evolution
Rapid and massive Rapid and massive reduction in number of reduction in number of genes:genes:
Transferred to nucleusTransferred to nucleusLostLost
80-90% of plastid 80-90% of plastid proteins are encoded in proteins are encoded in nucleusnucleusGreat overlap in gene Great overlap in gene content suggests that content suggests that last common ancestor of last common ancestor of cpDNA had ~300 genescpDNA had ~300 genes
SynechocystisSynechocystis3573 kbp3573 kbp
~3000 genes~3000 genes
PorphyraPorphyra chloroplast chloroplast201 kbp201 kbp
~250 genes~250 genes
Gene loss in chloroplast Gene loss in chloroplast evolutionevolution
45 genes present in all 45 genes present in all genomesgenomes
Unique losses (68) Unique losses (68) outnumbered by outnumbered by parallel losses (122)parallel losses (122)
Confirms that ancestral Confirms that ancestral plastid genome was plastid genome was already highly reduced already highly reduced from that of from that of cyanobacteriacyanobacteria
Zea Zea (75)(75)
Oryza Oryza (75)(75)
NicotianaNicotiana (76) (76)
Pinus Pinus (69)(69)
Marchantia Marchantia (84)(84)
Euglena Euglena (58)(58)
PorphyraPorphyra (200) (200)
Odontella Odontella (124)(124)
Cyanophora Cyanophora (136)(136)
1 (0)1 (0)
5 (2)5 (2)
12 (0)12 (0)
4 (0)4 (0)
1 (0)1 (0)
7 (5)7 (5)
34 (9)34 (9)
129 (34)129 (34)
20 (1)20 (1)
1 (0)1 (0)
77 (0)77 (0)
99 (3)99 (3)
AncestralAncestralplastidplastid((235)235)
14 (14)14 (14)
Chloroplast gene contentChloroplast gene content
Group 1
Gene expressionPhotosynthesis
Metabolism
Rhodophytes s. l.Glaucocystophytes
Group 1
Gene expressionPhotosynthesis
Metabolism
Rhodophytes s. l.Glaucocystophytes
Group 2
Gene expressionPhotosynthesis
Metabolism
Chlorophytes s. l
Group 2
Gene expressionPhotosynthesis
Metabolism
Chlorophytes s. l
Group 4
Gene expressionPhotosynthesis
Metabolism
Yet to be discovered(cf. Hydrogenosomes in mitochondria)
Group 4
Gene expressionPhotosynthesis
Metabolism
Yet to be discovered(cf. Hydrogenosomes in mitochondria)
Group 3
Gene expressionPhotosynthesis
Metabolism
Non-photosynthtic Chlorophytes(e.g. Epifagus) and apicomplexans
Group 3
Gene expressionPhotosynthesis
Metabolism
Non-photosynthtic Chlorophytes(e.g. Epifagus) and apicomplexans
Chloroplast genes (excluding Chloroplast genes (excluding ycfycf))
TotalTotal
Gene expressionGene expression rRNArRNA tRNAtRNA r-proteinr-protein OtherOther
PhotosynthesisPhotosynthesis RuBisCo/thylakoidRuBisCo/thylakoid ndhndh
Metabolism/misc.Metabolism/misc.
IntronsIntrons
Land PlantsLand Plants AlgaeAlgae
Photosyn.Photosyn. EpifagusEpifagus EuglenaEuglena OthersOthers PorphyraPorphyra
101-107101-107
4430-3230-322-212-215-65-6
29-3029-301111
1-51-5
18-2118-21
4040
441717151522
----
22
66
8282
332727212144
2626--
11
149+149+
113-166113-166
3328-3628-362121-44-44
66-9-9
3131-48-48-/-/1010
77-14-14
-/1/3-/1/3
181181
33353547471818
5353--
2525
--