Chloroplast Genome Evolution

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
Algal lineages
Primary (Double membrane) Secondary (Thre
e or more membranes)
Cryptophytes Heterokonts Haptophytes
Dinoflagellates Apicomplexans
Euglenoids Chlorarachniophytes
5
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
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
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
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
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
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 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
13
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