Evolution of chloroplast matK genes among lower land plants
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Evolution of chloroplast Evolution of chloroplast matK matK genes among lower lan genes among lower lan d plants d plants Shu-Lan Chuang ( 莊莊莊 ) and Jer-Ming Hu ( 莊莊莊 ) Institute of Ecology and Evolutionary Biology, National Taiwa n University The introns of chloroplast trnK UUU contain an open readi ng frame denoted as matK. The putative gene product MatK is the only one having maturase function in chloroplasts. However, only those chloroplasts of land plants and hi gher green algae such as Characeae have introns in their trnK genes, but not in other green algae examined. Chloro plast matK genes are indispensable since in nonphotosynt hetic parasitic plant, Epifagus virginiana, the chloroplast matK is functional even being a free-standing from with dismissed trnK exons. The chloroplasts of Psilotum, moss and liverworts all h ave trnK5’-matK-trnK3’ structure, but it is found that mat K is a pseudogene in hornwort Anthoceros formosae. We found a clear trnK5’-matK-trnK3’ structure in Ophioglossum petiolatu m, Lycopodiella cernua and Selaginella doederleinii . RT-PCR result s showed matK genes are expressed in Ophioglossum petiolatum and Lycopodiella cernua , but no signal detected in Selaginella doederleinii . So the function and expression of matK are no t consistent in lower land plants. Codon usage analysis showed that the use of codons in matK is in congruent with the average use of chloroplast genomes, showing a bias that can be explained by constra ints on GC contents. The result of correspondence analys is suggests the codon usage of chloroplast matK has some properties that is correlated with their evolutionary re lationship. Lycopodiella cernua and Selaginella doederleinii are placed into different group in matK phylogenetic analysis, but the i ncongruence is likely due to the disputable sequence ali gnment, which causes long branch attraction that will af fect phylogenetic inference. Nonetheless, the result sho wed that Pinus, Ginkgo, Cycas from a monophyletic group, w hich is sistered to angiosperms. Together they form a cl ade that is sistered to Gnetales. M R R I I M M R R I I L O L O L O L O L O L O RT-PCR Genomic DNA 500bp Fig. 3. Dot blot hybridization, indic ating that matK is likely present in all of the samples examined. Lycopodiella S e l a g i n e l l a Ophioglossum A d i a n t u m rbcL 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 1. Anthoceros formosae 2. Marchantia polymorpha 3. Equisetum ramosissimum 4. Isoetes taiwanensis 5. Selaginella doederleinii 6. Selaginella delicatula 7. Selaginella tamariscina 8. Selaginella involuens 9. Selaginella tamariscina 10. Lycopodiella cernua 11. Lycopodium pseudoclavatum 12. Ophioglossum petiolatum 13. Angiopteris palmiformis 14. Osmunda banksiifolia 15. Adiantum capillus-veneris 16. Dicranopteris linearis 17. Lygodium japonicum 18. Sphenomeris biflor 19. Nicotiana sylvestris 20. plasmid sd4 21. plasmid lyco8 22. plasmid ophio11 Fig 4. Codon usage analysis. (A, B) Correspondence analysi s of codon usage. Major group ings are indicated. (C) Nc-pl ot shows the bias of matK cod on usage is correlated to GC contents. 30.00 35.00 40.00 45.00 50.00 55.00 60.00 0.000 0.050 0.100 0.150 0.200 0.250 0.300 0.350 G C 3s Nc Nictm atK Aratm atK Atrbm atK Spiom aK O enem atK Lotjm atK Calfm atK M aggm atK Am btm atK Epivm atK Orysm atK Triam atK Zeam m atK Pintm atK Pinkm atK Cycpm atK Ginbm atK G nepm atK G nem m at Ephsm atK Adicm atK O phpm atK Seldm atK Lyccm atK Psinm atK Phypm atK M arpm atK Chagm atK Chacm atK (A) Maximum parsimony tree NictmatK AratmatK TroamatK AmbtmatK NymomatK MaggmatK OrysmatK TriamatK ZeammatK CycrmatK CycpmatK GinbmatK PintmatK PinkmatK GnegmatK GnepmatK GnemmatK WelmmatK EphsmatK OphpmatK PsinmatK SeldmatK LyccmatK PhypmatK MarpmatK Strict 86 75 100 100 100 92 73 99 100 99 100 82 100 89 96 90 99 84 100 Core eudicots Basal angiosperms Basal eudicots Monocots Ginkgo Lycophytes and ferns Bryophytes Cycads Gnetophytes Conifers (B) Bayesian inference tree 0.92 1.00 0.99 1.00 1.00 1.00 0.61 1.00 0.52 1.00 1.00 1.00 0.56 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 NictmatK AratmatK TroamatK OrysmatK TriamatK ZeammatK MaggmatK AmbtmatK NymomatK PintmatK PinkmatK CycrmatK CycpmatK GinbmatK GnegmatK GnepmatK GnemmatK WelmmatK EphsmatK OphpmatK PsinmatK SeldmatK LyccmatK PhypmatK MarpmatK Core eudicot s Basal eudicots Basal angiosperms Monocots Cycads Lycophytes and fe rns Bryophytes Conifers Ginkgo Gnetophytes Kishino-Hasegawa test Parsimony criteria Likelihood criteria Tree Length Diff . P* -ln L Diff. P* Tree Bayesian 5596 42 0.0034 * 23093.7295 2 (best) Tree Parsimon y 5554 (bes t) 23137.9230 1 44.1934 9 0.000 * P<0.05 * Abstract Abstract Fig. 6. Phylogenetic analyses of matK showed Gnetales is sister to other seed plants. Results Results Selaginella doederleinii M R I1 I 2 M R I1 I2 500bp RT-PCR Genomic DNA Fig. 2. Detection of chloroplast matK expression by RT-PCR. (A) Results from Lycopodiella cernua (L) and Ophioglossum petiolatum (O). O n the right showing a PCR of genomic DNA as controls. (B) Resul ts from Selaginella doederienii, and a PCR of genomic DNA is on the r ight. Chloroplast matKs are expressed in L. cernua and O. petiolatum, but not in S. doederienii. Abbreviations: M (matK), R (rbcL), I and I1 (intergenetic spacer: rbcL/atpB), I2 (trnL intron). (A ) (B ) Table 1. The results of Kishino-Hasegawa test show that the Tree Parsimony is preferred in parsimony crite ria, but the Tree Bayesian is favored by likelihood cr iteria, and both the alternative tree topologies a re rejected. The matK is present in the chloroplasts of lower land plants, but trnK5’-matK-trnK3 ’ structure may be lost in ferns due to chloroplast ge nome rearrangement. Chloroplast matKs are expres sed in Ophioglossum and Lycopo diella, but not expressed in Selaginella. Chloroplast matK follows ch loroplast average codon usa ge and the bias is influenc ed by GC content. Codon usage of matK does ha ve evolutionary properties. Phylogenetic analysis of m atK showed Gnetales is sist er to other seed plants. Nicotiana tabacum Atropa belladonna Epifagus virginiana Spinacia oleracea Arabidopsis thaliana Oenothera elata Lotus corniculatus Zea mays Oryza sativa Triticum aestivum Calycanthus floridus Amborella trichopoda Pinus koraiensis Pinus thunbergii Adiatum capillus-veneris Psilotum nudum Physcomitrella patens Marchantia polymorpha Anthoceros formosae Chaetosphaeridium globosum trnV clpP rpl2 rpl12 rpoC1 rps16 ycf3 ycf66 trnH trnG ndhB atpF ndhA ndhH petB petD rpl6 rpl16 rps12 ycf2 ycf10 trnA trnI trnK trnT trnL rrn23 Fig. 7. Distribution of chloroplast introns. A rrow A indicates the presence of trnK/matK in Chaetosphaeridium + land plant chloroplasts. A rrow B indicates matK being a pseudogene in Ant hoceros. A B Discussion Discussion Chara vulgaris (C) Intron No intron Free-standing matK pseudogene (A) Epifagus Axis 1 Axis2 Green algae Bryophytes Gnetophytes Gymnosperms* Monocots (B) Axis 1 Axis 2 Nictm atK Aratm atK Atrbm atK Spiom aK Oenem atK LotjmatK CalfmatK M aggm atK Ambtm atK Orysm atK TriamatK Zeam m atK Pintm atK PinkmatK Cycpm atK GinbmatK AdicmatK Ophpm atK SeldmatK LyccmatK PsinmatK Ferns and allies Gymnosperms Monocots Basal angiosperms
description
Core eudicots. Core eudicots. Basal eudicots. 90. Basal eudicots. Monocots. 73. 86. Basal angiosperms. Lycopodiella. Selaginella. 84. Gymnosperms. Basal angiosperms. 75. Basal angiosperms. 100. Monocots. Gnetophytes. Conifers. 100. Monocots. Cycads. 92. 0.92. 99. Cycads. - PowerPoint PPT Presentation
Transcript of Evolution of chloroplast matK genes among lower land plants
Evolution of chloroplast Evolution of chloroplast matKmatK genes among lower land plants genes among lower land plants
Shu-Lan Chuang (莊樹嵐 ) and Jer-Ming Hu (胡哲明 )Institute of Ecology and Evolutionary Biology, National Taiwan University
The introns of chloroplast trnKUUU contain an open reading frame denoted as matK. The putative gene product MatK is the only one having maturase function in chloroplasts.
However, only those chloroplasts of land plants and higher green algae such as Characeae have introns in their trnK genes, but not in other green algae examined. Chloroplast matK genes are indispensable since in nonphotosynthetic parasitic plant, Epifagus virginiana, the chloroplast matK is functional even being a free-standing from with dismissed trnK exons.
The chloroplasts of Psilotum, moss and liverworts all have trnK5’-matK-trnK3’ structure, but it is found that matK is a pseudogene in hornwort Anthoceros formosae. We found a clear trnK5’-matK-trnK3’ structure in Ophioglossum petiolatum, Lycopodiella cernua and Selaginella doederleinii. RT-PCR results showed matK genes are expressed in Ophioglossum petiolatum and Lycopodiella cernua, but no signal detected in Selaginella doederleinii. So the function and expression of matK are not consistent in lower land plants.
Codon usage analysis showed that the use of codons in matK is in congruent with the average use of chloroplast genomes, showing a bias that can be explained by constraints on GC contents. The result of correspondence analysis suggests the codon usage of chloroplast matK has some properties that is correlated with their evolutionary relationship.
Lycopodiella cernua and Selaginella doederleinii are placed into different group in matK phylogenetic analysis, but the incongruence is likely due to the disputable sequence alignment, which causes long branch attraction that will affect phylogenetic inference. Nonetheless, the result showed that Pinus, Ginkgo, Cycas from a monophyletic group, which is sistered to angiosperms. Together they form a clade that is sistered to Gnetales.
M M R R I I M M R R I I
L O L O L O L O L O L O
RT-PCR Genomic DNA
500bp
Fig. 3. Dot blot hybridization, indicating that matK is likely present in all of the samples examined.
Lycopodiella S
elaginella
Ophioglossum A
diantum
rbcL
1 2 3 4 5 6 7 8 9
10 11 12 13 14 15 16 17 18
19 20 21 22
1. Anthoceros formosae
2. Marchantia polymorpha
3. Equisetum ramosissimum
4. Isoetes taiwanensis
5. Selaginella doederleinii
6. Selaginella delicatula
7. Selaginella tamariscina
8. Selaginella involuens
9. Selaginella tamariscina
10.Lycopodiella cernua
11.Lycopodium pseudoclavatum
12.Ophioglossum petiolatum
13.Angiopteris palmiformis
14.Osmunda banksiifolia
15.Adiantum capillus-veneris
16.Dicranopteris linearis
17.Lygodium japonicum
18.Sphenomeris biflor
19.Nicotiana sylvestris
20.plasmid sd4
21.plasmid lyco8
22.plasmid ophio11
Fig 4. Codon usage analysis. (A, B) Correspondence analysis of codon usage. Major groupings are indicated. (C) Nc-plot shows the bias of matK codon usage is correlated to GC contents.
30.00
35.00
40.00
45.00
50.00
55.00
60.00
0.000 0.050 0.100 0.150 0.200 0.250 0.300 0.350
GC3s
Nc
NictmatK
AratmatK
AtrbmatK
SpiomaK
OenematK
LotjmatK
CalfmatK
MaggmatK
AmbtmatK
EpivmatK
OrysmatK
TriamatK
ZeammatK
PintmatK
PinkmatK
CycpmatK
GinbmatK
GnepmatK
Gnemmat
EphsmatK
AdicmatK
OphpmatK
SeldmatK
LyccmatK
PsinmatK
PhypmatK
MarpmatK
ChagmatK
ChacmatK
(A) Maximum parsimony tree
NictmatK
AratmatK
TroamatK
AmbtmatK
NymomatK
MaggmatK
OrysmatK
TriamatK
ZeammatK
CycrmatK
CycpmatK
GinbmatK
PintmatK
PinkmatK
GnegmatK
GnepmatK
GnemmatK
WelmmatK
EphsmatK
OphpmatK
PsinmatK
SeldmatK
LyccmatK
PhypmatK
MarpmatK
Strict
86
75
100
100
100
92
73
99
100
99
100
82
100
89
96
90
99
84
100
Core eudicots
Basal angiosperms
Basal eudicots
Monocots
Ginkgo
Lycophytes and ferns
Bryophytes
Cycads
Gnetophytes
Conifers
(B) Bayesian inference tree
0.92
1.00
0.99
1.00
1.001.00
0.61
1.00
0.52
1.00
1.00
1.00
0.56
1.00
1.00
1.00
1.00
1.00
1.00
1.00
1.00
NictmatK
AratmatK
TroamatK
OrysmatK
TriamatK
ZeammatK
MaggmatK
AmbtmatK
NymomatK
PintmatK
PinkmatK
CycrmatK
CycpmatK
GinbmatK
GnegmatK
GnepmatK
GnemmatK
WelmmatK
EphsmatK
OphpmatK
PsinmatK
SeldmatK
LyccmatK
PhypmatK
MarpmatK
Core eudicots
Basal eudicots
Basal angiosperms
Monocots
Cycads
Lycophytes and ferns
Bryophytes
Conifers
Ginkgo
Gnetophytes
Kishino-Hasegawa test
Parsimony criteria Likelihood criteria
Tree Length Diff. P* -ln L Diff. P*
TreeBayesian 5596 42 0.0034* 23093.72952 (best)
TreeParsimony 5554 (best) 23137.92301 44.19349 0.000*
P<0.05 *
AbstractAbstract
Fig. 6. Phylogenetic analyses of matK showed Gnetales is sister to other seed plants.
ResultsResults
Selaginella doederleinii
M R I1 I 2 M R I1 I2
500bp
RT-PCR Genomic DNA
Fig. 2. Detection of chloroplast matK expression by RT-PCR. (A) Results from Lycopodiella cernua (L) and Ophioglossum petiolatum (O). On the right showing a PCR of genomic DNA as controls. (B) Results from Selaginella doederienii, and a PCR of genomic DNA is on the right. Chloroplast matKs are expressed in L. cernua and O. petiolatum, but not in S. doederienii. Abbreviations: M (matK), R (rbcL), I and I1 (intergenetic spacer: rbcL/atpB), I2 (trnL intron).
(A)
(B)
Table 1. The results of Kishino-Hasegawa test show that the TreePars
imony is preferred in parsimony criteria, but the TreeBayesian is favored by likelihood criteria, and both the alternative tree topologies are rejected.
The matK is present in the chloroplasts of lower land plants, but trnK5’-matK-trnK3’ structure may be lost in ferns due to chloroplast genome rearrangement.
Chloroplast matKs are expressed in Ophioglossum and Lycopodiella, but not expressed in Selaginella.
Chloroplast matK follows chloroplast average codon usage and the bias is influenced by GC content.
Codon usage of matK does have evolutionary properties.
Phylogenetic analysis of matK showed Gnetales is sister to other seed plants.
Nicotiana tabacum
Atropa belladonna
Epifagus virginiana
Spinacia oleracea
Arabidopsis thaliana
Oenothera elata
Lotus corniculatus
Zea mays
Oryza sativa
Triticum aestivum
Calycanthus floridus
Amborella trichopoda
Pinus koraiensis
Pinus thunbergii
Adiatum capillus-veneris
Psilotum nudum
Physcomitrella patens
Marchantia polymorpha
Anthoceros formosae
Chaetosphaeridium globosum
trnVclpP rpl2 rpl12 rpoC1 rps16ycf3 ycf66 trnH trnGndhBatpF ndhA ndhH petB petD rpl6 rpl16 rps12 ycf2 ycf10 trnA trnI trnK trnTtrnL rrn23
Fig. 7. Distribution of chloroplast introns. Arrow A indicates the presence of trnK/matK in Chaetosphaeridium + land plant chloroplasts. Arrow B indicates matK being a pseudogene in Anthoceros.
A B
DiscussionDiscussion
Chara vulgaris
(C)
Intron
No intron
Free-standing matK
pseudogene
(A)
EpifagusAxis 1
Axis
2
Green algae
Bryophytes
Gnetophytes
Gymnosperms*
Monocots
(B)
Axis 1
Axi
s 2
NictmatK
AratmatK
AtrbmatK
SpiomaK
OenematK
LotjmatK
CalfmatK
MaggmatK
AmbtmatK
OrysmatK
TriamatK
ZeammatK
PintmatK
PinkmatK
CycpmatK
GinbmatK
AdicmatK
OphpmatK
SeldmatK
LyccmatK
PsinmatK
Ferns and allies
Gymnosperms
Monocots
Basal angiosperms
