Evolution of chloroplast matK 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
Abstract
NictmatK
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.
AratmatK
(A)
AtrbmatK
(B)
SpiomaK
Gymnosperms
Basal angiosperms
LotjmatK
CalfmatK
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.
Gnetophytes
MaggmatK
AmbtmatK
Axis 2
Axis 2
Monocots
Gymnosperms*
Green algae
OrysmatK
TriamatK
ZeammatK
PintmatK
CycpmatK
GinbmatK
AdicmatK
Ferns and allies
Bryophytes
OphpmatK
Epifagus
SeldmatK
Axis 1
Axis 1
LyccmatK
PsinmatK
NictmatK
60.00
AratmatK
(C)
AtrbmatK
SpiomaK
OenematK
LotjmatK
55.00
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.
CalfmatK
MaggmatK
AmbtmatK
EpivmatK
50.00
OrysmatK
TriamatK
Nc
ZeammatK
PintmatK
45.00
PinkmatK
CycpmatK
GinbmatK
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.
GnepmatK
40.00
Gnemmat
EphsmatK
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.
AdicmatK
OphpmatK
35.00
SeldmatK
LyccmatK
PsinmatK
PhypmatK
30.00
0.000
MarpmatK
0.050
0.100
0.150
0.200
0.250
0.300
0.350
GC3s
ChagmatK
ChacmatK
0.92
Basal eudicots
90
0.99
Basal eudicots
1.00
73
86
1.00
0.61
84
1.00
75
O
(B)
Genomic DNA
RT-PCR
L
Monocots
1.00
Basal angiosperms
Results
O
L
O
L
O
L
O
L
RT-PCR
O
100
Genomic DNA
Monocots
Basal angiosperms
0.52
Selaginella doederleinii
Conifers
100
M
M
R
Core eudicots
1.00
Core eudicots
L
PinkmatK
Monocots
The chloroplasts of Psilotum, moss and liverworts all have trnK5’-matKtrnK3’ 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.
(A)
OenematK
R
I
I
M
M
R
R
I
I
M
R
I1 I 2
M
R
I1 I2
1.00
Cycads
92
99
1.00
Ginkgo
100
Conifers
1.00
Ginkgo
99
1.00
100
1.00
Gnetophytes
99
500bp
96
Cycads
0.56
100
1.00
Gnetophytes
100
1.00
500bp
1.00
82
1.00
100
89
Lycophytes and ferns
1.00
Lycophytes and ferns
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).
Bryophytes
(A) Maximum parsimony tree
rbcL
2
3
7
8
9
10 11 12 13 14 15 16
17
18
19 20 21
4
5
6
No intron
pseudogene
Nicotiana tabacum
Atropa belladonna
Epifagus virginiana
Spinacia oleracea
Arabidopsis thaliana
Oenothera elata
Lotus corniculatus
Fig. 3. Dot blot hybridization, indicating that matK
is likely present in all of the samples examined.
22
Zea mays
Oryza sativa
Triticum aestivum
Calycanthus floridus
Amborella trichopoda
Kishino-Hasegawa test
Pinus koraiensis
Pinus thunbergii
Adiatum capillus-veneris
Parsimony criteria
Tree
TreeBayesian
Length
5596
TreeParsimony 5554
Diff.
42
P*
Likelihood criteria
-ln L
Diff.
A B
P*
0.0034* 23093.72952 (best)
Psilotum nudum
Physcomitrella patens
Marchantia polymorpha
Anthoceros formosae
(best)
23137.92301 44.19349 0.000*
Chaetosphaeridium globosum
Chara vulgaris
P<0.05 *
Table 1. The results of Kishino-Hasegawa test show that the
TreeParsimony is preferred in parsimony criteria, but the TreeBayesian is
favored by likelihood criteria, and both the alternative tree
topologies are rejected.
(B) Bayesian inference tree
Free-standing matK
atpF
clpP
ndhA
ndhB
ndhH
petB
petD
rpl2
rpl6
rpl12
rpl16
rpoC1
rps12
rps16
ycf2
ycf3
ycf10
ycf66
trnA
trnH
trnI
trnG
trnK
trnL
trnT
trnV
rrn23
Lycopodiella
Adiantum
Ophioglossum
Selaginella
1
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
Bryophytes
Fig. 6. Phylogenetic analyses of matK showed Gnetales is sister to other seed plants.
Intron
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
1.00
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.
Discussion
 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.