supplementary material - springer10.1007/s00239-012-9496... · unrooted ml tree based on the...
TRANSCRIPT
SUPPLEMENTARY MATERIAL-
Genes and Processed Paralogs Coexist in Plant Mitochondria
JournalofMolecularEvolution
A TGG TC C CT T A TGAAG TC T CTA T TGGT C T T A T T C T TA T T - A CTG TA C TAA TA TGTG TAGGT C CC TG TAA T T CGAG TGAGA T TG T CA TGG CGCAAAAGCAGATA TGG T T CGG TA T T CC C T TG T T C CC CGTATA T TGGT C T T A T T C T TA T T - A CTG TA C TAA TA TGTG TAGGT C CC TG TAA T T CGAG TGAGA T TG T CA TGG CGCAAAAGCAGATA TGG T T CGG TA T T CC C T TG T T C CC CGTA
T TGGT C T T A T T C T TA T T - A CTG TA C TAA TA TGTG TAGGT C CC TG TAA T T CGAG TGAGA T TG T CA TGG CGCAAAAGCAGATA TGG T T CGG TA T T CC C T TG T T C CC CGTAA TGG TC T CT T A TGAAG TC T CTA T TGGT C T T A T T C T TA T T - A CTG TA C TAA TA TGTG TAGGT C CC TG TAA CT CGAG TGAGA T TG T CA TGG CGCAAAAGCAGATA TGG T T CGG TA T T CC C T TG T T C CC CGK R
C T CT T A TGAGG TC T CTA T TGGT C T T A T T C T TA T T - A CTG TA C TAA TA TGTG TAGGT C CC TG TAA T T CGAG TGAGA T TG T CA TGG CGCAAAAGCAGATA TGG T T CGG TA T T CC C T TG T T C CC CGTAA TGG TC T CT T A TGAGG TC T CTA T TGGT C T T A T T C T TA T T - A CTG TA C TAA TA TGTG TAGGT C CC TG TAA T T CGAG TGAGA T TG T CA TGG CGCAAAAGCAGATA TGG T T CGG TA T T CC C T TG T T C CC CGTA
C T CT T A TGAGG TC T CTA T TGGT C T T A T T C T TA T T - A CTG TA C TAA TA TGTG TAGGT C CC TG TAA T T CGAG TGAGA T TG T CA TGG CGCAAAAGCAGATA TGG T T CGG TA T T CC C T TG T T C CC CGTAA TGG TC T CT T AAGAGG TC T CTA T TGGT C T T A T T C T TA T T - A CTG TA C TAA TA TGTG TAGGT C CC TG TAA T T CGAG TGAGA T TG T CA TGG CGCAAAAGCAGATA TGG T T CGG TA T T CC C T TG T T C CC CGTAA TGG TC T CT T A TGAAG TA T CTA T TGGT C T T A T T C T TA T T - A CTG TA C TAA TA TGTG TAGGT C CC TG TAA T T CGAG TGAGA T TG T CA TGG CGCAAAAGCAGATA TGG TA TGG TA T T CC C T TG T T C CCA TGG TC T CT T A TGAGG TC T CTA T TGGT C T T A T T C T TA T T - A CTG TA C TAA TA TGTG TAGGT C CC TG TAA T T CGAG TGAGA T TG T CA TGG CGCAAAAGCAGATA TGG T T CGG TA T T CC C T TG T T C CC CGTAA TGG TC T CT T A TGAGG TC T CTA T TGGT C T T A T T C T TA T T - A CTG TA C TAA TA TGTG TAGGT C CC TG TAA T T CGAG TGAGA T TG T CA TGG CGCAAAAGCAGATA TGG T T CGG TA T T CC C T TG T T C CC CGTAA TGG TC T CT T A TGAGG TC T CTA T TGGT C T T A T T C T TA T T - A CTG TA C TAA TA TGTG TAGGT C CC TG TAA T T CGAG TGAGA T TG T CA TGG CGCAAAAGCAGATA TGG T T CGG TA T T CC C T TG T T C CC CGTAA TGG TC T CT T A TGAGG TC T CTA T TGGT C T T A T T C T TA T T - A CTG TA C TAA TA TGTG TAGGT C CC TG TAA T T CGAG TGAGA T TG T CA TGG CGCAAAAGCAGATA TGG T T CGG TA T T CC C T TG T T C CC CGTAA TGG TC C CT T A TGAGG TC T CAA T CGGT C T T A T T C T TA T T - A CTG TA C TAA TA TGTG TAGGT C CC TG TAA T T CGAG TGAGA T TG T CA TGG CGCAAAAGCAGATA TGG T T CGG TA T T CC C T TG T T C CC CGTAA TGG TC T CT T A TGAGG TC T CTA T CGGT C T T A T T C T TA T T - A CTG TA C TAA TA TGTG TAGGT C CC TG TAA T T CGAG TGAGA T TG T CA TGG CGCAAAAGCAGATA TGG T T CGG TA T T CC C T TG T T C CC CGTAA TGG TC T CT T A TGAGG TC T CTA T TGGT C T T A T T C T TA T T - A CTG TA C TAA TA TGTG TAGGT C CC TG TAA T T CGAG TGAGA T TG T CA TGG CGCAAAAGCAGATA TGG T T CGG TA T T CC C T TG T T C CC CGTAA TGG TC T CT T A TGAGG TC T CTA T TGGT C T T A T T C T TA T T - A CTG TA C TAA TA TGTG TAGGT C CC TG TAA T T CGAG TGAGA T TG T CA TGG CGCAAAAGCAGATA TGG T T CGG TA T T CC C CTG T T C CC CGTAA TGG TC T CT T A TGAGG TC T CTA T TGGT C T T A T T C T TA T T - A CTG TA C TAA TA TGTG TAGGT C CC TG TAA T T CGAG TGAGA T TG T CA TGG CGCAAAAGCAGATA TGG T T CGG TA T T CC C T TG T T C CC CGTAA TGG TC C CT T A TGAGG TC T CTA T CGGT C T T A T T C T TA T T - A CTG TA C TAA TA TGTG TAGGT C CC TG TAA T T CGAG TGAGA T TG T CA TGG CGCAAAAGCAGATA TGG T T CGG TA T T CC C T TG T T C CC CGTAA TGG TC C CT T A TGAGG TC T CTA T CGGT C T T A T T C T TA T T - A CTG TA C TAA TA TGTG TAGGT C CC TG TAA T T CGAG TGAGA T TG T CA TGG CGCAAAAGCAGATA TGG T T CGG TA T T CC C T TG T T C CC CGTAA TGG TC T CT T A TGAAG TC T CTA T TGGT C T T A T T C T TA T T - A CTG TA C TAA TA TGTG TAGGT T CC TG TAA T T TGAG TGAGA T TG T CA TGG CGCAAAAGCAGATA TGG T T CGG TA T T CC C T TG T T C CC CGTAA TGG TC T CT T A TGAAG TC T CTA T TGGT C TGA T T C TGA T T - A CTG TA C TAA TA TGTG TGGGT T CT TG TAA T T TGAG TGAGA T TG T CA TGG CGCAAAAGCAGAT C TGG T T CGG TA T T CC C T TG T T C CC TGTAA TGG TC T CT T A TGAAG TC T CTA T TGGT C TGA T T C TGA T T - A CTG TA C TAA TA TGTG TAGGT T CT TG TAA T T TGAG TGAGA T TG T CA TGG CGCAAAAGCAGATA TGG T T CGG TA T T CC C T TG T T C CC TGTAA TGG TC T CT T A TGAGG TC T CTA T CGGT C TGA T T C TGA T T - A CTG TA C TAA T C TGTG TAGGT T CT TG TAA T T TGAG TGAGA T TG T CA TGG CGCAAAAGCAGATA TGG T T TGG TA T T CC C T TG T T C CC TGTAA TGG TC T CT T A TGAGG TC T CTA T CGGT C TGA T T C TGA T T - A CTG TA C TAA T C TGTG TAGGT T CT TG TAA T T T TAG TGAGA T TG T CA TGG CGCAAAAGCAGATA TGG T T TGG TA T T CC C T TG T T C CC TGTAA TGG TMT CT TA TGAGG TC T CTA T TGGT C TGA T T C T TA T T - A CTG T C C TAA T C TGTG TAGGT T CT TG TAA T T TGAG TGAGA T TG TGA TGG CGCAAAAGCAGATA TGG T T TGG TA T T CC C T TG T T C CC TGT CA TGG TC T CT T A TGAGG TC T CTA T TGGT C TGA T T C TGA T T - A CTG TA C T CA TA TGTG TAGGT T CT TG TAA T T TGAG TGAGA T TG T CA TGG CGCAAAAGCAGATA TGG T T CGG TA T T CC C T TG T T C CC CGTAA TGG TC T CT T A TGAGG TC T CTA T CGGT C TGA T T C TGA T T - A CTG TA C TAA T C TGTG TAGGT T CT TG TAA T T T TAG TGAGA T TG T CA TGG CGCAAAAGCAGATA TGG T T TGG TA T T CC C T TG T T C CC TGTAA TGG TC T CT T A TGAGG TC T CTA T TGGT C T T A T T C T TA T T - A CTG TA C TAA TA TGTG TAGGT C CC TG TAA T T CGAG TGAGA T TG T CA TGG CGCAAAAGCAGATA TGG T T CGG TA T T CC CA TGG TC C CT T A TGAGG TC T CTA T CGGT C TGA T T C TGA T T - A CTG TA C TAA TA TGTG TAGGT C CC TG TAA T T CGAG TGAGA T TG T CA TGG CGCAAAAGCAGATA TGG T T CGG TA T T CC C T TG T T C CC CGTA
1. Butomus2. Scheuchzeria3. Cymodocea4. Lilaea5. Heterozostera6. Zostera7. Phylospadix8. Potomageton9. Aponogeton10. Baldellia11. Luronium12. Echinodiorus13. Sagittaria14. Stratiotes15. Ottelia16. Blyxa17. Ruppia18. Syringodium19. Hydrocharis20. Limnobium21. Caldesia22. Limnocharis23. Hydrocleys24. Hydrilla25. Nechamandra26. Vallisneria27. Najas28. other paralogE29. Egeria30. Elodea2
intron
Figure S1 Alignment of the partial sequences of the exon B and C of nad1Reduced alignment including the ca. 130 pb used in our analyses. The location where the cis-spliced intron is inserted in sequences 1 to 20 is indicated. Edited sites experimentally observed are indicated with rectangles. Sequences 1 to 20 are paralog I sequences, and from 21 to 30 paralog E sequences.
0.01
Dioscoreales Dioscorea rockii
Araceae
Laurales Calycanthus floridus
Pandanales Pandanus tectorius
Fagales
Magnoliales Liriodendron tulipifera
Malpigiales
Apiales Chaerophyllum procumbens
Cucurbitales
Alismatids
Austrobaileyales Trimenia moorei
Liliales Androcymbium dregei
Poales
Caryophyllales
Rosales Pronus persica
Rosales Ziziphys obtusifolia
Tofeldiaceae
Oxalidales Hua gabonica
Dioscoreales Narthecium ossifragum
Asparagales
Ericales Actinidia deliciosa
Apiales Panax japonicus
Dioscoreales Tacca plantaginea
Gentaniales Apocynaceae sp.
Figure S2 Phylogenetic reconstruction of 71 angiosperm taxa based on intron nad1i477 Unrooted ML tree based on the partial sequences of nad1i477 using the GTR+G model. Clades and taxa were colored as follows: red lines for basal angiosperms, purple for Magnoliids, blue for Eudicots and green for Monocots. Generic names are indicated. The order Alismatales was split into the families To�eldeaceae, Araceae, and the remaining 12 families, all included in an informal clade named Alismatids. GenBank accession numbers available upon request.
0.06
CU
C 7
sp
+ S
OL
1 sp
ALI
Lim
noch
aris
RO
S Z
izip
hus
OX
A H
ua
AS
P O
rchi
dace
ae 4
sp
DIO
Nar
thec
ium
PA
RA
LOG
E
CE
L B
rexi
a
DIO
Hex
apte
rella
FAG
Jug
lans
ALI
Hal
ophi
la
MA
G L
iriod
endr
on
ALI
Het
eroz
oste
ra
RO
S P
runu
sLA
U C
alyc
anth
us
MA
L Li
cani
a
ER
I Prim
ula
MA
L R
affle
sia
ALI
Ege
ria
LIL
And
rocy
mbi
um
ALI
Cym
odoc
ea
ALI
Sag
ittar
ia
PO
A Z
izan
iops
is
PA
N P
anda
nus
ALI
Rup
pia
ALI
Syr
ingo
dium
ALI
Hyd
roch
aris
ALI
Stra
tiote
s
MA
L P
etal
ostig
ma
MA
L O
chna
MA
L E
ndod
esm
ia
GE
N A
pocy
nace
a
AP
I Pan
ax
PO
A (1
0sp)
+ A
LI A
race
ae (1
8sp)
+ D
IO (2
sp)
ALI
Zos
tera
ALI
Tof
ield
ia
ALI
Pot
amog
eton
ALI
Ech
inod
orus
DIO
Cam
pylo
siph
on
ALI
Val
lisne
ria
AS
P P
hrag
mip
ediu
m
DIO
Bur
man
nia
ALI
Naj
as
AC
O A
coru
s
ALI
Sym
ploc
arpu
sA
LI G
ymni
stac
hys
OX
A O
xalis
MA
L P
assi
flora
ZIG
Lar
rea
MA
L E
liea
ALI
Bly
xa
ALI
Elo
dea
ALI
Lur
oniu
m
MA
L M
anih
ot
ALI
Hyd
rilla
BR
A B
rass
ica
ALI
Pot
amog
eton
ALI
Cal
desi
a
MA
L S
auva
gesi
a
DIO
Thi
smia
GE
N P
agam
ea
ALI
Lila
ea
MA
L V
iola
CE
L Le
pido
botry
s
AS
P A
gave
CU
C C
ucum
is
PO
A T
ritic
um
ALI
Phy
llosp
adix
MA
L R
hiza
nthe
s
MA
L E
lvas
ia
DIO
Ste
nom
eris
DIO
Apt
eria
FAG
Fag
us
CO
M E
ichh
orni
a
ALI
Alis
ma
ALI
But
omus
ALI
Oro
ntiu
m
ALI
Lim
nobi
um
MA
L La
chno
styl
is
ALi
Otte
lia
AU
S T
rimen
ia
MY
R O
enot
hera
AM
B A
mbo
rella
ALI
Apo
noge
ton
AP
I Cha
erop
hyllu
GE
R G
eran
iace
ae 4
1 sp
AU
S A
ustro
baile
ya
DIO
Dio
scor
ea
ALI
Bal
delli
a
ALI
Hyd
rocl
eys
DIO
Geo
mitr
a
AS
P A
llium
DIO
Tac
ca
ALI
Naj
as
ER
I Act
inid
ia
Figure S3 Phylogenetic reconstruction of 181 angiosperm taxa based on nad1 exons
B and C.
Unrooted ML tree based on analysis of partial sequences of nad1 using a JC69+G model.
Paralog E and I sequences are indicated in yellow and green, respectively. Only one of
the twelve identical paralog E sequences was included in the analysis (indicated as
PARALOG E). Classification by order in accordance with APG III is indicated as
follows: AMB = Amborellales, AUS = Austrobaileyales, GER = Geraniales, CUC =
Cucurbitales, ROS = Rosales, ZIG = Zygophyllales, MAL = Malpigiales, CEL =
Celastrales, BRA = Brassicales, FAG = Fagales, OXA = Oxalidales, GEN = Gentianales,
API = Apiales, MAG = Magnoliales, ERI = Ericales, COM = Commelinales, DIO =
Dioscoreales, PAN = Pandanales, ACO = Acorales, LIL = Liliales, APS = Asparagales,
POA = Poales, ALI = Alismatales. To save space some clades were collapsed: from
bottom up: 1) 41 species of Geraniales, 2) seven species of Cucurbitales plus Solanum
(Solanales), 3) four orchid species (Asparagales), 4) ten species of Poales, plus 18 species
of Araceae (Alismatales), and two species of Dioscoreales.
TableS1.Primersusedforamplificationofnad1.
Name Position Sequence
Nad1EB ExonB GCATTACGATCTGCAGCTCA
Nad1ECr ExonC GGAGCTCGATTAGTTTCTGC
Nad1iB Intron2 GCTCCACCGGCCTAAACGAGGAGC
Nad1iB2 Intron2 CGCTCGATCGACGGGACGGAC
Nad1iB2 Intron2 GTCGAGCATACGACGATGCCGC
Nad1iB2R Intron2 GGCGGCATCGTCGTATGCTCG
Nad1p_E1_30F ExonA GCTGTTCCAGCGGAAATACT
Nad1p_E1_288R ExonA CCCAAGCGACCAGACTTAAC
Nad1p_E2_441F ExonB GCAGCTCAAATGGTCCCTTA
Nad1p_E5_971R ExonE AACACCTGAAACGGGGACTA
Primersnad1EBandnad1ECrweredevelopedbyref.[37].
TableS2.PlantmaterialandGeneBankaccessionnumbersusedinthisstudy
Family Taxon Voucher* Paralog I Paralog E
Acoraceae Acorus calamus C998 HM576887 absent
Acorus gramineus C2444 HM576888 absent
Araceae Arisaema amurense C1295 HM576827 absent
Gymnostachys anceps C205 HM576828 absent
Orontium aquaticum C2449 HM576829 absent
Symplocarpus foetidus C2450 HM576830 absent
Alismataceae Alisma plantago-aquatica C30 HM576848 absent
Baldellia ranunculoides C1082 HM576846 absent
Caldesia oligococca C246 absent HM576860
Echinodorus cordifolius C1526 HM576849 HM576881
Echinodorus uruguayensis C20 HM576850 HM576884
Luronium natans C2377 HM576847 absent
Ranalisma humile C2373 HM576851 absent
Sagittaria sagittifolia C1284 HM576852 HM576879
Aponogetaceae Aponogeton crispus C114 HM576845 HM576883
Butomaceae Butomus umbellatus C29 HM576844 absent
Cymodoceae Amphibolis griffithii C2375 HM576834 absent
Cymodocea nodosa C1260 HM576835 absent
Syringodeum isoetifolium C2376 HM576857 absent
Hydrocharitaceae Blyxa aubertii C107 HM576855 HM576880
Egeria naias C1525 absent HM576871
Elodea canadensis C798 absent HM576863
Elodea nutalii C2458 absent HM576873
Halophila sp. C864 absent HM576864
Hydrilla verticillata C112 absent HM576865
Hydrocharis morsus-ranae C524 HM576858 absent
Limnobium laevigatum C1449 HM576859 absent
Najas guadalupensis C1485 absent HM576868
Najas sp. C113 absent HM576869
Nechamandra alternifolia C111 absent HM576866
Ottelia ovalifolia C245 HM576854 HM576875
Stratiotes aloides C23 HM576853 absent
Vallisneria sp. C1139 absent HM576867
Limnocharitaceae Hydrocleys nymphoides C1434 absent HM576862
Limnocharis flava C1435 absent HM576861
Juncaginaceae Lilaea scilloides C25 HM576837 absent
Triglochin maritima C1440 - HM576872
Triglochin palustre C476 HM576838 HM576878
Posidoniaceae Posidonia oceanica C262 HM576836 HM576882
Potamogetaceae Potamogeton lucens C531 HM576842 -
Potamogeton natans C534 HM576843 HM576877
Zannichellia palustris C840 - HM576885
Ruppiaceae Ruppia cirrhosa C530 HM576856 HM576874
Scheuchzeriaceae Scheuchzeria palustris C522 HM576833 HM576870
Tofieldeaceae Tofieldia pusilla C462 HM576831 absent
Pleea tenuifolia C2448 - absent
Zosteraceae Heterozostera tasmanica C2374 HM576839 -
Phyllospadix scouleri C1093 HM576841 HM576876
Zostera sp. C2453 HM576840 HM576886
*AllvouchernumbersrefertotheCopenhagenUniversity’sHerbariumandDNAbank.