Curr Genet (2009) 55:323–337

DOI 10.1007/s00294-009-0249-7

RESEARCH ARTICLE

Loss of all plastid ndh genes in Gnetales and conifers: extent and evolutionary signiWcance for the seed plant phylogeny

Thomas Werner Anthony Braukmann · Maria Kuzmina · Sana StefanoviT

Received: 13 March 2009 / Revised: 22 April 2009 / Accepted: 27 April 2009 / Published online: 18 May 2009© Springer-Verlag 2009

Abstract The exact phylogenetic position of Gnetales, asmall, highly modiWed group of gymnosperms with anaccelerated rate of molecular evolution, is one of the mostchallenging issues for seed plant systematics. Recent resultsfrom entire plastid genome (ptDNA) sequencing revealedthe absence of the entire suite of plastid ndh genes in sev-eral species of Gnetales and the pine family (Pinaceae)potentially highlighting a major structural feature linkingthese two groups—concerted loss of all plastid genes forthe NADH dehydrogenase complex. However, the preciseextent of ndh gene loss in gymnosperms has not been sur-veyed. Using a slot-blot hybridization method, we probedall 11 ndh genes in 162 species from 70 of 85 gymnospermgenera. We Wnd that all ndh genes are absent acrossGnetales and Pinaceae, but not in any other group of gym-nosperms. This feature represents either a major synapo-morphy for a clade consisting of these two lineages or, lesslikely, a convergent loss. Our survey substantially extendsprevious inferences based on more limited sampling and, ifthe former evolutionary interpretation is correct, it provides

additional support for the contentious “gnepine” hypothe-sis, which places Gnetales as sister to Pinaceae.

Keywords Gnetales · Conifers · ndh genes · Phylogeny · Seed plants · Slot-blot hybridization

Introduction

Arguably the most vexing outstanding question for the seedplant phylogeny remains the placement of Gnetales, a smallgroup of gymnosperms currently circumscribed in threegenera (Ephedra, Gnetum, and Welwitschia), despite inten-sive cladistic investigations over past two decades. Multiplepermutations for the relationship of Gnetales to other extantlineages of spermatophytes (otherwise comprising Ginkgo,cycads, Pinaceae, cupressophyte conifers and Xoweringplants) have been proposed by diVerent studies, usingdiVerent types of data and/or diVerent analytical methods(reviewed by Magallón and Sanderson 2002; Soltis et al.2002; Burleigh and Mathews 2004, 2007a; Mathews 2009).However, because of their repeated recovery across manystudies, six particular hypotheses on the placement of Gne-tales stand out as the most frequently invoked ones (Fig. 1).A series of early cladistic analyses based on morphologicaldata and including relevant fossil taxa suggested the place-ment of Gnetales close to angiosperms (Crane 1985; Doyleand Donoghue 1986; Loconte and Stevenson 1990; Nixonet al. 1994), in accordance with the “anthophyte” hypothe-sis (Wettstein 1907). Later, some molecular studies recov-ered the same results, albeit only with weak support(StefanoviT et al. 1998; Rydin et al. 2002). However, mostearly analyses of molecular data resulted in so-called “gne-tales-sister” hypotheses, featuring Gnetales either sister tothe rest of gymnosperms (“gnetales-sister I”; Hasebe et al.

Communicated by R. Bock.

Electronic supplementary material The online version of this article (doi:10.1007/s00294-009-0249-7) contains supplementary material, which is available to authorized users.

T. W. A. Braukmann (&) · M. Kuzmina · S. StefanoviTDepartment of Biology, University of Toronto Mississauga, 3359 Mississauga Rd. N, Mississauga, ON L5L 1C6, Canadae-mail: thomas.braukmann@utoronto.ca

Present Address:M. KuzminaBiodiversity Institute of Ontario, University of Guelph, 579 Gordon St., Guelph, ON N1G 2W1, Canada

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http://dx.doi.org/10.1007/s00294-009-0249-7

324 Curr Genet (2009) 55:323–337

1992; Goremykin et al. 1996; Samigullin et al. 1999;Frolich and Parker 2000; Mathews and Donoghue 2000) orsister to the rest of seed plants, including angiosperms(“gnetales-sister II”; Hamby and Zimmer 1992; Albertet al. 1994; Rai et al. 2003, 2008). Subsequent analyses,based mainly on sequences from multiple genes andgenomes, suggested a “gnetifer” hypothesis, in which Gne-tales are found as sister to all conifers (Chaw et al. 1997,2000). But one of the most surprising results of molecularplant systematics placed Gnetales within conifers, as sisterto Pinaceae, in what became known as the “gnepine”hypothesis (Bowe et al. 2000; Chaw et al. 2000; Gugerliet al. 2001; Qiu et al. 2007). More recently, another hypoth-esis rendering conifers paraphyletic has gained somemomentum. According to the “gnecup” hypothesis, Gne-tales are also placed within conifers, but as sister tocupressophytes, not Pinaceae (see Nickrent et al. 2000;Rydin and Källersjö 2002; Doyle 2006; Chumley et al.2008).

One major cause of ambiguity for spermatophyte phy-logeny inference can be attributed to the ambiguous root-ing. While these six competing hypotheses seemsigniWcantly diVerent from one another when polarizedwith outgroups (i.e., rooted; Fig. 1a), they fall into only twocategories, each with an identical underlying unrooted tree(Fig. 1b). For example, it becomes apparent that there areno topological diVerences among the Wrst three major phy-logenetic hypotheses (anthophyte and gnetales-sister, I andII; Fig. 1a, 1–3) when the other land plant outgroups (repre-sented by grey arrows in Fig. 1) are pruned oV and theremainder is taken as an unrooted tree. Similarly, the only

diVerence between the remaining three alternative scenar-ios within seed plants (gnetifer, gnepine, and gnecuphypotheses; Fig. 1a, 4–6), is the placement of the root forthe clade comprising conifers and Gnetales. Besides rootingissues, another important source of ambiguity is due to thesubstantial sequence divergence among living lineages ofseed plants and their nearest outgroups (ferns and lyco-pods). In seed plants, this is particularly evident in longbranches leading to angiosperms, Gnetales, and Pinaceae asseen in most molecular trees, regardless of whether derivedfrom plastid, nuclear, or mitochondrial sequences (Chawet al. 1997, 2000; Bowe et al. 2000; Rydin et al. 2002; Gra-ham and Iles 2009). In conjunction, these two phenomenafrequently lead to the strongly supported yet spurious treerooting due to long-branch attraction or related artifacts(Felsenstein 1983; Hendy and Penny 1989). Further com-plicating the issue, diVerent methods of analyses and diVer-ent optimality criteria frequently support alternativetopologies, even though based on the same sequences(Bowe et al. 2000; Rydin et al. 2002; Burleigh andMathews 2004, 2007b). Surprisingly, the removal of mostrapidly evolving sequences or sites was shown to have littleto no eVect on the inferences on higher-order seed plantrelationships (Burleigh and Mathews 2004; Rai et al. 2008),raising the question of the limits of nucleotide data(Mathews 2009).

Molecular evidence is not limited only to primarysequence data. Additional sources of molecular data rele-vant for the number of open questions of seed plant phylog-eny can be sought from so-called “rare genomic markers”(e.g., Raubeson and Jansen 1992; Rokas and Holland 2000;

Fig. 1 Correspondence between competing rooted and unrooted seedplant phylogenetic hypotheses. a Six most prominent rooted hypothe-ses of relationships among major lineages of seed plants. Arrows indi-cate alternative root placements as in b, 1–6 Parsimony reconstructionsof gene losses for the ndh gene suite are mapped (oval) under theassumption of irreversibility. b Unrooted trees showing that the

underlying topologies for each of the two major sets of hypotheses areidentical when their respective outgroups, the other land plants (1–3)or other seed plants (4–6) are excluded. Note that these two unrootedtrees are incompatible. Taxon abbreviations: ANG angiosperms, CUPcupressophytes, CYC cycads, GIN Ginkgo, GNE Gnetales, GYM¡gymnosperms minus Gnetales, PIN Pinaceae

123

Curr Genet (2009) 55:323–337 325

Moreira and Philippe 2000; Gugerli et al. 2001). In thisregard, the plastid (pt) genome seems to be particularlypromising. In seed plants, this genome is highly conservedin size, structure, content, and synteny (Palmer 1991;Downie et al. 1991; Clegg et al. 1994). Because of theirrelatively infrequent evolutionary occurrence, any majorstructural mutation in the pt genome, such as inversions,gene/intron losses, and contractions/expansions of theinverted repeat (IR), are often considered to be more reli-able phylogenetic markers compared to sequences (e.g.,Downie et al. 1991; Downie and Palmer 1992; Raubesonand Jansen 1992; Doyle et al. 1995; Doyle et al. 1996;Bailey et al. 1997; Graham and Olmstead 2000a; Plunkettand Downie 2000; Jansen et al. 2007; but see McPhersonet al. 2004; Palmer et al. 2004 for cautionary views).

The loss of ndh genes from the pt genome of some seedplant represents one such potentially informative structuralchange. The ndh genes encode subunits of the plastidNAD(P)H-dehydrogenase (Ndh) complex, a homologue ofmitochondrial complex I (Shinozaki et al. 1986). In plas-tids, the Ndh complex seems to be primarily involved withtransfer of electrons from stromal reductants to a plastoqui-none pool, a process commonly known as “chlororespira-tion” (Bennoun 2002; Peltier and Cournac 2002). Inaddition, involvement of this complex in photooxidativestress reduction in high light intensity, regulation of photo-synthesis by modulating the activity of cyclic electron Xowaround photosystem I, and/or leaf senescence regulationhave also been suggested (Casano et al. 2001; Bukhov andCarpentier 2004; Zapata et al. 2005; Diaz et al. 2007;Tallon and Quiles 2007; Romeau et al. 2007; Endo et al.2008).

While the precise role of the Ndh complex is still uncer-tain, the ndh genes are known to be widespread in the auto-trophic seed plants and remain highly conserved over largeevolutionary distances, indicating the presence of strongselection pressure for their retention. Results of entire (orextensive) pt genome sequencing from a number of individ-ual studies indicate that the complete suite of ndh genes ispresent in Ginkgo (Leebens-Mack et al. 2005; Jansen et al.2007) and selected representatives of cycads (Wu et al.2007) and cupressophytes (Hirao et al. 2008) as well as in»60 species of diverse angiosperms (summarized mostrecently by Jansen et al. 2007). As suggested by Bungard(2004), the loss of ndh genes in Xowering plants seems tobe conWned only to parasitic plant lineages (dePamphilisand Palmer 1990; Olmstead et al. 2001; StefanoviT andOlmstead 2005; Funk et al. 2007; McNeal et al. 2007). Thislink with heterotrophy is further supported by the loss ofndh genes in a non-photosynthetic liverwort (Wickett et al.2008) and a green but potentially mycotrophic orchid(Chang et al. 2006). The absence of functional ndh genesfrom the pt genomes of fully autotrophic seed plants is

presently reported only from Gnetales (Wu et al. 2007,2009; McCoy et al. 2008) and several genera of Pinaceae(Wakasugi et al. 1994; Cronn et al. 2008; Rai et al. 2008;Wu et al. 2009). If inferred to have happened concurrently,this loss could represent a strong synapomorphy for Gne-tales and Pinaceae (Chaw et al. 2000; Burleigh andMathews 2004; Wu et al. 2007). Despite the potential ofthis rare structural genomic character to bear signiWcantlyon the seed plant relationships and help choose amongalternative phylogenetic hypotheses, the full extent of pres-ence or absence of ndh genes among living gymnosperms isunknown.

In the present study, we gathered data using a compre-hensive slot-blot hybridization survey of the complete suiteof plastid ndh genes with a dense sampling of gymno-sperms, the most extensive data matrix applied to this issueto date, in order to: (1) ascertain the extent and distributionof ndh gene losses across gymnosperms; and (2) assess theutility of these losses as phylogenetic markers for seedplant phylogeny.

Materials and methods

Taxon sampling

In total, 70 of the 85 genera and 162 of the »1,070 speciesof extant gymnosperms were sampled in this study(Table 1), corresponding to 82% of their generic- and 15%of their species-richness, respectively. Our samplingencompasses all four major lineages of living gymno-sperms; however, the percentage of diversity coveragediVers among these groups (compare with Table 1). Ginkgobiloba is the sole living representative of Ginkgoales. Coni-fers, including both Pinaceae and cupressophytes, are rep-resented by a total of 131 species (out of 680; 20%),grouped into 59 genera (out of 70; 85%), from all sevencurrently recognized families. The species-richness ofcycads is represented to a signiWcantly lesser degree, by 14out of 305 species (5%), but our sampling covers 64% ofgenera (7 out of 11). Finally, 16 species of Gnetales aresampled in total (out of the 92 species; 17%), including allthree recognized genera/families. Representatives of fourgenera of autotrophic angiosperms (Table 1), the lastremaining lineage of extant seed plants, were also includedin our surveys as positive controls.

DNA extraction and hybridization

Total genomic DNA was isolated using the modiWed 2£CTAB method (Doyle and Doyle 1987). Fresh leaf materialwas used where available, but approximately two-thirds ofthe samples were either from silica-gel dried tissue or

123

326 Curr Genet (2009) 55:323–337

Tab

le1

See

d pl

ant t

axa

surv

eyed

for

the

pres

ence

/abs

ence

of

plas

tid n

dh(A

-K)

gene

s

Tax

onV

ouch

ernd

hAnd

hBnd

hCnd

hDnd

hEnd

hFnd

hGnd

hHnd

hInd

hJnd

hK

exon

1ex

on 2

exon

1ex

on 2

5� e

nd3�

end

5� e

nd3�

end

Gin

kgoa

les

[1/1

; 100

%]

Gin

kgo

bilo

ba L

.Q

IU-9

4015

(IN

D)

++++

++++

++++

++++

++++

++++

++++

++

Cyc

adal

es [

7/11

;»64

%]

Cyc

as m

edia

R. B

r.N

o vo

uche

r++

++++

++++

++++

++++

++++

+++

++++

Cyc

as r

evol

uta

Thu

nb.

QIU

-940

51 (

IND

)++

++++

++++

++++

++++

++++

++++

++++

Cyc

as ta

iwan

iana

Car

ruth

.SS

-05-

53 (

TR

TE

)++

+++

+++

++++

++++

++++

++

+++

Dio

on s

pinu

losu

m D

yer

ex E

ichl

.SS

-03-

72 (

TR

TE

)++

+++

+++

++++

++++

++++

++

+++

Enc

epha

lart

os a

lten

stei

nii L

ehm

.SS

-05-

57 (

TR

TE

)++

+++

+++

++++

++++

++++

++

+++

Enc

epha

lart

os b

arte

ri C

arru

th. e

x M

iq.

SS-0

5-11

8 (T

RT

E)

++++

++

++++

++++

++++

+++

++

++

Enc

epha

lart

os fe

rox

Ber

tol.

f.SS

-05-

116

(TR

TE

)++

++++

++++

++++

++++

++++

++++

++++

Enc

epha

lart

os lo

ngif

oliu

s L

ehm

.Q

IU-9

5127

(IN

D)

++++

++++

++++

++++

++++

++++

++++

++

Mac

roza

mia

com

mun

is L

.A.S

. Joh

nson

SS-0

5-11

9 (T

RT

E)

++++

++

++++

++++

++++

++++

++

++

Cer

atoz

amia

mex

ican

a B

rong

n.Q

IU-9

4009

(IN

D)

++++

++

++++

++++

++++

++++

++

++

Stan

geri

a er

iopu

s (K

unze

) B

aill.

QIU

-940

78 (

IND

)++

++++

++++

++++

++++

++++

++++

++++

Zam

ia X

orid

ana

A.D

C.

QIU

-950

35 (

IND

)++

++++

++++

++++

++++

++++

++++

++++

Zam

ia fu

rfur

acea

Ait

.SS

-05-

56 (

TR

TE

)++

++++

++++

++++

++++

++++

++++

++++

Zam

ia p

umil

a L

.SS

-05-

58 (

TR

TE

)++

++++

++++

++++

++++

++++

++++

++++

Gne

tale

s [3

/3; 1

00%

]

Eph

edra

ant

isyp

hili

tica

Ber

land

ex

C.A

. Mey

.Q

IU-9

4004

(IN

D)

++

¡¡

+¡

¡+

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+¡

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¡E

phed

ra v

irid

is C

ovill

eSS

-05-

21 (

TR

TE

)¡

+¡

¡+

¡¡

+¡

¡+

¡¡

+¡

Eph

edra

tria

ndra

Tul

.SS

-05-

100

(TR

TE

)¡

+¡

¡+

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¡+

¡+

+¡

Eph

edra

sax

atil

is (

Sta

pf)

Roy

le e

x Fl

orin

SS-0

5-18

8 (T

RT

E)

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¡¡

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¡¡

+¡

¡¡

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phed

ra m

onos

perm

a J.

G. G

mel

. ex

C.A

. Mey

.SS

-05-

35 (

TR

TE

)+

+¡

¡+

+¡

¡¡

¡+

¡+

+¡

Eph

edra

sin

ica

Stap

fSS

-05-

112

(TR

TE

)+

+¡

¡+

¡¡

¡¡

¡+

¡+

¡¡

Eph

edra

dis

tach

ya L

.SS

-05-

25 (

TR

TE

)¡

+¡

¡+

¡¡

¡¡

¡+

¡+

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edra

cam

pylo

poda

C.A

. Mey

.SS

-05-

60 (

TR

TE

)¡

+¡

¡+

¡¡

¡¡

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Eph

edra

frag

ilis

Fre

sen.

SS-0

5-61

(T

RT

E)

++

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¡¡

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+¡

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phed

ra m

inut

a Fl

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SS-0

5-18

1 (T

RT

E)

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phed

ra p

roce

ra C

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SS-0

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(T

RT

E)

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netu

m g

nem

on L

.Q

IU-9

4005

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D)

++

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m le

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dii T

ul.

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IND

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tum

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9 (T

RT

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++

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netu

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la B

rong

n.SS

-06-

214

(TR

TE

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123

Curr Genet (2009) 55:323–337 327

Tab

le1

cont

inue

d

Tax

onV

ouch

ernd

hAnd

hBnd

hCnd

hDnd

hEnd

hFnd

hGnd

hHnd

hInd

hJnd

hK

exon

1ex

on 2

exon

1ex

on 2

5� e

nd3�

end

5� e

nd3�

end

Wel

wits

chia

mir

abili

s H

ook.

f.

SS-0

5-20

(T

RT

E)

++

¡¡

++

¡+

¡¡

+¡

+¡

¡

Pina

ceae

[10

/11;

»91

%]

Abi

es b

alsa

mea

(L

.) M

ill.

SS-0

5-20

8 (T

RT

E)

++

¡¡

+¡

¡¡

¡+

+¡

¡¡

+

Abi

es c

onco

lor

(Gor

don

& G

lend

.) H

ildeb

r.SS

-05-

157

(TR

TE

)+

++

¡+

¡¡

+¡

++

¡¡

¡+

Abi

es W

rma

Sieb

old

& Z

ucc.

QIU

-962

69 (

IND

)+

++

¡+

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+¡

++

¡¡

¡¡

Abi

es h

omol

epis

Sie

bold

& Z

ucc.

QIU

-962

24 (

IND

)+

++

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es k

orea

na E

.H. W

ilson

SS-0

5-39

(T

RT

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++

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+

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es la

sioc

arpa

(H

ook.

) N

utt.

SS-0

5-15

8 (T

RT

E)

++

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elee

ria

davi

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a B

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n.Q

IU-9

6248

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D)

++

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224

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TE

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abil

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-06-

206

(TR

TE

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suga

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RT

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ua M

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42 (

IND

)+

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Lar

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a (D

u R

oi)

K. K

och

SS-0

5-37

(T

RT

E)

++

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++

Pic

ea a

bies

(L

.) H

. Kar

st.

SS-0

3-99

(T

RT

E)

++

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Pic

ea e

xcel

sa L

ink.

SS-0

3-10

5 (T

RT

E)

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Pic

ea g

lehn

ii M

ast.

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5-15

5 (T

RT

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Pic

ea e

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man

nii P

arry

ex

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elm

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210

(TR

TE

)+

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Pic

ea g

lauc

a (M

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h) V

oss

SS-0

5-20

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RT

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Pic

ea p

unge

ns E

ngel

m.

SS-0

3-10

6 (T

RT

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Pic

ea m

aria

na B

ritto

n St

erns

& P

ogge

nb.

SS-0

5-15

6 (T

RT

E)

++

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++

Pic

ea o

mor

ika

(Pan

biT)

Pur

k.SS

-03-

96 (

TR

TE

)+

++

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++

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Pic

ea o

rien

tali

s (L

.) L

ink

SS-0

3-10

0 (T

RT

E)

++

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++

Cat

haya

arg

yrop

hyll

a C

hun

& K

uang

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3 (T

RT

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inus

ari

stat

a E

ngel

m.

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(T

RT

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Pin

us q

uadr

ifol

ia P

arry

ex

Parl

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222

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Pin

us c

embr

a L

.SS

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104

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TE

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¡+

¡¡

¡¡

¡+

¡¡

¡++

Pin

us p

arviX

ora

Sieb

. & Z

ucc.

SS-0

5-42

(T

RT

E)

++

¡¡

+¡

¡+

¡+

+¡

¡¡

++

Pin

us s

trob

us L

.SS

-05-

36 (

TR

TE

)+

+¡

¡+

¡¡

+¡

++

¡¡

¡++

Pin

us w

alli

chia

na A

.B. J

acks

.SS

-03-

97 (

TR

TE

)+

+¡

¡+

¡¡

¡¡

++

¡¡

¡++

Pin

us c

anar

iens

is C

. Sm

.SS

-05-

64 (

TR

TE

)+

+¡

¡+

¡¡

+¡

++

¡¡

¡++

Pin

us h

eldr

eich

ii C

hris

tSS

-03-

98 (

TR

TE

)+

+¡

¡+

¡¡

+¡

++

¡¡

¡+

Pin

us k

esiy

a R

oyle

ex

Gor

don

SS-0

6-22

3 (T

RT

E)

++

¡¡

+¡

¡¡

¡+

+¡

¡¡

¡

123

328 Curr Genet (2009) 55:323–337

Tab

le1

cont

inue

d

Tax

onV

ouch

ernd

hAnd

hBnd

hCnd

hDnd

hEnd

hFnd

hGnd

hHnd

hInd

hJnd

hK

exon

1ex

on 2

exon

1ex

on 2

5� e

nd3�

end

5� e

nd3�

end

Pin

us n

igra

J.F

. Arn

old

SS-0

3-10

7 (T

RT

E)

++

¡¡

+¡

¡+

¡+

+¡

¡¡

++

Pin

us p

inas

ter

Aito

nSS

-05-

65 (

TR

TE

)+

+¡

¡+

¡¡

+¡

++

¡¡

¡++

Pin

us p

inea

L.

SS-0

5-63

(T

RT

E)

++

¡¡

+¡

¡+

¡+

+¡

¡¡

++

Pin

us r

esin

osa

Aito

nSS

-05-

164

(TR

TE

)+

+¡

¡+

¡¡

+¡

++

¡¡

¡++

Pin

us c

onto

rta

Dou

glas

ex

Lou

don

SS-0

5-20

5 (T

RT

E)

++

¡¡

+¡

¡+

¡+

+¡

¡¡

++

Pin

us c

oulte

ri D

. Don

SS-0

5-28

(T

RT

E)

++

¡¡

+¡

¡+

¡+

+¡

¡¡

++

Pin

us r

adia

ta D

. Don

SS-0

5-99

(T

RT

E)

++

¡¡

+¡

¡+

¡+

+¡

¡¡

+

Ced

rus

atla

ntic

a M

anet

tiSS

-03-

101

(TR

TE

)¡

++

¡+

¡¡

¡¡

¡+

¡¡

¡¡

Ced

rus

deod

ara

(Rox

b. e

x L

ambe

rt)

G. D

onQ

IU-9

6265

(IN

D)

¡+

+¡

+¡

¡+

¡¡

+¡

¡¡

¡

Ara

ucar

iace

ae [

3/3;

100

%]

Aga

this

sp.

SS-0

5-66

(T

RT

E)

++++

++

++++

++++

++++

++++

+++

++

Aga

this

rob

usta

(F.

Mue

ll.)

F.M

. Bai

ley

SS-0

6-18

0 (T

RT

E)

++++

++

++++

++++

++++

++++

+++

++

Ara

ucar

ia a

rauc

ana

K. K

och

SS-0

5-11

7 (T

RT

E)

++++

++

++++

++++

++++

++++

+++

++

Ara

ucar

ia b

idw

illi

i Hoo

k.SS

-05-

67 (

TR

TE

)++

++¡

+++

++++

+++

++++

+++

+++

Ara

ucar

ia c

unni

ngha

mii

Aito

n ex

D. D

onSS

-05-

106

(TR

TE

)++

++¡

+++

++++

+++

++++

+?

+++

Ara

ucar

ia h

eter

ophy

lla

(Sal

isb.

) Fr

anco

QIU

-962

20 (

IND

)++

+++

+++

++++

++++

++++

+++

++++

Ara

ucar

ia r

ulei

F. M

uell.

SS-0

5-10

1 (T

RT

E)

++++

++

++++

++++

++++

++++

?++

++

Ara

ucar

ia s

p.SS

-05-

21 (

TR

TE

)++

++¡

+++

++++

++++

++++

++?

++++

Wol

lem

ia n

obil

is W

.G. J

ones

K.D

. Hil

l & J

.M.A

llen

SS-0

5-17

6 (T

RT

E)

++++

¡+

++++

++++

++++

++++

+++

++

Podo

carp

acea

e [1

4/19

;»74

%]

Phy

lloc

ladu

s al

pinu

s H

ook.

f.

SS-0

6-23

1 (T

RT

E)

++++

?+

++++

++++

++++

++++

+++

++

Phy

lloc

ladu

s as

plen

ifol

ius

(Lab

ill.)

Hoo

k.f.

SS-0

6-19

9 (T

RT

E)

++++

??

++++

++++

++++

++++

+++

++

Hal

ocar

pus

bidw

illii

(Hoo

k. f

. ex

T. K

irk)

Qui

nnSS

-06-

201

(TR

TE

)++

+++

+++

++++

++++

++++

+++

++++

Lag

aros

trob

os c

olen

soi (

Hoo

k.)

Qui

nnSS

-06-

187

(TR

TE

)++

+++

+++

++++

++++

++++

+++

++++

Pru

mno

pity

s an

dina

(P

oepp

. ex

End

l.) d

e L

aub.

SS-0

6-18

8 (T

RT

E)

++++

++

++++

++++

++++

++++

+++

++

Sund

acar

pus

amar

a (B

lum

e) C

·N. P

age

SS-0

6-17

7 (T

RT

E)

++++

++

++++

++++

++++

++++

+++

++

Saxe

goth

ea c

onsp

icua

Lin

dl.

QIU

-962

43 (

IND

)++

+++

+++

++++

++++

++++

++++

++++

Mic

rost

robo

s W

tzge

rald

ii (

F.M

uell

.)

J.G

arde

n &

L.A

.S. J

ohns

onSS

-06-

232

(TR

TE

)++

+++

+++

++++

++++

++++

+++

++++

Acm

opyl

e pa

nche

ri P

ilg.

SS-0

6-18

2 (T

RT

E)

++++

??

++++

++++

++++

++?

+?

++

Dac

ryca

rpus

dac

rydi

oide

s (A

.Ric

h.)

de L

aub.

SS-0

6-18

6 (T

RT

E)

++++

¡+

++++

++++

++?

++++

+++

++

Dac

rydi

um c

upre

ssin

um S

ol. e

x L

amb.

SS-0

5-12

0 (T

RT

E)

++++

++

++++

++++

++++

++++

+++

++

Fal

cati

foli

um s

p.SS

-06-

179

(TR

TE

)++

+++

+++

++++

++++

++++

+++

++++

Pod

ocar

pus

cori

aceu

s R

ich.

& A

. Ric

h.SS

-05-

111

(TR

TE

)++

++

+++

++++

++++

++++

+++

++++

123

Curr Genet (2009) 55:323–337 329

Tab

le1

cont

inue

d

Tax

onV

ouch

ernd

hAnd

hBnd

hCnd

hDnd

hEnd

hFnd

hGnd

hHnd

hInd

hJnd

hK

exon

1ex

on 2

exon

1ex

on 2

5� e

nd3�

end

5� e

nd3�

end

Pod

ocar

pus

cost

alis

C. P

resl

QIU

-961

49 (

IND

)++

+++

+++

++++

++++

++++

+++

++++

Pod

ocar

pus

elat

us E

ndl.

SS-0

5-10

7 (T

RT

E)

++++

¡+

++++

++++

++++

++++

++

++

Pod

ocar

pus

falc

atus

(T

hunb

.) M

irb.

SS-0

5-11

4 (T

RT

E)

++++

¡+

++++

++++

++++

++++

++

++

Pod

ocar

pus

fasc

icul

us d

e L

aub.

QIU

-961

48 (

IND

)++

+++

+++

++++

++++

++++

++++

++++

Pod

ocar

pus

gray

ae d

e L

aub.

SS-0

6-20

4 (T

RT

E)

++++

¡+

++++

++++

++++

++++

++

++

Pod

ocar

pus

lati

foli

us R

. Br.

SS-0

5-17

9 (T

RT

E)

++++

¡+

++++

++++

++++

++++

++

++

Pod

ocar

pus

mac

roph

yllu

s (T

hunb

.) D

. Don

QIU

-950

06 (

IND

)++

+++

+++

++++

++++

++++

+++

++++

Pod

ocar

pus

niva

lis

Hoo

k.SS

-05-

103

(TR

TE

)++

+++

+++

++++

++++

++++

+++

++++

Pod

ocar

pus

sp.

SS-0

3-39

(T

RT

E)

++++

¡¡

++++

++++

++++

++++

¡+

++

Pod

ocar

pus

tota

ra G

. Ben

n. e

x D

. Don

SS-0

5-17

8 (T

RT

E)

++++

++

++++

++++

++++

++++

++++

++

Nag

eia

nagi

Bri

tton

& P

. Wils

onQ

IU-9

6146

(IN

D)

++++

++

++++

++++

++++

++++

++++

++

Afr

ocar

pus

grac

ilio

r (P

ilg.)

C·N

. Pag

eSS

-03-

55 (

TR

TE

)++

+++

+++

++++

++++

++++

++++

++++

Ret

roph

yllu

m c

ompt

onii

(B

uchh

.) C

·N. P

age

SS-0

6-18

1 (T

RT

E)

++++

??

++++

++++

??

++?

++?

++

Ret

roph

yllu

m m

inor

(C

arri

ère)

C·N

. Pag

eSS

-06-

178

(TR

TE

)++

++?

?++

++++

++?

?++

?+

?++

Tax

acea

e [3

/5; 6

0%]

Am

ento

taxu

s fo

rmas

ana

H.L

. Li

SS-0

6-21

1 (T

RT

E)

++++

++

++++

++++

++++

++++

+++

++

Tax

us b

acca

ta L

.SS

-05-

109

(TR

TE

)++

+++

+++

++++

++++

++++

+++

++++

Tax

us c

anad

ensi

s M

arsh

all

SS-0

5-41

(T

RT

E)

++++

++

++++

++++

++++

++++

+++

++

Tax

us c

uspi

data

Sie

b. &

Zuc

c.SS

-05-

38 (

TR

TE

)++

+++

+++

++++

++++

++++

++++

++++

Tax

us £

med

ia R

ahde

rQ

IU-9

6218

(IN

D)

++++

++

++++

++++

++++

++++

++++

++

Tor

reya

cal

ifor

nica

Tor

r.SS

-05-

121

(TR

TE

)++

+++

+++

++++

+++

++++

+++

++++

Tor

reya

nuc

ifer

a S

ieb.

& Z

ucc.

SS-0

5-18

0 (T

RT

E)

++++

¡¡

++++

+++

++++

++++

+¡

++

Tor

reya

taxi

folia

Arn

.Q

IU-9

6251

(IN

D)

++++

+++

++++

++++

++++

++++

+++

++

Cep

halo

taxa

ceae

[1/

1; 1

00%

]

Cep

halo

taxu

s ha

rrin

gton

ia K

. Koc

hSS

-03-

102

(TR

TE

)++

+++

+++

++++

++++

++++

+++

++++

Cep

halo

taxu

s fo

rtun

ei H

ook.

SS-0

6-22

1 (T

RT

E)

++++

++

++++

++++

++++

++++

+++

++

Scia

dopi

tyac

eae

[1/1

; 100

%]

Scia

dopi

tys

vert

icill

ata

Sieb

. & Z

ucc.

QIU

-960

87 (

IND

)++

++++

++++

++++

++++

++++

++++

++++

Cup

ress

acea

e s.

l. [2

7/30

; 90%

]

Cun

ning

ham

ia la

nceo

lata

Hoo

k.Q

IU-9

6254

(IN

D)

++++

+++

++++

++++

+++

++++

++++

++

Tai

wan

ia X

ousi

ana

Gau

ssen

QIU

-962

66 (

IND

)++

+++

++++

++++

++++

++++

++++

++++

Ath

rota

xis

sp.

SS-0

6-23

0 (T

RT

E)

++++

?+

++++

++?

++++

++++

++++

++

Sequ

oia

sem

perv

iren

s E

ndl.

QIU

-960

91 (

IND

)++

+++

++++

++++

++++

+++

++++

++++

Sequ

oiad

endr

on g

igan

teum

(Lin

dl.)

J. B

uchh

olz

QIU

-960

89 (

IND

)++

+++

++++

++++

++++

++++

++++

++++

123

330 Curr Genet (2009) 55:323–337

Tab

le1

cont

inue

d

Tax

onV

ouch

ernd

hAnd

hBnd

hCnd

hDnd

hEnd

hFnd

hGnd

hHnd

hInd

hJnd

hK

exon

1ex

on 2

exon

1ex

on 2

5� e

nd3�

end

5� e

nd3�

end

Cry

ptom

eria

japo

nica

D. D

onQ

IU-9

6267

(IN

D)

++++

+++

++++

++++

+++

++++

++++

++

Gly

ptos

trob

us p

ensi

lis

(lin

eatu

s) K

. Koc

hQ

IU-9

6264

(IN

D)

++++

+++

?++

++++

++++

++++

?++

++

Tax

odiu

m d

isti

chum

H·B

. & K

.SS

-05-

113

(TR

TE

)++

+++

++++

++++

++++

+++

++++

++++

Aus

troc

edru

s ch

ilen

sis

(D.D

on) F

lori

n &

Bou

telje

SS-0

6-19

0 (T

RT

E)

++++

++

++++

++++

+++

++++

++++

++

Lib

oced

rus

plum

osa

Dru

ceSS

-06-

196

(TR

TE

)++

+++

+++

++++

++++

+++

++++

++++

Pil

gero

dend

ron

uvif

erum

Flo

rin

SS-0

6-20

2 (T

RT

E)

++++

++

??

?++

?++

++++

?++

++

Act

inos

trob

us a

rena

rius

C.A

. Gar

dner

SS-0

6-22

6 (T

RT

E)

++++

++

++++

++++

+++

++++

+++

++

Cal

litri

s dr

umm

ondi

i (Pa

rl.)

F. M

uell

.Q

IU-9

6250

(IN

D)

++++

++

++++

++++

++++

++++

++++

++

Dis

elm

a ar

cher

i Hoo

k. f

.SS

-06-

203

(TR

TE

)++

+++

+++

++++

++++

++++

++++

++++

Fit

zroy

a cu

pres

soid

es I

.M. J

ohns

t.SS

-06-

200

(TR

TE

)++

++¡

+++

++++

++++

?++

++++

++++

Thu

ja o

ccid

enta

lis L

.Q

IU-9

6223

(IN

D)

++++

++

++++

++++

+++

++++

++++

++

Thu

ja o

rien

tali

s L

.SS

-05-

69 (

TR

TE

)++

+++

+++

++++

++++

+++

++++

++++

Thu

ja p

lica

ta D

onn

ex D

. Don

SS-0

5-21

1 (T

RT

E)

++++

++

++++

++++

+++

++++

++++

++

Thu

jops

is d

olab

rata

Sie

bold

& Z

ucc.

QIU

-962

46 (

IND

)++

+++

+++

++++

++++

+++

++++

++++

Fok

ieni

a ho

dgin

sii A

. Hen

ry &

H·H

. Tho

mas

SS-0

6-19

8 (T

RT

E)

++++

¡¡

++++

++++

+++

+++

++

++

Cha

mae

cypa

ris

obtu

sa S

iebo

ld &

Zuc

c.SS

-05-

187

(TR

TE

)++

+++

+++

++++

++++

+++

++++

++++

Cha

mae

cypa

ris

pisi

fera

(S

iebo

ld &

Zuc

c.)

End

l.SS

-05-

161

(TR

TE

)++

+++

+?

++++

++++

?++

++++

++++

Cha

mae

cypa

ris

thyo

ides

(L

.)

Bri

tton

Ster

ns &

Pog

genb

.SS

-05-

74 (

TR

TE

)++

+++

+++

++++

++++

+++

++++

++++

Tet

racl

inis

art

icul

ata

Mas

t.SS

-05-

72 (

TR

TE

)++

+++

+++

++++

++++

+++

++++

++++

Cal

oced

rus

decu

rren

s (T

orr.

) Fl

orin

QIU

-962

45 (

IND

)++

+++

+++

++++

++++

+++

++++

++++

Mic

robi

ota

decu

ssat

a K

om.

QIU

-962

52 (

IND

)++

+++

++++

++++

++++

+++

++++

++++

Pla

tycl

adus

ori

enta

lis

(L.)

Fra

nco

SS-0

6-19

2 (T

RT

E)

++++

++

++++

++++

+++

++++

++++

++

Cup

ress

us s

empe

rvir

ens

L.

SS-0

5-12

2 (T

RT

E)

++++

++

++++

++++

+++

++++

++++

++

Cup

ress

us c

ashm

eria

na R

oyle

ex

Car

rier

eSS

-06-

01 (

TR

TE

)++

++?

+++

++++

++++

?++

++?

++++

Cup

ress

us d

upre

zian

a A

. Cam

usSS

-05-

70 (

TR

TE

)++

+++

+++

++++

++++

?++

++?

++++

Juni

peru

s ch

inen

sis

L.

SS-0

5-18

3 (T

RT

E)

++++

¡+

++++

++++

++++

++++

?++

++

Juni

peru

s co

mm

unis

L.

SS-0

5-83

(T

RT

E)

++++

+++

++++

++++

+++

++++

++++

++

Juni

peru

s ho

rizo

ntal

is M

oenc

hSS

-05-

160

(TR

TE

)++

+++

++++

++++

++++

+++

++++

++++

Juni

peru

s in

dica

Ber

tol.

QIU

-962

70 (

IND

)++

++++

++++

++++

++++

++++

++++

++++

Juni

peru

s pr

ocum

bens

Sie

bold

SS-0

5-15

9 (T

RT

E)

++++

+++

++++

++++

+++

++++

++++

++

Juni

peru

s sa

bina

L.

SS-0

5-16

3 (T

RT

E)

++++

++

++++

++++

++++

++++

++++

++

Juni

peru

s sc

opul

orum

Sar

g.SS

-05-

162

(TR

TE

)++

+++

++++

++++

++++

+++

++++

++++

Juni

peru

s vi

rgin

iana

L.

SS-0

5-84

(T

RT

E)

++++

+++

++++

++++

++++

++++

++++

++

123

Curr Genet (2009) 55:323–337 331

herbarium specimens. Quality of DNA varied signiWcantly,from high molecular weight to considerably degraded(from some herbarium material). Because of the poor qual-ity of a number of samples, frequently accompanied also bylimited quantity, the standard restriction endonucleasedigestion followed by electrophoretic separation approachto Southern hybridization (Sambrook et al. 1989) could notbe used. Instead, the slot-blot hybridization method wasused, as described in detail by Doyle et al. (1995).

In brief, a slot-blot apparatus (Bio-Rad) was used tomake seven sets of pseudoreplicate Wlter-blots, followingthe manufacturer’s protocol. Approximately 500–800 ng oftotal DNA (per sample and per set) was bound to Immobi-lon-Ny + nylon membrane (Millipore). DNAs from severalspecies with sequenced pt genomes (e.g., Nicotiana, Aco-rus, Amborella, Ginkgo, or Welwitschia) were included oneach membrane as positive or negative controls. Mem-branes were prehybridized and hybridized at 60°C–62°C in5£ standard saline citrate (SSC), 0.1% SDS, 50 mM Tris(pH 8.0), 10 mM EDTA, 2£ Denhardt’s solution, and 5%dextran sulfate. After hybridization, Wlters were washedtwice for 30–45 min in 0.5% SDS and 2£ SSC at thehybridization temperature. Probes were labeled with 32Pusing random oligonucleotide primers (Invitrogen). Autora-diography was carried out using intensifying screens at¡80°C for 18–48 h. Filters were stripped of probe betweenhybridizations by boiling twice for 5–10 min in 0.1% SSC.The absence of carryover signal from previous hybridiza-tions was assured by an overexposure (3–5 days) prior tonew rounds of hybridization.

Hybridization probes for all 11 plastid-encoded ndhgenes and small plastid ribosomal subunit (16S rDNA; usedas a control probe) were derived from tobacco via polymer-ase chain reaction (PCR). Primer names and sequences areprovided in Supplementary Table 1. A total of 17 probeswere constructed and their relative positions are indicatedin Supplementary Fig. 1. For the two ndh genes, usuallyinterrupted by introns (ndhA and ndhB), two probes wereused, each covering one exon. Two additional longer ndhgenes (ndhD and ndhH) were surveyed with two probes sit-uated at the 5�- and 3�-ends, respectively. In addition, toestimate the unspeciWc background hybridization levels, aninitial negative hybridization control was performed underthe same stringency conditions (see above) and the sameamount of 32P, but without probe added.

Results

Interpretation of slot-blots

The slot-blot data ranged from no diminution to completeabsence of signal and were for the most part readilyT

able

1co

ntin

ued

Num

bers

in s

quar

e pa

rent

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l num

ber

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n an

d th

e ap

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imat

e pe

rcen

tage

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With

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ajor

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ts, s

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es a

re a

rran

ged

acco

rdin

g to

the

ir p

resu

mpt

ive

phyl

ogen

etic

rel

atio

nshi

ps (

see

text

for

det

ails

). B

ased

on

slot

-blo

t re

sults

, a

“++

” sy

mbo

l in

dica

tes

pres

ence

of

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hybr

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f hy

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tion

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ajor

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e) a

re s

how

n in

Fig

.1. A

bbre

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of

herb

aria

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low

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ex H

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onV

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Cal

litr

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(Je

ps.)

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tle

SS-0

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Cal

litr

opsi

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.) D

.P. L

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-05-

190

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)++

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+++

++++

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++++

++++

Ang

iosp

erm

s

Am

bore

lla tr

icho

poda

Bai

ll.N

o vo

uche

r++

++++

++++

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++++

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Vic

tori

a sp

.N

o vo

uche

r++

++++

++++

++++

++++

++++

++++

++++

Aco

rus

gram

ineu

s So

land

.SS

-03-

70 (

TR

TE

)++

++++

++++

++++

++++

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++++

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Gly

cine

max

(L

.) M

err.

No

vouc

her

++++

++++

++++

++++

++++

++++

++++

++

123

332 Curr Genet (2009) 55:323–337

interpretable. The presence or absence of ndh genes wasdetermined by eye, by comparison of hybridization signalto the corresponding 16S probe, which is used as a controlto establish the presence of signiWcant amounts of ptDNAon the blots. For each blot set and probe combination, thestrength of signal was estimated by comparison with anumber of positive and negative controls; namely, the spe-cies known to contain functional ndh genes (e.g., Ginkgo,Amborella, Acorus, etc.) or to lack these genes (e.g., Wel-witschia, Pinus spp., etc.), based on previously availableentire ptDNA sequence data.

Representative hybridization results, arranged phyloge-netically, are shown in Fig. 2, and the scores for all surveyedspecies and probes are summarized in Table 1. For everyprobe, the relative presence or absence of signal was scoredfor each taxon as showing either full (++), diminished (+),or absent (¡) hybridization in comparison to their respective16S positive controls (Table 1). Full hybridization strengthis assumed to indicate that the gene is present and func-tional. For genes that have two probes (i.e., two exons or5�- and 3�-end) full hybridization to both probes is requiredto indicate that the gene is functional. Diminished signals,where hybridization is weaker than the control but there isdeWnite signal presence, can be interpreted in two diVerentways. It can indicate that the gene is divergent with respectto tobacco but still present and functional or that the gene ispresent but pseudogenized (i.e., rendered nonfunctional).Absence was scored if no detectable hybridization to theprobe was observed. Under our experimental conditions,plants in which a gene has been transferred to the nucleuswould fail to produce a detectable hybridization signal whencompared to a plant that retains the gene in its plastidgenome, due to signiWcant reduction in copy number and anincrease in nucleotide substitution rates (Wolfe et al. 1987).Hence, the absence of signal implies either outright loss ofgenes or their functional transfer to the nucleus. Given thegenerally conservative substitution rates of ptDNA, it is lesslikely that the absence of signal represents a highly diver-gent yet functional gene. Lastly, in certain cases we wereunable to determine the presence or absence of signal andwe scored these taxa as unknown (“?”; see Table 1). Theseambiguities are due to insuYcient amounts or poor qualityof ptDNA for a given pseudoreplicate.

Altogether, these assumptions on the presence orabsence of genes can lead to potential underestimates oroverestimates of gene losses. For example, signals thatappear present could potentially represent relatively recentpseudogenized genes while signiWcantly diminished signalsmight be due to divergent but functional genes. Neverthe-less, despite these caveats, a hybridization approachremains a cost eVective and eYcient method for surveyingnumerous and diverse samples (Doyle et al. 1995; Adamset al. 2002).

Distribution of ndh gene losses

As expected, the full hybridization signal was observed forall taxa used as positive controls. Based on results fromwhole pt genome sequencing, the entire ndh gene suite isknown to be present in autotrophic angiosperms, indicatingthat its presence is the shared ancestral condition for thisgroup of plants (Jansen et al. 2007). The presence of all 11ndh genes is conWrmed here across the representatives cho-sen to span the basal nodes of Xowering plant diversity(Fig. 2; Table 1). Also, for Ginkgo, the hybridization to allprobes derived from the ndh genes was similar in strengthto the control DNA (Fig. 2; Table 1). This was expected aswell, given the known presence of these genes based onextensive sequencing of its pt genome (Leebens-Mack et al.2005; Jansen et al. 2007). In addition, the relative strengthof the hybridization of tobacco-derived probes to Ginkgoillustrates the conserved nature of the ndh genes acrosslarge phylogenetic distances, including the angiosperm-gymnosperm divergence (>325 Mya; Judd et al. 2002;Palmer et al. 2004).

As a group, cycads strongly hybridized to seven of 11ndh genes. For a few taxa (Table 1), the signal was dimin-ished with probes for ndhB (both exons), ndhH 3, ndhI, andndhJ. Although some of the hybridizations are weaker thanthe positive controls, they do not necessarily indicate lossof function of these ndh genes but rather that these genesare divergent to some degree in these taxa. The presence offunctional ndh genes in cycads is expected given that theyare found as open reading frames (ORFs) in the sequencedptDNA of Cycas taitungensis (Wu et al. 2007).

In contrast to the previous lineages, the evidence for lossof ndh genes from pt genomes is widespread in Gnetalesand Pinaceae. In Gnetales, there was no signiWcant hybrid-ization signal for most of the probes (Fig. 2; Table 1). Forsome taxa weak signal was present for ndhA (both exons),ndhC, and ndhH 5�-end. This pattern indicates that the lossof the ndh genes is common to all Gnetales (Fig. 2), inaccordance with the results of entire ptDNA sequencesfrom a small number of select representatives of this group(McCoy et al. 2008; Wu et al. 2009). Similarly, there was agenerally weak to absent hybridization signal observed formost probes across Pinaceae. In particular, ndhI and ndhJare absent from all surveyed taxa. Substantially diminishedsignal was common for probes derived from ndhA (bothexons), ndhD, ndhE, ndhH, and ndhI genes. However,ndhB (most notably, the 5� end), ndhC, and ndhK appearedpresent in many (but not all) taxa. Given what is knownfrom the entire plastid genome sequences of several Pinusspp. (Wakasugi et al. 1994; Cronn et al. 2008), Picea sitch-ensis (Cronn et al. 2008), and Keteleeria davidiana (Wuet al. 2009) species, it can be deduced that the presence ofweak to moderate hybridization signal observed for these

123

Curr Genet (2009) 55:323–337 333

Fig

.2A

utor

adio

grap

hs s

how

ing

slot

-blo

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brid

izat

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all p

last

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eren

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nea

r ab

senc

eof

hyb

ridi

zatio

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on a

bbre

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ions

are

the

sam

e as

in F

ig.1

123

334 Curr Genet (2009) 55:323–337

ndh genes (Fig. 2; Table 1) corresponds to pseudogenes.Compared to Pinaceae, Gnetales appear to have fewer rem-nants of ndh genes (Fig. 2; Table 1), which is expected,given the highly elevated rates of molecular evolutionobserved in Gnetales plastids generally (Rydin et al. 2002;Burleigh and Mathews 2007a; McCoy et al. 2008).

Unlike Gnetales and Pinaceae, the general trend acrosscupressophytes was a strong hybridization to almost all ndhprobes, indicating that the entire suite of ndh genes is pres-ent and conserved within this group (Fig. 2; Table 1). Thisis fully in agreement with the only published entirelysequenced ptDNA from cupressophytes, Cryptomeriajaponica (Cupressaceae s. lat.; Hirao et al. 2008). However,some members of Araucariaceae, Podocarpaceae, Taxa-ceae, and Cephalotaxaceae hybridized weakly to ndhB (oneor both exons) and ndhI, while Cupressaceae s. lat. exhibitdiminished hybridization signal to ndhG but not ndhI (seeTable 1). In these cases, diminished signal is most likelydue to the elevated sequence divergence of ndh genes, asevidenced by the presence of ndhB and ndhF ORFs in fewrepresentative species from these families that are currentlysequenced (Rai et al. 2008).

Discussion

Implications of ndh losses for spermatophyte relationships

The ndh genes comprise about one-tenth of the »120 genesretained in plastids of most photosynthetic seed plants.Based on numerous entirely sequenced pt genomes ofangiosperms (see Jansen et al. 2007 for the most recentsummary) as well as a limited number of gymnosperms(Wakasugi et al. 1994; Wu et al. 2007, 2009; Cronn et al.2008; McCoy et al. 2008; Hirao et al. 2008), it appearedthat the loss of the ndh genes was restricted to Gnetales(McCoy et al. 2008; Wu et al. 2009) and Pinaceae(Wakasugi et al. 1994; Cronn et al. 2008; Wu et al. 2009).The results of our survey extend the previous inferences ofthe ndh gene absence to be common to all of Gnetales andPinaceae, but not to other gymnosperms (nor to autotrophicangiosperms). While the losses of ndh genes from the plas-tids is rare in autotrophic plants, their absence has beenobserved repeatedly in heterotrophic angiosperms(Olmstead et al. 2001; StefanoviT and Olmstead 2005).Extrapolating from those cases, it seems that the ndh genesare generally lost as a suite (Bungard 2004; Krause 2008).Hence, from a phylogenetic point of view, the entire suiteshould be considered as a single loss (StefanoviT andOlmstead 2005) and not as 11 independent losses.

Given the extent and distribution of presence andabsence of the ndh genes among spermatophytes, the mostparsimonious solution suggests that the loss of these genes

is a synapomorphy for Gnetales and Pinaceae, a sharedderived character inherited from their common ancestor(Fig. 1) supporting the gnepine hypothesis. Each of the Wvealternatives for the Gnetales relationships with the otherseed plants (i.e., anthophyte, gnetales-sister, gnetifer, andgnecup hypthotheses) would require a minimum of twoindependent losses of ndh genes, one in Gnetales and one inPinaceae (Fig. 1). While the possibility that ndh genes werelost more than once in gymnosperms cannot be positivelyexcluded, the low frequency of loss of these genes, and inparticular the near-absence of loss among autotrophic seedplants, argues against such a scenario.

Additional lines of evidence supporting the gnepinehypothesis are provided by a couple of other plastid struc-tural characters, each with putatively the same phylogeneticdistribution among seed plants as that observed for the lossof ndh genes. First, an expansion of the inverted repeat (IR)that includes the duplication of trnI-CAU and a partialduplication of the psbA gene region situated at the end ofthe large single copy (LSC) is found in several sequencedmembers of Gnetales and Pinaceae but is not known fromany other land plant (Wu et al. 2007, 2009; McCoy et al.2008; Hirao et al. 2008). Second, both Gnetales and Pina-ceae appear to share a common loss of rps16, to the exclu-sion of other gymnosperms and basal angiosperms lineagesfrom which the presence of this gene is ascertained (Waka-sugi et al. 1994; Wu et al. 2007, 2009; Jansen et al. 2007;McCoy et al. 2008). However, contrary to the above exam-ples, one particular structural genomic marker does not sup-port the gnepine phylogeny. The loss (or a signiWcantreduction) of the IR is reported from both cupressophytesand Pinaceae, but not from Gnetales (Raubeson and Jansen1992; Wu et al. 2007, 2009; McCoy et al. 2008; Hirao et al.2008). This ptDNA feature favors the phylogenetic inter-pretation according to which the loss of the ndh genesoccurred independently in Gnetales and Pinaceae.

Future directions

Although the preponderance of genomic structural changescurrently supports the gnepine hypothesis, caution is stillwarranted because most of these features have only beenobserved in a subset of exemplar taxa. Hence, their full dis-tribution across seed plants and their evolutionary signiW-cance remains poorly understood. To determine theirrelative importance, all of these underexamined markersrequire further in-depth surveys across a broader taxonsample, as was done here for the ndh genes. In particular,additional ptDNA sequences are needed from the represen-tatives of Araucariaceae and Podocarpaceae, to help trian-gulate the ancestral conditions for many of these potentiallyphylogenetically important characters in cupressophytes. Itwould also be valuable to survey for ndh genes in Parasit-

123

Curr Genet (2009) 55:323–337 335

axus usta (Podocarpaceae), the only known mycohetero-trophic conifer (Feild and Brodribb 2005). We predict thefunctional absence of all ndh genes in this highly derivedpodocarp species (Sinclair et al. 2002), which would repre-sent an independent loss of the Ndh complex in conifers,related to its shift to a fully heterotrophic nutritional mode.

Acknowledgments For providing generous access to their live plantcollections, the authors are grateful to directors/managers of the fol-lowing institutions: Humboldt State University (Acrata, CA) green-house, Indiana University (Bloomington, IN) greenhouse, Universityof Alberta (Edmonton, AB) greenhouse, University of Toronto (Toron-to, ON) greenhouse, University of Washington (Seattle, WA) green-house and Arboretum, University of Guelph Arboretum (Guelph, ON),Devonian Botanic Garden (Devon, AB), Jardin botanique de Montréal(Montréal, QC), University of Belgrade Arboretum (Belgrade, Serbia),Vienna Botanical Garden (Vienna, Austria), and Carleton University(Ottawa, ON) greenhouse. We also thank curators/directors of ALTA,IND, and TRT for supplying plant material. Special thanks are due toSean Graham and two anonymous reviewers for their valuable sugges-tions that improved the earlier versions of the manuscript. Financialsupport from the Natural Sciences and Engineering Research Councilof Canada, Canada Foundation for Innovation and Ontario ResearchFunds to S. StefanoviT is gratefully acknowledged.

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Loss of all plastid ndh genes in Gnetales and conifers: extent and evolutionary signiWcance for the seed plant phylogenyAbstractIntroductionMaterials and methodsTaxon samplingDNA extraction and hybridization

ResultsInterpretation of slot-blotsDistribution of ndh gene losses

DiscussionImplications of ndh losses for spermatophyte relationshipsFuture directions

References

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