Evolution of the Phytochrome Gene Family and Its Utility for Phylogenetic Analyses of Angiosperms

26 Pages·1995·21.6 MB·English

by  Sarah Mathews

THE
EVOLUTION OF
PHYTOCHROME GENE
AND
FAMILY
ITS
FOR
UTILITY
PHYLOGENETIC ANALYSES OF
ANGIOSPERMS
1
\HSTH\i
I
Bptorprotwri8thatservemanyfuiKii.il .mi
Hi phyt< famil ncobV ph iln ;)«• hi
toi
I - i
m
plant. From studies of the align the family has been modeled as comprising five loci, Pt
s,
- '
Mn
"/'..
II. .. ./i. i-rins, one locus, or at most two, is present ei.ii
I
.
Um
m
\l.ih: /../ s^ IU...I--I .|..<-. ii .1 ..iii|..i-ie|-. iepi..-eiil -,..in.' ,ir,-i.,^|.ei ,.,,.,,[.- .1 ev.mipa- u|.Iit:<w ,;-.. /'//) r
• I
,11m
h> /'//) and /'//}/; //..'/./. /../.sm have ex, .Urd in.ir, ,,, ml nigiosperms, and mc
<>t
I I , , i I ,
PHYD
may PHYE.
angiosperms (as well as Piper) lack orthologs of Arabidopsis and Nonetheless, for stud
lull vl HI, _
I , v I I I I ... i I I I I I I I II , ll I \
I
occur as single copy sequences, and prelum, the various loci are evolving independently,
i i i t
plant family Fabaceae, phytochrome data are ha ..lution to a taxonomically very di
k
I
|
U
l-ltrci.t l-.-pi. ,U\ r 'i I ci. i td.,1 in. lude M, .',!>:'. I .',,';... .(•/.,/ .. iixl / »< -f . - I ll .idililh •!) In i u, I,'. .1 1< |e -. ,1-1 it I
>" insertion - v „-
phvlogeiielie.illv iMli.rni.il .-Jul leii-tieii l.elpcil tn . lela'ion In] it, this .-,•.,, ,,| mii,
> . I « , |i,
f
the presence prove to phylogenetically informative on
ol lie
il
i I
DNA DNA
The
from chloroplast or nuclear ribosomal low copy fraction of nuclear remains
se-
When
quences. discordance between molecular underexplored phvlogcneiic studies of plants,
in
!
DNA
phvlogenies occurs, phenomena such as and investigations sequences from
biological initial
introgressive hybridization or lineage sorting from multigene families have revealed some potential
may
polymorphic ancestry explain the disparity problems related to concerted evolution (sensu Zim-
&
mer
Harrison 987; Rieseberg Brunsfeld, 980). For example, an analysis of rbcS
(e.g., et al., et al.,
1 1
1992; Soltis et al., 1992). Such differences also nucleotide sequences (Meagher et al., 1989) in-
may Mo<
result from lack of resolution in one of the <h .in- ;/. have
f
I ,
data sets (e.g., Olmstead, 1989), or from mistaken occurred in ea< ading u. regions
,t 1, I.
< i
Goodman
orthology 1979; Doyle, of "partial homology" (Patterson, 1987) and thus
(e.g., et al.,
1992). Thus, determining organismal relationships to the possibility of mistaken orthology. Sanderson
Du
requires that evoln derived from vie 1992) suggested, however, that the prob-
v\
i • (
Pam-
single genes be tested with further data (e.g., ability of recoi n ible organismal phy-
i
& DNA DNA
Nei, 1988; Takahata, 1989). sequences logeny high from sequences of multigene
ilo is
genome
from the low copy fraction of the nuclear families which concerted evolution infrequent,
in
is
potentially provide novel phylogenetic resolution, Preliminary data indicate that this the case in
is
specifically at the organismal level, since certain such gene families as actin (Shah et 1983;
al.,
&
of the processes that lead to incongruence of spe- Drouin Dover, 1990; McElroy et 1990) and
al.,
&
uniparental inheritance, phytochrome (Sharrock Quail, 198'J; hi.
I I ,
This work was sup >rted b is lalScien lationGrani H 15897 (to RAS) and BSR-91 18785
' tv I N
I
We
(to ML), and the MONTS/EPSCoR program. thank Paul Manos, Pam Soltis, and Randy Woodson for providing
DNAs Pam
Lemna,
of Quercus, nthus, Elaine Tobin for providing tissue of Jeff Doyle, Soltis,
/ I
,
,
and an anonymous reviewer for providing helpful comments on the manuscript, and Carol Bult and Leslie Gottlieb
lor providing pertinent insights.
M
Department ..I liiol \l<.i,i...n It../.. n nt.ina 59717, U.S.A.
.
Ann. 296
Missouri Bot. Card. 82: 321
&
1991; Heyer Gatz, 1992a, Clack dopsis chrc
b; et al.,
al.,
PHY
Adam
1994; 1993); consequently, these and no evidence for pseudogenes was found.
et
al.,
PHYA PHYB
Homologs Arabidopsis and have
multigene families should yield data pertinent to of
(Adam
studies of organismal phylogenies. Furthermore, an been characterized in other angiosperms et
&
advantage of multigene families in phylogenetic 1993; Christensen Quail, 1989; Dehesh et
al.,
&
reconstruction is that, in addition to nucleotide al., 1991; Hershey et al., 1985; Heyer Gatz,
Kay
substitution and insertion/deletion characters, the 1992a, b; et 1989; Sato, 1988; Sharrock
al.,
A
presence or absence of loci can be phylogenetically et 1986). putative pseudogene most similar
al.,
PHYA
Pisum
to has been reported in (Sato, 1990),
cDNA
The photochromes are photoreceptors for red and a clone from Zea containing a partial
PHY
and red land plants and green algae fragment has been interpreted as a pseudo-
far- light in
all
&
Each
(reviewed Quail, 1991; Furuya, 1993). gene (Christensen Quail, 1989). Overall, these
in
studies suggest that the gene family increases in
iof 1100 complexity from nonangiosperms angiosperms.
r to 2 to
ise.- |.r..| a
i»i
,.i
a covalently attached linear tetrapyrrole chromo- This suggestion consistent with data recently
is
GenBank
interconvertible submitted to (see Results).
-
i , i i
PHY
forms, Pr, the red light-absorbing form, and Pfr, Nearly all genes that are fully character-
the far-red light-absorbing and biologically active ized share high sequence identity (App. 1) and
Arabidopsis
form, phytochrome mediates diverse developmen structural similarity with the loci (Fig.
nonanmo-penns
responses throughout the plant's cycle. These Peptide fragments from the
tal life 1).
Anemia
include germination, seedling hypocotyl Psilotum (Hanelt et 1992), phyllitidis
al.,
-
< j» i «
(Maucher
elongation, stem cell differentiation, plastid devel- (L.) Sw., and Dryopteris filix-mas et al.,
opment, flavonoid pigment synthesis, and 1992) share high sequence identity with the Ar-
floral in-
N-termnn
duction in response to photoperiod. Modulation of abidopsis phytochromes in their
\|'[>
(
PHY
plant gene expression by phytochrome well doc- and small internal peptides from the
is 1, 2),
umented (Nagy et 1988). While the mecha- alga Mesotaeniu Lagerh.) Hansg.
al.,
(
nisms whereby phytochrome participates in cellular are highly similar to both N- and C-terminal pep-
signalling remain unknown, regions of the poly- tides of other phytochromes (Morand et al., 1993).
PHY
Two
chromophore attachment. genes have been described
peptide required for exceptional
PHY
and dimeri- nonangiosperms. The gene sequence from
spectral integrity, biological activity, in
zation have been identified (Cherry et 1993; the alga Mougeotia scalaris Hiissel (Winands et
al.,
&
Edgerton Jones, 1992). 1992) contains additional introns in the N-ter-
al.,
PHY
Several reports have described the presence of minal coding sequence, and in the gene from
PHY
only a single gene in certain nonangiosperms the moss Ceratodon purpureus (Hedw.) Brid. the
(Hanelt 1992; Kolukisaoglu et 1993;
et al., al.,
Morand 1993; Okamoto 1993; highly divergent C-terminal coding region (Fig.
et al., et al., 1),
Thummler et al., 1992; W.nands et al., 1992), which encodes a putative light-regulate.! (troiem
PHY
while evidence of two genes reported for kinase (Thummler et 1992). However, in an-
al.,
is
Maucher w H >
other nonangiosperms. For example, other moss,
et
I'/i \ 1 1 • I . ) < . ,
al. (1992) refer to a putative second gene in the the C-terminal coding region is similar to all other
PHY
No
unusual
fern Dryopteris filix-mas L., although the frag- genes (Kolukisaoglu et al., 1993).
PHY
ment remains uncharacterized. Two unpublished have been described in angiosperms.
loci
PHY PHYA-E
nudum
sequence fragments from Psilotum The genes in Arabidopsis are differ-
X74930,
(L.) Griseb. (GenBank accessions entially expressed in response to the light environ-
&
Somers
X74931) from one another the region of ment (Sharrock Quail, 1989; et al.,
differ in
overlap; and two P/ZTcDN As from Pin us pa lust r in 1 99 Clack et al., 1 994), and unique physiological
1 ;
reportedly have been cloned and partially
Mill,
PHY
A
Phytochrome
sequenced (Furuya, 1993), while a single proteins. controls the far-red high-
cDNA from Gingko biloba L. cited in the same irradiance response (Nagatani et al., 1993; Parks
is
&
Whitelam whereas
report. However, in angiosperms, five related se- Quail, 1993; et al., 1993),
quences encoding phytochrome proteins designated
PHYAPHYE
have been characterized from Ar- length and flowering time, and the end-of-day far-
&
Wester
abidopsis thaliana (D.C.) Schur (Sharrock Quail, red light response (Reed et al., 1993; et
1989; Clack et al., 1994). The genes for these al., 1 994). This functional divergence together with
phytochromes have been mapped Arabi- high sequence divergence (approximately .'>()',
five to
:
kb
1
FIGURE Phytochrome gene
structi
1.
1992), from N-terminus to C-term Ungl.-s).
(left)
,
mil, !. ophore attachment m ..md-
;.;,-,: ,.' in-1' -; ir.l llir
,i i i|> > »
,
f
among the and I'HYC suggests su Cronquist, 19£ and, from legum \)\\
I'll) I'll) II. loci)
/.
homologous recombination infrequent were sampled include two three divergent
to to
rii.ii hi is
PHY
among members and
genes of Arabldopsis. If the loci are ol the tribes bobuiieae, Millettieae,
make
evolving independently distinguishing orthologs Dalbergieae order to preliminary evalua-
in
&
To
from paralogs should not be tion hiogeographic hypotheses Lavin
difficult. test this (e.g.,
..I
Luckow, The two sampled from
1993). species
PHY M
PCR
Dunn
of sequence data, (polymerase chain Millet tin (M. durti and in
I
&
reaction) was used -ample multiple /'//) D. Du Puy Labat) and Sesbania
to loci (Baill.)
J. J.
DNAs
from genomic seshtm Morr. and
of diverse species of land (>' resit (Jae<| iKIIioti
(I..) .S tiriti
plants lor sequence information, and these data are not thought to he closely related within each
were subjected to phylogenetic analysis.
peptidi
M
\|.. n|i
\ i; \ ,
I I
DNA
was from
Total isolated fresh, lyophilized,
or dried herbarium material of taxa
listed
&
methods
pendix 3 by standard (Doyle Doyle.
1987). Aliquots were extracted once with phenol
DNAs
chloroform-isoamyl alcohol (1:1 volume), and th. plify all possible target sequences in template
HY-
aqueous portions were purified over sepharo flanked h\ served upstream peptide
th<
»K New PATDIP(5'-CA[TC]TA[TC][TC]CICCIACICA
(Pharmacia, Piscataway, Jersey) columns.
K
PFPLRYAC
Toassess phytochrome and downstream
diversity in early lai plan) 1-VI1 T( :A ]CC-3')
il
|
>\ .jiienecs from different nonangiosperm phy- cv c| \(.|cak;g[ag]taic[gt]ia[ag]igg[ag]
\
I
\T|\ICC
la available in the literature (Appendix 2 ar These peptide sequences are con-
.'.
i
I
lukisaoglu et al., 1993) were included in th< served in tnihitlttp.sis phytochromes and in the
ill
yses with those determined during the present studv amino acid sequences inferred from other
fully
.
The most complete /'//) sequence from Psilotum sequenced and monocot genes, and they flank
dic.ot
GenBank X74931,
obtained from (accession lack- a region comprising variation likely to be phylo-
PCR
510 3417
ing 3' nucleotide sites out of the geneiK allv nihil inative. Standard protocols
otitic sites in the lull length sequence data set) was (1'erkni Klini-r. \orwalk, Connecticut) were mod-
was whu
used in phylogenetic analyses, but no! included ilied to include an initial cycles in h nine ding
.*>
in final alignments because did not si- u temperatures were less stringent (e.g., 45-49°C).
ll\
it
.
PHY
PCR
affect the consensus sequence. Likewise, the The products were converted to blunt-end
DNA
T4
sequences from Physvomitrella and from the an- fragments with polymerase (BRL, Gaith-
giosperm Nicotiana (GenBank accessions X66784, ershurg, Maryland) and were fitoRV-cut
ligated to
M13KRV8.2. M13KRV8.2
L101 14), were used in phylogenetic analyses, hut bacteriophage carries
.DMAs
were not included Vppcndix were sam- an l'<ok assette screening of non-
in that facilitates
I i
re<-omhinunts an which in/
eoli -Irani
pl.-.l hi].-.. hi /•'. is \\'
t
Number
Volume
2
82,
Gene
Phytochrome
Family
(Waye 1985). Transformation of E. coli distic, and rate analyses are available on request
et
al.,
with the ligation product yielded a population of from the first author. Tree analysis and graphical
PHY
M MacClade (Maddison
genomic output were performed with
M'll) clones containing amplified
I
COMPONENT
&
were and Maddison, 1992) and (Page,
sequences. Individual clones cultured,
DNA
double stranded phage was isolated from bac- 1993). However, tree mapping procedures based
Goodman
terial pellets by alkaline-lysis minipreparation. In- on the model of et al. (1979), which
cut from Ml 3 vectors using £coRI and evaluate whether incongruence of gene and species
serts
3%
/Will were resolved on NuSieve (FMC, trees could be due to sampling error (Page, 1990),
2%
agarose were not performed because of the preliminary
Rockland, Maine), or standard, gels,
and some cases were further screened by re- nature of this study.
in
enzyme digestion to avoid sequencing du- For the cladistic analysis of the full length se-
striction
PHY
DNAs
Sanger quences, trees were rooted by designating
Single-stranded for
plicate clones.
USB, sequences from Physcomitrella, Selaginella, and
dideoxy sequencing (Sequenase version 2.0,
Adiantum capiUus-veneris (Okamoto
Cleveland, Ohio) were isolated from L. et al.,
m
PHY
the,
carrying putative inserts. In
.
PHY
were determined, and lulK characterized genes from nonangio-
quences of both ori
i
PCR sperms. For analysis of partial sequences in angio-
prodt
multiple
per ms, Selaginella was retained as an outgroup,
s
PHY
gymno-
PCR sequences were mul- along with the sequences from the
and Peptide
Mori errors.
&
ALIGN Education -penns Cingko and Pseudotsuga that were deter-
aligned using (Scientific
tiply
GDE
Pennsylvania) and 2.2
Software, State Line,
and were
(Steven Smith and University of Illinois)
adjusted by eye; peptide alignments were the basis codon positions were equally weighted for the fol-
determined
sequence alignments, h-i lowing reasons. First, empirically tran-
multiple nucleotide
for
sequence coinpan en gaps certain
.iliginnei in
i
.
between
from any comparisons except
regions of insertion/deletion were deleted, while 1.0 for lot
were
yans could be identified closely related legume sequences that diller
that
<3%
entiated by very few total substitutions (e.g.,
were Second, result- from
.V nucleotide sites were not included in the data of all sites variable).
under weight-
matrices used in cladistic and distance analyse- clad i- tic analyses certain differential
Sequences were compared using maximum par- ing schemes are apparently the same as those from
when
PHYLIP schemes
analyses under equal weighting tax-
simony algorithms available in (Felsen-
PAUP
Hennig86 1988), and onomic sampling adequate (Albert et al., 1993;
1993), (Farris, is
stein,
&
Minimal Cracraft Helm-Bychowski, 1991). Finally, all
(Swofford, 1993). length trees result. ug
may
codon positions exhibit similar levels of ho-
from search options available in either
heuristic
PHY- moplasy Chase 1993); thus a rationale
Hennig86 (mh*, bb* with no upper limit set), (see et al.,
(DNAPARS), PAUP (CLOSEST RAN- excluding or differentially weighting codon po-
LIP or or loi
in
DOM HOLD
data addition sequence, option set for rtions is difficult to define. In these analyses, third
many
STEEPEST DESCENT, codon and perhaps of the synon-
when positions,
5 applicable,
trees
MULPARS, TBR vmou- were determined by bootstrap
and branch swapping options -institutions,
resampling analyses to be phylogenetically very
MAXTREES
and 10,000) were used informative, with confidence intervals for just the
set at
trees,
PAUP 90 and 100%,
analyses )S third codon position of between or
further
as starting trees for ((
!l <
STEEPEST
EST DE- as high as the values obtained for the first
data addition sequence, at least
MULPARS TBR
SCENT,
and options activated,
branch swapping on nonminimal trees), with
with
Support
the latter resulting in shorter trees. for
monophyly was evaluated using bootstrap
of clades
PHY
The sequenced genes
1985) and decay analysis orthology of fully
resampling (Felsenstein,
PHY
from
were estimated from various species to individual loci
(Bremer, 1988). Pairwise distances
m commonly
been established
Arabidopsis has
Kimura 2-parameter option available
using the
:
&
Heyer
MEGA 1991;
(Kumar 1993) and absolute and overall -i.ii.lai.tv (Del.esl, et al.,
et
al.,
1992a, 1991; Furuya, 1993). Sim-
were calculated by the Gatz, b; Quail,
evolutionary rates
relative
Wu & have
and
gene expression regulation
methods Kimura (1981) and Li (1985) ilarities in
of
imply orthology (Furuya,
been used secondarily to
matrices subject to distance, ela
respectively. All
may
1993). However, overall similarity not reflect i.-imihr: Retention of a clade in a strict consensus
phylogeny, and phylogenetically related loci may tree (Figs. 2 5), resulting from the mhennig and
ddlei in function due to itiulal im is in < is refill. iloi - bran, Ii -and -bound search options in Hennig86 or
& PAUP
from
regions (e.g., Doyle, 1991; Li Noll, 1994). Since heuristic options available in (see
orthology best determined by shared ancestry, above), was considered good evidence of mono-
is
as evidenced by synapomorphies, cladistic analysis phyl) Results from bootstrap resampling and de-
was used to determine the orthology of available cay analyses revealed that some clades were strong-
all
PHY
>
(>95%,
length sequences to those characterized ly supported d 5 20).
full
PHYA
A
from Arabidopsis. most parsimonious The tiabidopsis sequence was included
single tree
was generated analysis and
(Fig. 2) in this re-
it
gram n l«l. mono-
solved the following monophyletic clades with strong (Fig phylogenetic analysis of
(90-100%) monocot PHYAs, sequences monocot holo^s 77
bootstrap support: col (f 01
all i; ."". ), I <>| / I /
PHYAs + PHYA.
PHYAs, PHYAs,
dicot Ara- (Fig. 2) were substituted for Arabidopsis
all all all
PHYB PHYD PHYA
bidopsis PHYC, just and of Ara- Likewise, Arabidopsis was replaced by Pi-
PHYBs PHYD, sum
bidopsis, just and Arabidopsis I'll) in the analysis of legume sequences
i
PHYE
+ PHYBs
and Arabidopsis (Fig. also based on results depicted in Figure
sis all 5),
'.
PHYD, PHYs A
angiosperm PHYs, angiosperm 2. notable finding was that from three plant taxa,
all all
+ PHYs +
Psilotum, and angiosperm Psilotum Ceratophyllaceae, Caryophyllaceae, and Fabaceae,
+ PCR
Adiantum. Seventy-eight trees were found by two differenl products were amplified that
<30
keeping trees that were steps longer than were determined to be most closely related to Ar-
all
These
I'/l) are interpreted to be du-
I
A
in trees that are 20 steps longer, except for .healed I'll) loci, and in legumes, the additional
all
I
PHYC + PHYA'
Arabidopsis PHYAs. The two locus here designated These
trees (Fig.
all is 5).
PHYA
that were one step longer than the minimal length -related sequences appear to have
PHYC
tree varied in their placement of as the Iq odenl the three plant groups (Figs.
rise] in in
PHYA PHYB/D/E
sister group of either the or 4, 5). For example, the legume phytochrome phy-
clade. These results thus suggest that, for example, logeny (Fig. 5) depicts this iuoiioiiIin lelii I'll) !'
PHYAs
the dicot and monocot are orthologous, as clade as being derived from within the legume
PHYBs.
are the dicot and rice Additionally, evi- I'll) lineage (which thus paraphyletic). Also,
is
\
95%,
dence provided for the sister group relationship well supported by a bootstrap value of
is it is
PHYE PHYB + PHYD, PHYA'
of with and for a later and, in a global analysis of legume with all
PHYB
duplication giving rise to Arabidopsis or othei hi: 'losperm loci, is most closely related to
it
PHYD.
lei'iime I'll) liown). thus ap-
in It
I ..lid. •:".!. i'i: 'i
. i
Using degenerate primers and amplification by pears die evolution of the phytochrome gene
at
il
PCR, sequences from
target five
all //<
PHY
A A
genes, as well as from multiple genes of other of the I'll) locus. similar argument can be
made
angiosperms, were recovered in single cloning ex- 7/5 unit's in Cerato-
I !
PHY
periments. Single sequences were obtained im. nd .jihvlla. eai lug. 4). In the
I'h III I
i (
PHYA
from the nonangiosperms Equisetum and Pseu- subfamily, and in other cases described be-
dotsuga and two were obtained from Gingko. In- low, this all. tii ot diversification attributed to
is
|.
270 350 new
serts varied from to bp, and a region of the evolution of a locus rather than to allelic
insertion and deletion corresponding to residues diversity. With the exception of genes that are
398 to 415 (App. was eliminated from broad under frequency-dependent selection, such as
1) al-
MHC-
comparisons because nucleotide site homologies leles of the S-locus (Ioerger et al., 1 990) and
among
could not be determined llowevei this region could loci (Klein et al., 1993), levels of divergence
,
&
be retained narrower comparisons, where Gaut
in site loci
,
homologies were more readily established, as in the L993)
I
PHYA
Fabaceae data (App. duplicated
set 4). ie
Similarly to the analysis of full-length sequences,
PHYC
Sequences homologous Arabidopsis
to
cladistically analyzed to determine their orthology were amplified commonly in monocots (Fig. In
3).
PHY
DNA
to the loci of Arabidopsis (Figs. 3-5). Each dieots, (.uly of Dianthus yielded a sequence
sequence occurred in a monophyletic clade that homnloi-oii l!,;!>!tlops>s I'll) homologs
I.. * II
.
PHY PHYC
included a single, specific locus of Arabi- of in monocots were identified by their close
PHYC
iinfisis. providing evident for distinct /'//) -u\> relationship with just Arabidopsis in a global
i
Physcomitrella
Selaginella
Adiantum
Psilotum
PHYB
Arabidopsis
|
[PHYD
Arabidopsis
|
PHYB
Nicotiana
PHYB
Solanum
PHYB
Oryza
[PHYE
Arabidopsis"]
PHYA
Avena
PHYA
Oryza
PHYA
Zea
[PHYA
Arabidopsis
|
PHYA
Pisum
PHYA
Nicotiana
PHYA
Solanum
PHYACucurbita
[PHYC
Arabidopsis~l
m.-M ,m:.,moi] .tin >m analysis of 2637 variable nucleotide sites from the full-length
Sin-I.-
in |»;n
.'..
, ,
The
ochrome sequences. length 11,376,
is
GenBank X66784 and L1011
accessions
i
1
Missouri Botanical Garden
100
d>5
Qfi
d>5
100
d>5
Oryza
*
b
Muscari
Orya
d=4
100
A
d>5
d>5
C
—
—J
Figure
3.
= = HZ
The
tes. length is 799, the CI 0.44, and the RI 0.52. Bootstrap values (from 500 replica
jces are included on the best supported clades. Single uppercase letters to the right of the generic n
Photochrome Gene
Family
Selaginella
Gingko
Gingko
Pseudotsuga
Ceratophyllum
Ceratophyllum
Urtica
PH
[Arabidopsis
Hebestigma
Myrospermum
Pisum
Dianthus
Dianthus
Spinacia
Antirrhinum
Lycopersicon
Solanum
Aquilegia
Cucurbita
Daucus
Dianthus
PHYC|
lArabidopsis
Ceratophyllum
Quercus
Hebestigma
Myrospermum
Urtica
Antirrhinum
Lycopersicon
Aqu
ilegia
PHYE]
lArabidopsis
Aquilegia
Daucus
Dianthus
Spinacia
Antirrhinu
Daucus
Daucus
PHYBl
lArabidopsis
PHYD|
lArabidopsis
rsimonious trees from analysis of dicot sequence
all
= =
743, the CI 0.23, and the RI 0.49. Bootstrap
^
included on the best supported clades. Single uppercase letters
PHY
ibidopsis
loci.
PHYC
The and homology
analysis (cladogram __.iplified in dicots, the
..j
.
PHYE
molog in Dianthus was identified by sister sequences to was readily established
its
g
PHYC me PHYE
Arabidopsis ny Arabidopsis mono-
relationship with (Fig. 4). inclusion oi /i in
PHYE
Sequences homologous to Arabidopsis phyletic gene lineages ~. .„„.wv. ~
& ., - .& «,. B
v .
PHYE
were not amplified monocots using the primer Arabidopsis sequence was not included in
in
set described above. However, such homologs were the legume data set (Fig. 5), two representative
Myrospermum
| E
Xeroderris
Sesbania
Sesbania
Poitea
Hybosema
Caragana
Wisteria
Lonchocarpus
Tipuana
Myrospermum
Poitea
Hybosema
Hebestigma
Lennea
Sesbania
Sesbania
Piscidia
Lonchocarpus
Derris
Kunstleria
Caragana
Wisteria
Pisum
Lathyrus
Clianthus
Myrospermum
Hebestigma
Lennea
Kunstleria
Xeroderris
Lonchocarpus
Sin,-! ,,:^.-m.mi> (.".(ill in nn.,1 ,-i^\U
>,i
. I
= =
on the 174 informative sites of the Fabace lata set. Length 545, CI
i (
lues (from 1000 replications) and decay es are included on the best supported
ii
>
Phytochrome Gene
Family
legumes were included in the dicot analysis shown nd in magnoliids with uniaperturate pol-
in Figure 4, and these were part of the monophy-
letic gene lineage that included Arabidopsis PHYE. The relationships angiosperm and
a
PHY
In the legume gene phylogeny, the bootstrap value nonangiosperm lineages were evaluated
in
PHYEdade
for the was 100%, thus revealing how two additional types of analysis: parsimony anal-
( 1 )
PCR
strongly this lineage is supported by the data in yses of nucleotide sites homologous to the
PHYA-
target fragment, including angiosperm
all
E
PH)
and nonangiosperm
paralogs sequenee-.
all
The
evolution of genes related to Arabidopsis for which there were corresponding nucleotide data
PHYB
has been more complex, with the apparently (about 330 bp); and parsimony and distance
(2)
independent duplication and divergence /'.'/) />' analyses of amino acid sites homologous to the
<>l
related genes some dicot lineages. 1ml perhaps Mougeotia fragment (App. about 300 amino
in 2,
Tl„- acids), including from angiosperms shown Ap-
in
, |,
I
pendix and from gymnosperms determined
1, in
/'// I> ipiences are sister grou this study (with sites coded as missing). Patterns
! <
nii Id. Imi' ilicots (Figs. 2, 4), and togetber with the that emerged from the nucleotide sequence anal-
Myrospermum
sequence from are the sister group vm-. included: Ceratodon, Physcomitrella, Se-
(1)
PHYB/ PHYD
of the other sequences. Note Equisetum, Gingko, and
-re\aied laginella, /'><
PHYB/D-
that two related sequences occur Ly- most commonly occurred as groups of a
in sister
PHYB/D/E
copersicon, forming a monoplivlelic elade. with clade; Mougeotia, when not des-
(2)
,i
f7/Ftf -related sequence from Solarium, that sep- ignated as the outgroup, was the lineage of
sister
is
PHYC
PHYCs
arate from the clade containing Arabidopsis PHYfi were and
the clade; basal para-
(3)
PHYD; PHYB/
and two of the D-related sequences phyletic many cladograms rooted Mougeotia;
in at
from Daucus also form a monophyletic clade (Fig. in others, or Mougeotia was removed from anal-
if
PHYB/D + PHYEdade PHYA +
This pattern could from nonhomologous and
4). result a a
v
. ,
PHYC
recombination between loci, but the hypothesis of clade were most often resolved. Results of
recent divergence consistent with the putative
is
PHYA + PHYC PHYB/
absence of addih .equences between and
Iron) split the
i
PHYD D/E
monocots. Arabidopsis each nonangiosperms
Additionally, in clade, with a set of as
is
apparently evidenced
functionally as
distinct,
l>\
PHYB
compensate was between
its failure to for the loss of sets of analyses the close relationship
phyB
function in null mutants of Arabidopsis (Reed the sequences available from Gingko and Pseu-
PHYB/D/E
1993; Wester dotsuga and
et et 1994). the clade. Further, the
al., al.,
robustness to perturbation of the data, which
is
PHYE
PIIYH
is the sister group to the I'll) found in the analysis of the full-length sequence
I
PHYD PHYE
clade. Since and have not been am- data set (Fig. lost in these broad comparisons
2), is
from monocots, when number
plified the diversification of this the of sites limited.
is
may
part of the phytochrome gene family have Recently, phytochrome sequence
single frag-
taken place only during the diversification dieots. ments (561-654 bp) from a number of nonangio-
< > I
Further sampling from Nymphaeales, hedra, were
Piperales, de-
GenBank
Winterales, Laurales, and Magnoliales should ad- posited in (Kolukisaoglu et
al.,
dress the question of whether the presence of just bringing the number of non-
total
lied),
ibl
PHYC PHY
PHYA, PHYB,
and the ancestral con- angiosperm homologous sequence fragments
is
dition in angiosperms. Notably, however, prelimi- available for nucleotide analysis to 15. Preliminary
nary analysis of three sequences from Piper re- analyses of these sequences indicate that the data
GenBank
cently submitted to (Kolukisaoglu et al., are still too fragmentary to draw conclusions re-
unpublished), derived using a different primer pair. garding evolution of specific loci, especialU as -oine
suggests that they are orthologs of \rahidopsis of the nonangiosperm taxa represented by a single
PHY
PHYA, PHYB, PHYC.
and Alternatively, the sequence are have more than one
in- likely to
PHYD PHYE
ability to amplify and horn monocots gene. Furthermore, organismal relationships de-
mean
(and Piper) could that the oligonucleotide picted these cladograms and neighbor-joining
in
+
primers designed in recent studies do not recognize trees, except for the pairs Ceratodon Funaria
PHYD PHYE
+
and amplify and homologs. This (both mosses) and Metasequoia Picca (both
all
.aluated in sub- conifers), are not well supported in bootstrap anal-
gene
Iannis
in
•