International Journal of Bioinformatics Research, ISSN: 0975–3087, Volume 1, Issue 2, 2009, pp-27-36
Molecular phylogeny of angiospermic plant families using RBCL gene
sequences
B. Uma Reddy*
Department of Bioinformatics, Gulbarga University, Gulbarga, India
E. mail: [email protected], Ph. No: +91-9449329266
Abstract: The present study was undertaken to assess the role of plastid-rbcL (ribulose-1, 5-bisphosphate
carboxylase large-subunit) gene sequences in addressing the evolutionary relationships within the
angiosperms at inter and intra-familial levels using computational experiment. In order to elucidate the
relationships, a set of 92 chloroplast rbcL sequences representing from 90 taxa of 12 genera and 10
angiospermic plant families (dicot and monocots) were withdrawn from the GenBank database. The multiple
sequence alignment was performed using Genebee-ClustalW service to findout the regions of conserved or
indels among the sequences. The phylogenetic tree was inferred from these sequences by employing
Bootstrap method of UPGMA (Unweighted Pair Group Method with Arithmetic Mean) using MEGA
(Molecular Evolutionary Genetics Analysis) software. The consistency of these generic-wise groupings was
further confirmed by the MP (Maximum-Parsimony), ME (Minimum-Evolution) and NJ (Neighbor-Joining)
methods. The analysis of these studies strongly indicates that, out of the 12 selected genera Trichosanthes
(Cucurbitaceae), Phyllanthus (Phyllanthaceae), Austrobryonia (Cucurbitaceae), Solanum (Solanaceae),
Piper (Piperaceae) and Saxifraga (Saxifragaceae) are grouped into separate clusters and
exhibiting
monophyletic conditions. Where as, Drypetes (Putranjivaceae), Asparagus (Asparagaceae), Cassia
(Caesalpinioideae, sub-family), Canna (Cannaceae), Mentha (Lamiaceae), are paraphyletic and the
members of the Salvia (Lamiaceae) are distributed throughout these hiraeoid clades, confirming the
polyphyly of this large genus. Similar observations were noticed in all four methods. Thus, chloroplast rbcL
gene sequences can unambiguously resolve the relationships, as well as provided a good indication of
major supra-generic groupings among the selected angiospermic plant families and also gave many clues
for future studies.
Key Words: rbcL gene, monophyletic, paraphyletic, polyphyletic, Phylogenetic relationship, MEGA
INTRODUCTION
The use of DNA nucleotide sequence data has
awakened a quickly growing interest in molecular
systematic analyses. Since last decade
molecular systematics in plants has progressed
rapidly with in-vitro DNA amplification and direct
sequencing methods. In angiosperm systematics,
this molecular approach has been effective in
addressing many phylogenetic questions that had
not been solved only by using phenotypic
characters. The gene for the large subunit of the
ribulose-bisphosphate
carboxylase/oxygenase
(rbcL), located on the chloroplast genome, is an
appropriate choice for inference of phylogenetic
relationships at higher taxonomic levels [1—3].
Because of its slow synonymous nucleotide
substitution rate in comparison with nuclear
genes and its functional constraint that reduces
the evolutionary rate of non-synonymous
substitution [4]. The substitution rate of rbcL
appears appropriate for studies involving taxa
that diverged from 10’s of million years [5]. In
recent years, there has been a growing interest in
using sequences of the gene coding for the large
subunit
of
ribulose-1,
5-bisphosphate
carboxylase/ oxygenase (rbcL) to estimate the
plant phylogenies [6]. Several research groups
have shown the usefulness of this gene for
solving
intergeneric
and
interspecific
relationships among flowering plants example,
Cucurbitaceae
[7],
Orchidaceae
[8],
Rhamnaceae [9], Araucariaceae [10]. The
present study was undertaken to evaluate the
relationships at the intra and inter familial,
intergeneric and interspecific levels, and also to
examine the rates, patterns and types of
nucleotide substitutions within the rbcL gene in all
the selected taxa of each genera, through a
computational experiment using 92 chloroplast
rbcL gene sequences from 90 taxa, 12 genera,
10 families, and discussed the utilization of
plastid-rbcL gene for molecular phylogeny.
MATERIALS AND METHODS
Cladistic parsimony analyses of a total 92 rbcL
nucleotide sequence data
representing 90
species (Spp) and 2 duplicates from
Austrobryonia micrantha and Mentha longifolia of
12 genera, 10 angiospermic plant families (both
dicots and monocots) are presented here in the
table-1, were withdrawn from GenBank
database). The multiple sequence alignment was
performed using Genebee-ClustalW service. All
gap characters were scored as missing data
rather than a fifth character. Phylogenetic
analyses of the sequence data was analyzed with
UPGMA using MEGA software. The consistency
of these generic wise groupings was further
confirmed by the MP, NJ and ME methods as
implemented in MEGA 4.1 software [11]. Tree
statistics included the consistency index (CI) [12],
retention index (RC) [13] and rescaled
Bioinfo Publications, International Journal of Bioinformatics Research, ISSN: 0975–3087, Volume 1, Issue 2, 2009
Molecular phylogeny of angiospermic plant families using RBCL gene sequences
consistency index (RCI) [13]. Branch lengths
(ACCTRAN optimization with equal weights) and
the level of support for branches of the
phylogenetic trees was evaluated with the
bootstrap analysis [14] to verify the strength of
the branches based on 100 replicates, using
branch and bound search. Bootstrap percentages
are described as high (85-100%), moderate (75 –
84%) or low (50 – 74%) [15]. The number of
nucleotide substitutions per site was estimated by
Kimura’s two parameter method [16] with the
DNADIST program.
RESULTS
The 12 genera of angiosperms namely,
Trichosanthes (4 Spp), Solanum (2 Spp),
Austrobryonia (4 Spp and 5 sequences), Piper
(11 Spp), Phyllanthus (9 Spp.), Saxifraga
(2
Spp.), Drypetes (10 Spp), Asparagus (3 Spp),
Salvia (35 Spp.), Cassia (4 Spp), Canna (3 Spp),
Mentha (3 Spp and 4 sequences) were selected
for the study are highly divergent in several
respects from one another. But the properties,
such as, biochemical, morphological and
cytological characteristics of species within each
genus are exhibiting greater level of similarity.
This in turn inferred that the molecular makeup of
these organisms at the generic and family levels
is also highly conserved. The analysis of the
above studies strongly indicates that, out of the
12 selected genera, the members of
Trichosanthes,
Austrobryonia,
Phyllanthus,
Solanum, Piper and Saxifraga are nested into a
separate clusters as a monophyletic group, within
the major clades and sub-clades in the tree
topology, this is strongly supported by high
bootstrap replications (100%). Where as,
Drypetes, Asparagus, Cassia, Canna, Mentha
are paraphyletic and the members of the Salvia
are distributed throughout these hiraeoid clades,
confirming the polyphyletic condition of this large
genus. These observations were noticed in all
UPGMA, MP, ME and NJ methods, but only the
positions of the generic-wise clusters were
altered into the tree topology in all these
methods. The members of the Asparagus
(Asparagales) and Canna (Cannaceae) were
nested within the angiospermic dicot plant
families also exhibiting the paraphyletic
conditions of these genera with selected dicot
plant families. The total length of the tree is
14029. Of the 92 sequences ranging between
968 – 1471 in the data matrix, of which only 877
nucleotide residues were used to infer the
phylogenetic relationships among the selected
taxa and were shown to be invariant and 305
were variable. These trees were characterized by
a consistency index (CI) of 0.187540, retention
index (RI) of 0.733592 and the rescaled
consistency index i.e., RCI = 0.137578 (for all
sites). The strict consensus of these weighted
trees is shown in the Fig 1-4. Branch lengths
28
(ACCTRAN optimization with equal weights) and
bootstrap are shown. The composition of adenine
(A)-0.27, thymine (T)-0.29, guanine (G)-0.25 and
cytosine (C)-0.19 nucleotides were observed as
constant in all the test genera. But slight changes
were noticed in the ratio of transition and
transversion substitutions. In case of Saxifraga
the ratio of transition and transversion is 1.83,
Asparagus is 0.7, Cassia is 1.33, Drypetes is
1.63, Salvia is 2.7, Mentha is 1.8, Trichosanthes
is 0.5, Piper is 1.0, Phyllanthus is 0.7. Perhaps
the members within genera of Austrobryonia,
Solanum and Canna are exhibiting highest level
of similarity, the rate of transition and
transversion ratios are almost negligible. In these
selected taxa, there is no significant cluster at the
level of subclass was found, particularly, there is
no clear-cut segregation between monocots and
dicotyledonous plants was observed in the tree
topology. The members of the genera Canna and
Asparagus belongs to monocotyledons are
nested within the clades of the dicot plant
families. The length of the rbcL gene sequence in
the members of few genera included in the
present study possess fixed number of nucleotide
residues, which is evident from the genus
Trichosanthes is 1356, Phyllanthus -1408,
Saxifraga – 1346 and 1377, Solanum – 1370,
Austobryonia – 1355, Piper – 1428. Where as,
considerable variation in substitution rates and
length of the sequences were observed in some
other selected genera namely, Saxifraga stellaris
and S. integrifolia– 1346 and 1377, respectively.
Similar observations were found with Asparagus
officinalis, A. cochinchinensis and A. capensis –
1206, 1369 and 1340, respectively, Drypetes –
1398, except D. littoralis and D. roxburghii -1331
and 1420, respectively. Canna indica and C.
glauca – 1327 but C. tuerckheimii – 1334;
Mentha rotundifolia, longifolia (2) – 1420 and M.
suaveolens, M. longifolia – 1402; Cassia senna,
C. didymobotrya – 1368, C. grandis – 1421, C.
fistula- 1465. However, the sequence length of
rbcL in 35 members of the genus Salvia is
ranging between 968 -1474. But the members
of this genus located in the subclades-I of CladeV are strictly containing 1323 and subclades-I of
Clade-I containing 1371 nucleotide residues only,
and these exhibited highest level of sequence
similarity and originated from one common
ancestral forms. Where as, the members of this
genus located in the sub-clade-IV of clade-I,
clade-II, and clade – III are found to be highly
variable. The UPGMA method of phylogenetic
analysis strongly suggests that, the members of
the genus Trichosanthes are evolved first and
forms a primitive, and then Phyllanthus,
Drypetes, Saxifraga, Solanum, Austrobryonia are
evolved in a sequential order. Where as, the
members of the genus Piper are found to be late
evolved and inferred them as highly advanced
among the selected genera. Where as, the
Bioinfo Publications, International Journal of Bioinformatics Research, ISSN: 0975–3087, Volume 1, Issue 2, 2009
B. Uma Reddy
members of the genus Mentha are evolved twice
with the members of Salvia. Mentha suaveolens
and M. longifolia are early evolved, they are
found in the cluster-I and forms a basal group.
But the M. rotundifolia and M. longifolia (2) are
late evolved and nested in a cluster-V indicating
that they are advanced. Among the four species
of the Cassia, only the C. senna and C.
didymobotrya exhibited high level of similarity,
this is supported by high bootstrap values of
100% and occupying in the basal group. Where
as, Cassia grandis nested with in the members of
Salvia in clade-II and Cassia fistula originated
sisterly with the members of the genus Saxifraga.
Similarities between these individuals are
strongly supported with bootstrap values as 96%.
In case of the genus Canna, only the C. indica
and C. glauca are highly similar, supporting with
bootstrap values of 100% and located in the
major clade-I. Another member of the same
genus C. tuerckheimii is located in the clade-IV.
Due to high sequence diversity among the three
selected species of Asparagus are distributed
distantly into the tree topology and indicated that,
this is evolved several times during evolution. A.
capensis is found in clade-I and referred as less
evolved
or
primitive,
where
as,
A.
cochinchinensis in the cluster III and A. officinalis
is in Clade-V and this A. officinalis is inferred as
highly evolved among other selected species.
Among the 35 species, the members located in
the subclade-I of clade-I and members in the
subclade –I of clade-V are exhibiting greater level
of sequence similarity, members of the same
genus located in the other clades and subclades
are displaying much variable. It is evident that the
members of this large genus evolved several
times and are distributed into several patches all
along the tree topology (FIG -1). The similar
monophyletic, paraphyletic and polyphyletic
conditions of these selected genera were also
confirmed through other
NJ, MP, and ME
methods, indicating that these conditions are
strictly conserved. Only the relative position of
these generic level groupings was altered (FIG 2-4).
DISCUSSION
The study presented here is an attempt to
employ a set of 92 plastid rbcL gene sequences
of 90 taxa belonging to 12 genera of 10
angiospermic plant families to address intra
familial relationships. The analyses of rbcL
nucleotide sequences presented here provide a
great deal of support for previous hypotheses of
relationships within the family and generic levels
of some angiospermic plants. The members of
the genera belongs to Asparagus (Asparagales)
and Canna (Cannaceae) belongs to the subclass monocotyledonous were nested within the
angiospermic dicot plant families also exhibiting
the paraphyletic conditions of these genera with
selected dicot plant families. The present data
also reject the views of Burger, 1997; Taylor and
Hickey, 1992 [17–18], that Piperaceae are basal
among most of the primitive angiosperms and
that, the monocots included in the present study
were derived from them. In contrast to the ShuMiaw et al., 1997 [19], that the monocots
included in the present studies are not clustered
into a separate monophyletic group. The
members of the genera Canna and Asparagus
belongs to monocotyledons are nested within the
major clades of the dicot plant families.
Therefore, the plastid-rbcL gene sequence data
lend support to Hutchinson’s view that “the single
cotyledon, parallel-veined leaves, absence of
cambium, dissected stele and the adventitious
root system of monocots are all regarded as
apomorphies within the angiosperms. Moreover
monocots are regarded as derived from dicots,
the point of origin being Ranales [20]. These
results show that analyses of the chloroplast
DNA rbcL is a useful approach for inferring
phylogenetic relationships especially at the
supra-generic level.
CONCLUSION
However, the present study, the tree relations
among the genera are well resolved and
providing support for the monophyly of large
clades and subclades for many of the selected
plant
genera
such
as
Trichosanthes,
Austrobryonia, Saxifraga, Solanum, Phyllanthus
and Piper. The polyphyletic condition of the
genus Salvia is supported by the higher rate of
the transition and transversion ratio is 2.7, 554
gaps as well as significant variation in the total
number nucleotide residues in the different
members of the genus Salvia among 35 species
(i.e., 968 in Salvia nubicola to 1474 in Salvia
divinorum).
The present investigation also
concludes that, the gene plastid-rbcL alone is not
likely to provide robust estimates of phylogeny.
Data from additional molecular (complete nuclear
and
chloroplast
genetic
systems)
and
morphological sources and their combined
analyses are necessary to establish a stable and
firm base for a plant systematics (Family
classification) that better reflects phylogenetic
relationships.
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Bioinfo Publications, International Journal of Bioinformatics Research, ISSN: 0975–3087, Volume 1, Issue 2, 2009
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Table: List of the rbcL sequences using figure-1
Sl.
No
01
02
03
04
05
06
07
08
09
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
Accession
Number
(GenBank)
AY663611
AY663610
AY663609
AY663608
AY663607
AY663606
AY663605
AY663603
AB233921
EF450315
EF450314
EF450313
EF450312
EF450310
EF450309
EF450311
EF450308
EF450307
EF450305
EF450304
EU155605
EU155604
EU155603
EU155602
EF487553
EF487552
No of
base
pairs
1408
1408
1408
1408
1408
1408
1408
1408
1331
1428
1428
1428
1428
1428
1428
1428
1428
1428
1428
1428
1356
1356
1356
1356
1355
1355
27
EF487551
1355
28
29
30
31
32
33
34
35
36
37
38
EF487550
EF487549
AF378764
AF378763
AF378774
AY570390
Z37417
Z37415
U28876
L14407
AB295077
39
TAXA USED
REFFERENCES
FAMILY
Phyllanthaceae
Phyllanthaceae
Phyllanthaceae
Phyllanthaceae
Phyllanthaceae
Phyllanthaceae
Phyllanthaceae
Phyllanthaceae
Phyllanthaceae
Piperaceae
Piperaceae
Piperaceae
Piperaceae
Piperaceae
Piperaceae
Piperaceae
Piperaceae
Piperaceae
Piperaceae
Piperaceae
Cucurbitaceae
Cucurbitaceae
Cucurbitaceae
Cucurbitaceae
Cucurbitaceae
Cucurbitaceae
[21]
[21]
[21]
[21]
[21]
[21]
[21]
[21]
[22]
Yang et al.,
Yang et al.,
Yang et al.,
Yang et al.,
Yang et al.,
Yang et al.,
Yang et al.,
Yang et al.,
Yang et al.,
Yang et al.,
Yang et al.,
[23]
[23]
[23]
[23]
[23]
[23]
Cucurbitaceae
[23]
1355
1355
1334
1327
1327
1371
1420
1420
1402
1474
1323
Phyllanthus polyphyllus
Phyllanthus nutans
Phyllanthus nummariifolius
Phyllanthus lokohensis
Phyllanthus juglandifolius
Phyllanthus fluitans
Phyllanthus flagelliformis
Phyllanthus calycinus
Phyllanthus flexuosus
Piper nigrum
Piper chinense
Piper laetispicum
Piper hainanse
Piper hancei
Piper sarmentosum
Piper betle
Piper kadsura
Piper wallichii
Piper austrosinense
Piper longum
Trichosanthes schlechteri
Trichosanthes pentaphylla
Trichosanthes cucumerina
Trichosanthes bracteata
Austrobryonia pilbarensis
Austrobryonia
micrantha
HS4V
Austrobryonia
micrantha
HS411
Austrobryonia centralis
Austrobryonia argillicola
Canna tuerckheimii
Canna indica
Canna glauca
Mentha longifolia
Mentha rotundifolia
Mentha longifolia (2)
Mentha suaveolens
Salvia divinorum
Salvia plebeia
Cucurbitaceae
Cucurbitaceae
Cannaceae
Cannaceae
Cannaceae
Lamiaceae
Lamiaceae
Lamiaceae
Lamiaceae
Lamiaceae
Lamiaceae
AB295076
1323
Salvia glabrescens
Lamiaceae
40
AB295073
1323
Salvia nipponica
Lamiaceae
41
AB295070
1323
Salvia arisanensis
Lamiaceae
42
AB295069
1323
Salvia hayatana
Lamiaceae
43
AB295068
1323
Salvia pygmea
Lamiaceae
44
AB295067
1323
Salvia lutescens
Lamiaceae
45
46
47
AY570451
AY570450
AY570449
1162
1368
1353
Salvia viscosa
Salvia viridis
Salvia staminea
Lamiaceae
Lamiaceae
Lamiaceae
[23]
[23]
[24]
[24]
Prince (Unpublished)
[25]
[26]
[26]
[27]
[28]
Sudarmono and Okada
(Unpublished)
Sudarmono and Okada
(Unpublished)
Sudarmono and Okada
(Unpublished)
Sudarmono and Okada
(Unpublished)
Sudarmono and Okada
(Unpublished)
Sudarmono and Okada
(Unpublished)
Sudarmono and Okada
(Unpublished)
[25]
[25]
[25]
(Unpublished)
(Unpublished)
(Unpublished)
(Unpublished)
(Unpublished)
(Unpublished)
(Unpublished)
(Unpublished)
(Unpublished)
(Unpublished)
(Unpublished)
International Journal of Bioinformatics Research, ISSN: 0975–3087, Volume 1, Issue 2, 2009
31
Molecular phylogeny of angiospermic plant families using RBCL gene sequences
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
AY570448
AY570447
AY570446
AY570445
AY570444
AY570443
AY570442
AY570439
AY570438
AY570437
AY570436
AY570435
AY570434
AY570433
AY570432
AY570431
AY570430
AY570427
AY570428
AY570426
AY570425
AY570424
AY570423
AY570422
AY663639
AY663638
AY663637
AY663636
AY663635
AY663634
AY663633
AY663632
M95757
AB233926
AM234244
U74195
Z70155
Z70154
AY149374
1187
1349
1365
1356
1371
1350
1371
1349
1371
1177
1364
1126
1371
1186
1371
1355
968
1182
1113
1371
1357
1296
1115
1135
1398
1398
1398
1398
1398
1398
1398
1398
1420
1331
1421
1465
1368
1368
1206
Salvia tiliifolia
Salvia texana
Salvia sylvestris
Salvia taraxacifolia
Salvia summa
Salvia subincisa
Salvia spathaceae
Salvia sclarea
Salvia roemeriana
Salvia ringens
Salvia pratensis
Salvia polystachya
Salvia pentstemonoides
Salvia palaestina
Salvia pachyphylla
Salvia officinalis
Salvia nubicola
Salvia nilotica
Salvia misella
Salvia lyrata
Salvia lycoides
Salvia involucrate
Salvia verbenaca
Salvia hirsuta
Drypetes staudtii
Drypetes lateriflora
Drypetes gilgiana
Drypetes floribunda
Drypetes fallax
Drypetes diversifolia
Drypetes deplanchei
Drypetes brownie
Drypetes roxburghii
Drypetes littoralis
Cassia grandis
Cassia fistula
Cassia senna
Cassia didymobotrya
Asparagus officinalis
Lamiaceae
Lamiaceae
Lamiaceae
Lamiaceae
Lamiaceae
Lamiaceae
Lamiaceae
Lamiaceae
Lamiaceae
Lamiaceae
Lamiaceae
Lamiaceae
Lamiaceae
Lamiaceae
Lamiaceae
Lamiaceae
Lamiaceae
Lamiaceae
Lamiaceae
Lamiaceae
Lamiaceae
Lamiaceae
Lamiaceae
Lamiaceae
Putranjivaceae
Putranjivaceae
Putranjivaceae
Putranjivaceae
Putranjivaceae
Putranjivaceae
Putranjivaceae
Putranjivaceae
Putranjivaceae
Putranjivaceae
Caesalpinioideae
Caesalpinioideae
Caesalpinioideae
Caesalpinioideae
Asparagaceae
87
88
89
90
91
92
AB029849
AM234843
AF374732
L01953
FJ914175
FJ914174
1369
1340
1346
1377
1370
1370
Asparagus cochinensis
Asparagus capsensis
Saxifraga stellaris
Saxifraga integrifolia
Solanum chilense
Solanum pennellii
Asparagaceae
Asparagaceae
Saxifragaceae
Saxifragaceae
Solanceae
Solanceae
32
[25]
[25]
[25]
[25]
[25]
[25]
[25]
[25]
[25]
[25]
[25]
[25]
[25]
[25]
[25]
[25]
[25]
[25]
[25]
[25]
[25]
[25]
[25]
[21]
[21]
[21]
[21]
[21]
[21]
[21]
[21]
[21]
[29]
[22]
[30]
[31]
[31]
Kaess, (Unpublished).
McPherson
et
al.,
(Unpublished)
[32]
[30]
[33]
[33]
Dillon et al., (Unpublished)
Dillon et al., (Unpublished)
Bioinfo Publications, International Journal of Bioinformatics Research, ISSN: 0975–3087, Volume 1, Issue 2, 2009
B. Uma Reddy
Pipe r nigrum
22
0.0000
53 0.0000
Pipe r a ustrosine nse
0.0000
56 0.0006
13
Pipe r lae tispicum
0.0006
Pipe r sa rmentosum
81
0.0000
0.0013
Pipe r longum
0.0000
18
0.0004
53
33
0.0009
0.0000
Pipe r w allichii
0.0000
0.0007
0.0001
100
P ipe r
[Pipe rac e a e ]
S ubc la de - I I
Pipe r kadsura
0.0006
Pipe r chinense
62
0.0000
0.0006
Pipe r hancei
0.0000
Pipe r betle
0.0514
0.0018
100
Pipe r haina ne nse
CLADE - V
0.0019
2.9732
Asparagus officinalis
0.0500
53
0.0033
Mentha rotundifolia
0.0125
100
0.0375
0.0042
7
Mentha longifolia
0.0083
87
Salvia plebeia
0.0070
47
100
0.0013
0.3018
0.0000
0.0042
64
0.0000
0.0029
0.0040
33
0.0001 92
2
0.0011
Salvia glabrescens
Subclade - I
Salvia nipponica
Salvia arisanensis
Salvia [Lamiaceae]
Salvia lutescens
Salvia hayatana
0.0029 92
0.0000
0.0011
Salvia pygmaea
0.0000
2.9073
36
2.3685
0.6579
2.3685
0
Salvia [Lamiaceae]
Salvia involucrata
Salvia lycioides
3.3282
3.5798
Salvia tiliifolia
Salvia misella
4.5465
Austrobryonia pilbarensis
17
0.0000
17 0.0000
Austrobryonia micrantha
0.0000
86 0.0000
Austrobryonia micrantha (2)
S ubclade - I V
Austrobryonia ce ntra lis
14
0.0011
0.4800
33
0.2998
4
1.4746
Salvia officinalis
2.2921
Sola num chilense
100
0.0000
2.2921
Sola num penne llii
0.0000
Subclade - III
S olanum
Canna tuerckheimii
2.3779
CLADE - IV
Sa xifra ga ste lla ris
100
0.0093
96 0.0263
Sa xifra ga inte grifolia
0.0093
0.0134
37
0.3442
[S ola na c e a e ]
Salvia hirsuta
2.7221
6
0.3498
1.8296
[Cuc urbita c e ae ]
Austrobryonia a rgillicola
0.0000
2.5908
0
Austrobryonia
0.0000
100 0.0011
2
1.6889
Sa xifra ga
[S a xifra ga c ea e ]
Subclade - II
Cassia fistula
0.0356
Drypetes staudtii
18
0.0023
18 0.0000
Drypetes fallax
0.0023
28 0.0006
100
2.3289
0.0023
0.0011
0.0029
100
0.0451
1.3224
Drypetes gilgiana
Drypetes
37
0.0023
Drypetes
19 0.0009
0.0023
0.0008
Drypetes
27
0.0029
0.0003
Drypetes
0.0029
14
3.0102
4.9248
0
1.8802
3.0102
Drypetes
[Putanjivaceae] Subclade - I
lateriflora
deplanchei
diversifolia
brownii
Salvia pratensis
Out group
Asparagus cochinchinensis
Salvia texana
100
0.0000
Salvia sclarea
14 2.9688
0.0000
4.9662 47
Salvia subincisa
2.3426
0.6262
Salvia verbenaca
2.3426
26
2.8156
5.4417
0
2.8156
3.3875
Drypetes floribunda
3.1560
5
5.1013 14
2.8919
Salvia
[Lamiaceae] CLADE - III
Salvia viscosa
Cassia grandis
Salvia palaestina
Salvia
[Lamiaceae] CLADE - II
Salvia polystachya
Salvia staminea
0.2641 100
0.0006
2.8913
Salvia ringens
0.0006
100
0.0000
9.0506
0.0000
Canna indica
Canna
[Cannac eae]
Subclade - VII
Canna glauca
Phylla nthus nutans
57
0.0029
30 0.0009
Phylla nthus jugla ndifolius
0.0029
34 0.0005
Phylla nthus polyphyllus
0.0037
26 0.0014
32
0
Phylla nthus fluita ns
0.0056
42
0.0009
100
3.9166
Phylla nthus fla ge lliformis
0.0042
0.0012
0.0317
P hylla nthus
[P hyllantha c ea e ]
Phylla nthus calycinus
Subclade - VI
0.0058
Phylla nthus fle xuosus
0.0011
0.0058
100
51
2.4614
Phylla nthus nummulariifolius
0.0058
Phylla nthus lokohensis
0.0020
32
0.0058
2.5010
Drypetes littoralis
0.0395
Salvia sylvestris
2.5009
Salvia viridis
100
0.0516
23 2.5299
Asparagus capensis
0.0516
1
4.0488
1.3161
2.5815
37
1
2.3166
0.9530
1.1042
2.3166
Out group
Subclade - V
Salvia [Lamiaceae]
Subclade - IV
CLADE - I
Salvia nilotica
0.0006
76 0.0009
Trichosanthes cucume rina
0.0006
100 0.0016
6
[Lamiaceae]
Salvia nubicola
Trichosanthes pentaphylla
71
0.6282
Salv ia
Salvia taraxacifolia
T ric hosa nthe s
[Cuc urbita c e a e ]
Subc lade - I I I
Trichosanthes schlechte ri
0.0014
2.6454
Trichosanthes bra cte ata
0.0031
27
0.6211
Drypetes roxburghii
0.0574
100
100
0.0034
0.0371
2.5911
0.0034
85
100
0.0332
0.0003
0.0058
0.0040
72
[Caesalpinoideae]
Subclade - II
Salvia spathacea
100
0.0000
25 0.0058
Salvia pachyphylla
0.0000
42
0.0012
Cassia
Cassia didymobotrya
Salvia divinorum
0.0073
0.0168
Cassia senna
0.0021 74
0.0019
0.0021 59
Mentha suaveolens
Mentha longifolia
Out group
Out group
Salvia
[Lamiaceae]
Subclade - I
Salvia lyrata
Salvia pentstemonoides
0.0011
0.0008 92 0.0000 Salvia summa
0.0011
Salvia roemeriana
0.0000
Fig -1 Phylogenetic tree from 92 rbcL sequences representing 90 taxa of family Cucurbitaceae, were inferred using UPGMA method.
Bootstrap percentages and branch lengths are indicated above and below the branches, respectively.
International Journal of Bioinformatics Research, ISSN: 0975–3087, Volume 1, Issue 2, 2009
33
Molecular phylogeny of angiospermic plant families using RBCL gene sequences
86
Salvia summa
Salvia roemeriana
60
Salvia (Lamiaceae)
Salvia pents temonoides
69
36
Salvia lyrata
59
Mentha longifolia (2)
99
Mentha s uaveolens
Salvia divinorum
40
Salvia (Lamiaceae)
Salvia spathac ea
39
94
99
Salvia pac hy phylla
Cas sia senna
99
1
Cassia (Caesalpinioideae - sub family)
Cas sia didymobotry a
Drypet es rox burghii
Salvia taraxacifolia
Trichosa nthes bracte ata
11
3
Trichosa nthes schl echte ri
99
0
T ric hosa nthe s ( Cuc urbit a c e a e )
Trichosa nthes pentaphylla
62
70
Trichosa nthes cucumerina
Salvia nilotic a
2
Salvia nubic ola
Salvia verbenac a
Salvia subincis a
0
Asparagus c apensis
5
99
18
Salvia staminea
Salvia (Lamiaceae)
Salvia ringens
Drypet es litt oralis
14
Phylla nthus fl agel liformis
9
99
14
37
Phylla nthus nuta ns
Phylla nthus fl uitans
99
Phylla nthus jugl andi fol ius
82
30
Phylla nthus nummul ari ifolius
Phylla nthus ( Phylla nt ha c e a e )
Phylla nthus lokohe nsis
Phylla nthus polyphyl lus
33
Phylla nthus calyci nus
30
74
Phylla nthus fl ex uosus
Mentha rotundifolia
3
99
Mentha longifolia
94
Salvia glabresc ens
50
Mentha (Lamiaceae)
Salvia nipponic a
Salvia plebeia
33
Salvia viridis
57
83
Salvia sylves tris
Salv ia (Lamiac eae)
Salvia lutesc ens
99
Salvia hay at ana
70
72
Salvia pygmaea
Salvia aris anensis
99
Asparagus offic inalis
Pipe r ka dsura
2
18
29
Pipe r chine nse
Pipe r ha ncei
99
23
28
Pipe r ha ina ne nse
Pipe r be tle
65
49
Pipe r sarmentosum
P ipe r ( Pipe ra c e a e )
Pipe r longum
Pipe r nigrum
5
Pipe r austrosine nse
66
Pipe r lae tispi cum
15
11
Pipe r wa lli chii
Canna tuerc kheimii
0
Asparagus c oc hinchinens is
0
99
Salvia tex ana
Salv ia {Lamiac eae)
Salvia sclarea
0
99
3
Canna indica
Canna (Cannaceae)
Canna glauc a
Salvia polys tac hy a
21
Cas sia grandis
12
Salvia tiliifolia
3
Salvia visc os a
1
0
Salvia (Lamiaceae)
Salvia involucrata
0
Salvia palaestina
1
8
Salvia lyc ioides
Austrobryonia centra lis
0
Austrobryonia pilbarensis
99
Austrobryonia micrantha
56
Austrobryonia ( Cuc urbit a c e a e )
Austrobryonia micrantha(2)
15
13
99
Austrobryonia a rgi lli col a
Salvia officinalis
Salvia hirs ut a
Salvia pratensis
Salvia mis ella
0
99
75
Sax ifraga ste lla ris
Sa xif ra ga ( Sa xif ra ga c e a e )
Sax ifraga i nte grifolia
10
Cas sia fis tula
Drypet es brownii
99
49
13
99
Drypet es lat eriflora
Drypet es deplanc hei
Drypet es divers ifolia
Drypetes (Putranjivaceae)
Drypet es staudtii
56
Drypet es gilgiana
50
Drypet es floribunda
51
21
Drypet es fallax
Solanum chilense
Solanum pennellii
Fig-2 Phylogenetic tree from 92 rbcL sequences representing 90 taxa of family Cucurbitaceae, were inferred using the Maximum
Parsimony method (length = 14029, CI = CI = 0.187540; RI = 0.733592; RCI = 0.137578 (for all sites).
34
Bioinfo Publications, International Journal of Bioinformatics Research, ISSN: 0975–3087, Volume 1, Issue 2, 2009
B. Uma Reddy
21
10
Salvia polys tachya
Salvia palaest ina
3
Salvia involucrata
1
Salv ia (Lamiaceae)
Salvia tiliifolia
0
Salvia vis cosa
0
Cas sia grandis
0
Salvia plebeia
0
Mentha longifolia (2)
0
Salvia py gmaea
0
Salvia hayatana
0
Salvia glabres cens
0
Salvia nipponica
0
Salvia lutes cens
0
Salvia arisanens is
0
Mentha rotundifolia
0
Asparagus officinalis
0
Piper hancei
0
Piper kadsura
0
Piper chinens e
0
Piper hainanense
Piper sarment os um
0
14
0
Piper longum
Piper betle
0
Piper laetis pic um
0
Piper wallic hii
0
Piper austrosinense
Piper nigrum
0
Asparagus cochinc hinensis
Asparagus capensis
0
Salvia viridis
0
90
0
Salvia st aminea
Salv ia (Lamiac eae)
Salvia ringens
Dry petes lit toralis
6
Phyll anthus fla ge lliformi s
67
Phyll anthus nutans
47
Phyll anthus jugla ndifolius
27
Phyll anthus ca lycinus
17
Phyll anthus polyphyllus
Phylla nt hus (P hylla ntha c e a e )
13
Phyll anthus lokohensi s
5
Phyll anthus fle xuosus
12
Phyll anthus nummula riifoli us
12
18
Phyll anthus fluita ns
17
Austrobryoni a pil ba rensi s
Austrobryoni a mi cra ntha
66
Austrobryoni a mi cra ntha (2)
83
17
13
Austrobryonia (Cuc urbita c e a e )
Austrobryoni a a rgill icola
Austrobryoni a centrali s
Solanum chi lense
3
88
S ola num (Sola na c e a e )
Solanum pe nnell ii
Salvia hirsuta
1
Sax ifraga s tellaris
Sax ifraga integrifolia
55
Dry petes deplanchei
33
Dry petes lateriflora
29
Dry petes floribunda
18
Dry petes diversifolia
13
Dry petes s taudtii
3
Drypetes (Putranjivaceae)
Dry petes fallax
6
Dry petes brownii
2
Dry petes gilgiana
2
13
5
0
Cas sia fistula
Canna tuerckheimii
Salvia (Lamiaceae)
Salvia ly cioides
Salvia officinalis
7
0
Salvia sy lvest ris
Salvia pratens is
0
Salvia (Lamiaceae)
Salvia verbenaca
92
12
0
Salvia texana
Salvia sc larea
Salv ia (Lamiaceae)
5
Salvia subincisa
Salvia misella
Salvia nilotica
0
Salvia tarax ac ifolia
26
0
53
Tri chosa nthe s schle chteri
Tri chosa nthe s cucume rina
T ric hosa nthe s (Cuc urbita c e a e )
91
0
Tri chosa nthe s pe nta phyl la
Tri chosa nthe s bra ctea ta
Salvia nubic ola
0
97
1
Canna indic a
Canna (Cannaceae)
Canna glauca
Mentha s uaveolens
7
Mentha longifolia
85
Salvia roemeriana
9
Salvia summa
3
Salvia pachyphy lla
1
Salvia spat hac ea
4
Salvia ly rat a
0
Salvia (Lamiaceae)
Salvia pent stemonoides
3
Dry petes roxburghii
0
Salvia divinorum
7
Cas sia s enna
11
Cassia (out group from Salv ia)
41
Cas sia didy mobotry a
Fig -3 Phylogenetic tree from 92 rbcL sequences belongs to 90 taxa of 12 genera and 10 families by the Neighbor-Joining method.
Numbers above branches indicate percentage of 500 bootstrap replications. Horizontal bar indicates the nucleotide substitution scale
International Journal of Bioinformatics Research, ISSN: 0975–3087, Volume 1, Issue 2, 2009
35
Molecular phylogeny of angiospermic plant families using RBCL gene sequences
7
0
Piper ni grum
Piper w all ichii
0
Piper ka dsura
0
Piper la eti spi cum
0
Piper sa rmentosum
P ipe r ( Pipe ra c e a e )
0
Piper longum
0
Piper chinense
0
Piper ha ncei
0
Piper be tle
0
Piper austrosine nse
0
Salvia arisanensis
0
Salvia plebeia
0
Asparagus officinalis
0
Salvia hayatana
3
Salvia py gmaea
0
Piper hainanense
2
Salvia nipponic a
3
Salvia glabresc ens
11
Mentha rotundifolia
65
Salvia lut es cens
Mentha longifolia
16
13
0
Austrobryonia micra ntha(2)
Austrobryonia a rgilli cola
61
Austrobryonia micra ntha
86
Austrobrypnia ( Cuc urbit a c e a e )
Austrobryonia pilbarensis
Austrobryonia centra lis
Salvia hirsuta
2
87
6
Sol anum chil ense
Sola num (S ola na c e a e )
Sol anum penne lli i
Sax ifraga integrifolia
8
Dry petes floribunda
72
0
Dry petes diversifolia
12
Sax ifraga st ellaris
1
Cas sia fistula
1
Dry petes brownii
5
Dry petes lateriflora
7
0
Dry petes deplanc hei
3
Drypetes (Putranjivaceae)
Dry petes st audtii
5
Dry petes gilgiana
7
7
Dry petes fallax
Asparagus coc hinchinens is
Canna tuerc kheimii
Salvia officinalis
0
Salvia (Lamiaceae)
3
Salvia lyc ioides
5
Salvia vis cosa
Salvia involucrata
Salvia tiliifolia
0
Salvia (Lamiac eae)
Cas sia grandis
1
Salvia polys tac hy a
8
21
Salvia palaestina
95
Salvia tex ana
10
Salvia sc larea
3
Salvia subincis a
Salvia misella
0
Salv ia (Lamiac eae)
Salvia verbenaca
Salvia sy lvestris
1
6
Salvia pratensis
Asparagus capensis
0
Salvia viridis
11
6
0
Phylla nthus flex uosus
4
Phylla nthus l okohensis
8
Phylla nthus pol yphyllus
8
P hylla nthus ( Phylla nt ha c e a e )
Phylla nthus cal yci nus
14
0
Phylla nthus nummul ari ifolius
Phylla nthus flui tans
8
Phylla nthus j uglandi fol ius
37
Phylla nthus nutans
79
Phylla nthus flagel liformis
5
Dry petes lit toralis
Salvia staminea
Salvia (Lamiaceae)
89
Salvia ringens
20
Trichosa nthe s schlechteri
47
Trichosa nthe s cucumerina
T ric hosa nthe s ( Cuc urbit a c e a e )
90
0
Trichosa nthe s penta phyll a
9
Trichosa nthe s bra cte ata
Salvia tarax acifolia
96
0
4
Canna indic a
Canna (Cannaceae)
Canna glauc a
Salvia nubic ola
Salvia nilotic a
0
Mentha s uaveolens
16
Salvia pents temonoides
88
Salvia summa
12
Salvia roemeriana
3
Salvia spathac ea
1
Salvia pachyphylla
6
Salvia lyrata
0
Mentha longifolia (2)
5
Dry petes roxburghii
2
Salvia divinorum
7
Cas sia s enna
12
Cassia (Caesalpinioide)
40
Cas sia didy mobotry a
Fig -4 Phylogenetic tree from 92 rbcL sequences belongs to 90 taxa of 12 genera and 10 families using Minimum Evolution method.
Numbers above branches indicate percentage of 500 bootstrap replications.
36
Bioinfo Publications, International Journal of Bioinformatics Research, ISSN: 0975–3087, Volume 1, Issue 2, 2009