Transcript RICE PHYLOGENY REVISITED

RICE PHYLOGENY
REVISITED
N. K H I R I P E T
V. POTLURI
AND
Some Background
Rice is staple for more than half of the
world’s population
Large collection of germplasm [ >10000
accessions] held at IRRI
Plant breeders/genecists use these to
develop news cultivars
For this purpose, evolutionary
history/phylogeny is important
Rice genetics
Rice is usually a diploid, but tetraploids are
not uncommon
The diploid genome is classified as
AA,BB,CC,DD,EE,FF,GG,HH.KK
The tetraploids are mostly allo
BBCC,CCDD,HHJJ,HHKK
Taxa in the Genus Oryza: the species and
genome groups
Table 1-1. Taxa in the genus Oryza: the species and genome groups. [From IRRI]
Species2nGenomeDistribution
Sect. Oryza Ser. Sativae
O. barthii
O. glaberrima
O. glumaepatula
O. longistaminata
O. meridionalis
O. nivara
O. rufipogon
O. sativa
Ser. Latifoliae
O. eichingeri
O. alta
O. grandiglumis
O. latifolia
O. minuta
O. punctata
O. rhizomatis
24
24
24
24
24
24
24
AA
AA
AA
AA
AA
AA
AA
Sub-Saharan Africa
West Africa
South, Central America
Sub-Saharan Africa
Tropical Australia
Tropical, Subtropical Asia
Tropical, Subtropical Asia, Tropical Australia
24
24
48
48
48
48
24, 48
24
AA
CC
CCDD
CCDD
CCDD
BBCC
BB, BBCC
CC
Worldwide
South Asia, East Africa
South, Central America
South, Central America
South, Central America
Philippines, Papua New Guinea
Sub-Saharan Africa
Sri Lanka
O. officinalis
24,48 CC, BBCC Tropical, Subtropical Asia
Ser. Australienses
O. australiensis
24
EE
ropical Australia
Sect. Brachyantha Ser. Brachyanthae
O. brachyantha
24
FF
Sub-Saharan Africa
Sect. Padia Ser. Meyerianae
O. granulata
24
GG
South, Southeast Asia
O. meyeriana
24
GG
Southeast Asia
O. neocaledonica
24
??
New Caledonia
Ser. Ridleyanae
O. longiglumis
48
HHJJ
Indonesia (Irian Jaya), Papua New Guinea
O. ridleyi 48HHJJSoutheast Asia
Ser. Schlechterianae
O. schlechteri
48
HHKK
Indonesia (Irian Jaya), Papua New Guinea
So, What is the Problem?
No problem really, but
We would like to have a better tool to
understand the interrelationships of
various cultivars
Which in turn should help breeders and
genecists
Well then, what is the plan?
We chose four important enzymes, viz
Maturase
Integrase
Alcohol dehydrogenase I and
Alcohol dehydrogenase II
Then,
We got the protein sequence data [from
NCBI]for these enzymes for 8 cultivars
O. sativa
Ser. Latifoliae
O. eichingeri
O. alta
O. grandiglumis
O. latifolia
O. minuta
O. punctata
O. rhizomatis
24
AA
Worldwide
24
48
48
48
48
24, 48
24
CC
CCDD
CCDD
CCDD
BBCC
BB, BBCC
CC
South Asia, East Africa
South, Central America
South, C. America
South, C.America
Philippines, PN G
Sub-Saharan Africa
Sri Lanka
Hold On
Change of Speaker
Methods [contd.]
We constructed a phylogenetic tree for
each enzyme using Workbench using
Clustalw
We calculated the distance matrix from
this tree using ClustalDist
[Methods-contd.]
We converted the distance matrix to
digital form to be used in JBenzer and
GDE using PERL scripts.
Threshold
We used a median point between the
distance values as a threshold. We will
discuss the implications of changing the
threshold after presenting the results
Finally [methods contd.]
We combined all the distance matrices
and combined in to one matrix and
Digitized the matrix for use in JBenzer and
GDE to obtain a single Benzer plot
Biology Workbench
clustalw
clustdist
clustdist2benzer.pl
sequences
benzer2gde.pl
Clustdist2benzer.pl
OL
OG
OA
OE
OR
OS
OP
OM
(1)
(2)
(3)
(4)
(5)
(6)
(7)
(8)
0.000
0.002
0.002
0.008
0.006
0.013
0.015
0.015
0.002
0.000
0.000
0.006
0.004
0.012
0.013
0.013
0.002
0.000
0.000
0.006
0.004
0.012
0.013
0.013
0.008
0.006
0.006
0.000
0.002
0.013
0.015
0.015
0.006
0.004
0.004
0.002
0.000
0.012
0.013
0.013
JBENZER
8
1,1,1,0,0,0,0,0,OL
1,1,1,0,1,0,0,0,OG
1,1,1,0,1,0,0,0,OA
0,0,0,1,1,0,0,0,OE
0,1,1,1,1,0,0,0,OR
0,0,0,0,0,1,0,0,OS
0,0,0,0,0,0,1,1,OP
0,0,0,0,0,0,1,1,OM
0.013
0.012
0.012
0.013
0.012
0.000
0.015
0.015
0.015
0.013
0.013
0.015
0.013
0.015
0.000
0.000
0.015
0.013
0.013
0.015
0.013
0.015
0.000
0.000
Benzer2gde.pl
JBENZER
8
1,1,1,0,0,0,0,0,OL
1,1,1,0,1,0,0,0,OG
1,1,1,0,1,0,0,0,OA
0,0,0,1,1,0,0,0,OE
0,1,1,1,1,0,0,0,OR
0,0,0,0,0,1,0,0,OS
0,0,0,0,0,0,1,1,OP
0,0,0,0,0,0,1,1,OM
"OL","OG"
"OL","OA"
"OG","OL"
"OG","OA"
"OG","OR"
"OA","OL"
"OA","OG"
"OA","OR"
"OE","OR"
"OR","OG"
"OR","OA"
"OR","OE"
"OS","OS"
"OP","OM"
"OM","OP"
Maturase
OL
OG
OA
OE
OR
OS
OP
OM
Integrase
OA
OG
OL
OS
OP
OE
OR
OM
Alcohol dehydrogenase I
OP
OA
OG
OS
OR
OE
OL
OM
Alcohol dehydrogenase II
OL
OG
OA
OM
OP
OS
OE
OR
Combined Matrix
0
0.159
0.146
0.138
0.103
0.131
0.141
0.185
0.159
0
0.055
0.137
0.118
0.16
0.179
0.264
0.146
0.055
0
0.135
0.092
0.138
0.158
0.253
0.138
0.137
0.135
0
0.124
0.066
0.047
0.223
0.103
0.118
0.092
0.124
0
0.127
0.147
0.225
0.131
0.16
0.138
0.066
0.127
0
0.04
0.228
0.141
0.179
0.158
0.047
0.147
0.04
0
0.238
0.185
0.264
0.253
0.223
0.225
0.228
0.238
0
0.128
0.157
0.135
0.059
0.124
0.007
0.047
0.234
OP
OE
OR
OL
OM
OA
OG
OS
Back to the
Beginning
Conclusions
The phylogenetic trees and JBenzer differ
in some respects
JBenjer plots show O.sativa [2n=24,AA]to
be unique but in phylogenic trees,it is
clustered with O.punctata [4x,48,BBCC] or
O.grandiglumis and O.alta[4x,48,CCDD]
BUT
Remember the threshold values?
We used a median value from a matrix
table and it does give relationships which
can be related to their genomes.
IF we change the threshold value, the
Benjer plot will change which brings the
question whether relationships based on
distance matrices need re-visitation
We realize that phylogenetic trees based
on distance matrices have been used for
so long
However, different scientists calculate and
interpret the distance matrix results
differently
Does it help if the input data is obtained
differently from the beginning in binary
format
We used a very limited data to compare
but it does indicate that we may have to
look at the phylogenetic relationships
using improved methods to minimize and
/or to understand better varied
interpretations
Finally
A Gigabyte of Thanks to
ALL THE BIOQUEST STAFF AND THE
PARTICIPANTS OF THIS WORKSHOP
WHO MADE OUR PARTICIPATION IN
THE WORKSHOP A MEMORABLE AND
REWARDING EXPERIENCE