Comparative Sequence Analysis of Genes from Rice ssp. indica
and japonica ---- A Case Study
Longjiang Fan1,2（樊龙江）
Jianbin Wang1（王建斌） Yang Zhang1 (张扬)
（Bioinplant Lab, 1. Institute of Bioinformatics / 2. Institute of Seed Science, Zhejiang University,
Hangzhou 310029; E-mail fanlj@zju.edu.cn / bioinplant@zju.edu.cn）
Comparative sequence analysis of genes from oryza sativa L. ssp. indica and japonica is an important
part in rice genomics research. The releases of draft genome sequences of indica rice cultivar 9311
and about half genome sequences of japonica rice cultivar Nipponbare make the analysis available.
As a case study, here we compared the sequences of superoxide dismutase (SOD, EC1.15.1.1) gene
from the two subspecies respectively and offer some clues for large scale comparative research of
them.
Rice SOD gene sequences in public databases
SOD catalyzes the first step in the scavenging system of active oxygen species by the
disproportionation of superoxide anion radical to hydrogen peroxide and molecular oxygen. SOD has
multiple isoforms, which are classified by their metal co-factor as copper/zinc (Cu/Zn), manganese
(Mn) and iron (Fe) forms. These isoforms are distributed in different subcellular locations. In higher
plants, Cu/Zn-SOD is localized mainly in plastids and cytosol. Mn-SOD is localized predominantly in
the mitochondrial matrix, and Fe-SOD is observed in chloroplasts. In rice, the cDNAs and genes
corresponding to most SOD isoforms have been isolated and characterized (Kaminaka et al., 1999). In
GenBank, There are total 13 rice SOD entries which are mostly from japonica rice (Table1). Genes
from Nipponbare were searched against the Rice GD (http://btn.genomics.org.cn/rice), using BLAST
(2002-3-20). We were fortunate that all of them were found in contigs of the database (all E-values
equal to 0).
Table 1 Entries of rice SOD mRNA/gene sequences in GenBank and the Rice GD
mRNA
SOD isoforms
Cu/Zn-SOD
Plastid
CytosolA
CytosolB
Mn-SOD
Mn-SODA
Mn-SODB
Fe-SOD
japonica
(Nipponbare)
D85239
D00999
D01000
L19436
AB014056
Genomic DNA
indica
(IR36)
japonica
(Nipponbare)
indica
(9311)
L36320
AB026724
L19435
L19434
Contig20429
Contig7075
Contig11946
AB026725
Contig736
AP000399
Contig5035 and
Contig13401
L34038
L34039
UniGene Clusters
UniGene is an experimental system for automatically partitioning GenBank sequences into a
non-redundant set of gene-oriented clusters. Each UniGene cluster contains sequences that represent a
unique gene. All sequences from GenBank in Table1 fall into five UniGene clusters (Table2). Same
SOD isoform gene sequences from japonica and indica rice all fall into same cluster (see Os.186 and
Os.4610)
Table 2 UniGene clusters of rice SOD gene sequences
UniGene
Os.186
Os.4169
Os.5522
Os.4610
Os.3583
mRNA/GENE
SEQUENCES
Description
Oryza sativa mRNA for copper/zinc-superoxide
dismutase, complete cds, clone:RSODA
Oryza sativa mRNA for copper/zinc-superoxide
dismutase, complete cds, clone:RSODB
Oryza
sativa
mRNA
for
plastidic
copper/zinc-superoxide dismutase, complete cds
Rice mitochondrial manganese-superoxide
dismutase (sodAOs1) mRNA, complete cds
Oryza sativa mRNA for iron-superoxide
dismutase, complete cds
D00999 /L19435/L36320
D01000/L19434
D85239/AB026724
L19436/ AB026725
/L34038/L34039
AB014056/AP000399
Differences in genomic DNA level
The Rice GD BLAST results of all SOD genes from Nipponbare were summarized (Table3). In
general, the differences between SOD gene sequences from japonica and indica rice are small in
genomic level (gene/promoter) with a view to SNP density and sequencing errors, etc. Mn-SOD gene
may be an exception and there is a big gap (856bp) between the genes from japonica and indica rice
(see figure). The gap doesn’t belong to exon region of Mn-SOD gene by and large based on its mRNA
sequence. There is a 102bp-overlapped region between two matched regions in a contig for CytosolA
(Cu/Zn-SOD) genes. This may be a wrong assembling in the Rice GD.
M1-337bp
unM-23bp
M2-154bp
unM2-856bp
M3-764bp
unM3-43bp
M4-2280bp
Mn-SOD Genes from
indica (upper) and
japonica (down)
rice
0
500
1000
1500
2000
2500
3000
Gene size (bp)
3500
4000
4500
Table 3 Differences between SOD gene sequences from japonica and indica rice in genomic
level*
Gene (bp)
Promoter (bp)
Gene
size
Identity(%)
of
matched region
Unmatched
region/gap
Before
ATG
Identity(%) of
matched
region
Cu/Zn-SOD
CytosolA
CytosolB
Plastid
1548
1172
2626
100/100
100
99.7/98.7/100
102,overlapped
20,14/
-605
-600
-610
99.7
100
99.1/100§
Mn-SOD
Mn-SODA
3352
23/856,43
-602
98.3
Fe-SOD
1472
99.7/99.4/99.9/9
9.0
100/100
/38, two contigs
-600
100
SOD isoforms
*based on the Rice GD BLAST research with default value;
§there
is a 30bp unmatched region
Differences in mRNA and protein level
SOD
isoforms
Cu/Zn-SOD
CytosolA
Mn-SOD
Mn-SODA
mRNA sequence(bp)
Protein sequence(aa)
G+C content
CDS size
Different
number
Size
Different
number
japonica/indica
(%)
459
1
152
0
52.1/52.1
696
2
231
1
58.0/58.0
Conclusions
Difference between genes from japonica and indica rice is small in this case (SOD gene). Particular,
this difference is few at mRNA and protein sequence level. But the things make sense are what
make for the difference between the two subspecies. Do regulatory sequences or transcription
factors play important roles in it?
SOD genes are single-copy genes in the indica rice genome. Only one significant sequence (contig)
was returned for all SOD gene sequences in BLAST search from the Rice GD. It was reported that
Mn-SOD gene is a single-copy gene in rice ((Kaminaka et al., 1999).
The Rice GD contributes a comprehensive functional coverage of rice genome based on this research.
第一作者简介
樊龙江，37 岁，博士，浙江大学生物信息学研究所/种子科学与工程研究所副教
授，目前主要从事水稻基因组生物信息学、数量遗传等方面研究。已发表 SCI
论文 4 篇，国内一级学报论文 10 篇，获国家教委科技进步二等奖(1991)和农业
部(1999)、浙江省(2001)科技进步三等奖各一次。
实验室（Bioinplant Lab）主页:
http://www.cab.zju.edu.cn/depart/nx/Bioinplant/bioinplant_page.htm
E-mail: fanlj@zju.edu.cn 或 bioinplant@zju.edu.cn