Oryza Sativa Japonica Research Articles

Stress-induced cytokinin synthesis increases drought tolerance through the coordinated regulation of carbon and nitrogen assimilation in rice.

The effects of water deficit on carbon and nitrogen metabolism were investigated in flag leaves of wild-type and transgenic rice (Oryza sativa japonica 'Kitaake') plants expressing ISOPENTENYLTRANSFERASE (IPT; encoding the enzyme that mediates the rate-limiting step in cytokinin synthesis) under the control of P(SARK), a maturation- and stress-induced promoter. While the wild-type plants displayed inhibition of photosynthesis and nitrogen assimilation during water stress, neither carbon nor nitrogen assimilation was affected by stress in the transgenic P(SARK)::IPT plants. In the transgenic plants, photosynthesis was maintained at control levels during stress and the flag leaf showed increased sucrose (Suc) phosphate synthase activity and reduced Suc synthase and invertase activities, leading to increased Suc contents. The sustained carbon assimilation in the transgenic P(SARK)::IPT plants was well correlated with enhanced nitrate content, higher nitrate reductase activity, and sustained ammonium contents, indicating that the stress-induced cytokinin synthesis in the transgenic plants played a role in maintaining nitrate acquisition. Protein contents decreased and free amino acids increased in wild-type plants during stress, while protein content was preserved in the transgenic plants. Our results indicate that the stress-induced cytokinin synthesis in the transgenic plants promoted sink strengthening through a cytokinin-dependent coordinated regulation of carbon and nitrogen metabolism that facilitates an enhanced tolerance of the transgenic plants to water deficit.

Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data

BackgroundRice research has been enabled by access to the high quality reference genome sequence generated in 2005 by the International Rice Genome Sequencing Project (IRGSP). To further facilitate genomic-enabled research, we have updated and validated the genome assembly and sequence for the Nipponbare cultivar of Oryza sativa (japonica group).ResultsThe Nipponbare genome assembly was updated by revising and validating the minimal tiling path of clones with the optical map for rice. Sequencing errors in the revised genome assembly were identified by re-sequencing the genome of two different Nipponbare individuals using the Illumina Genome Analyzer II/IIx platform. A total of 4,886 sequencing errors were identified in 321 Mb of the assembled genome indicating an error rate in the original IRGSP assembly of only 0.15 per 10,000 nucleotides. A small number (five) of insertions/deletions were identified using longer reads generated using the Roche 454 pyrosequencing platform. As the re-sequencing data were generated from two different individuals, we were able to identify a number of allelic differences between the original individual used in the IRGSP effort and the two individuals used in the re-sequencing effort. The revised assembly, termed Os-Nipponbare-Reference-IRGSP-1.0, is now being used in updated releases of the Rice Annotation Project and the Michigan State University Rice Genome Annotation Project, thereby providing a unified set of pseudomolecules for the rice community.ConclusionsA revised, error-corrected, and validated assembly of the Nipponbare cultivar of rice was generated using optical map data, re-sequencing data, and manual curation that will facilitate on-going and future research in rice. Detection of polymorphisms between three different Nipponbare individuals highlights that allelic differences between individuals should be considered in diversity studies.Electronic supplementary materialThe online version of this article (doi:10.1186/1939-8433-6-4) contains supplementary material, which is available to authorized users.

Rice Annotation Project Database (RAP-DB): An Integrative and Interactive Database for Rice Genomics

The Rice Annotation Project Database (RAP-DB, http://rapdb.dna.affrc.go.jp/) has been providing a comprehensive set of gene annotations for the genome sequence of rice, Oryza sativa (japonica group) cv. Nipponbare. Since the first release in 2005, RAP-DB has been updated several times along with the genome assembly updates. Here, we present our newest RAP-DB based on the latest genome assembly, Os-Nipponbare-Reference-IRGSP-1.0 (IRGSP-1.0), which was released in 2011. We detected 37,869 loci by mapping transcript and protein sequences of 150 monocot species. To provide plant researchers with highly reliable and up to date rice gene annotations, we have been incorporating literature-based manually curated data, and 1,626 loci currently incorporate literature-based annotation data, including commonly used gene names or gene symbols. Transcriptional activities are shown at the nucleotide level by mapping RNA-Seq reads derived from 27 samples. We also mapped the Illumina reads of a Japanese leading japonica cultivar, Koshihikari, and a Chinese indica cultivar, Guangluai-4, to the genome and show alignments together with the single nucleotide polymorphisms (SNPs) and gene functional annotations through a newly developed browser, Short-Read Assembly Browser (S-RAB). We have developed two satellite databases, Plant Gene Family Database (PGFD) and Integrative Database of Cereal Gene Phylogeny (IDCGP), which display gene family and homologous gene relationships among diverse plant species. RAP-DB and the satellite databases offer simple and user-friendly web interfaces, enabling plant and genome researchers to access the data easily and facilitating a broad range of plant research topics.

A map of rice genome variation reveals the origin of cultivated rice

Crop domestications are long-term selection experiments that have greatly advanced human civilization. The domestication of cultivated rice (Oryza sativa L.) ranks as one of the most important developments in history. However, its origins and domestication processes are controversial and have long been debated. Here we generate genome sequences from 446 geographically diverse accessions of the wild rice species Oryza rufipogon, the immediate ancestral progenitor of cultivated rice, and from 1,083 cultivated indica and japonica varieties to construct a comprehensive map of rice genome variation. In the search for signatures of selection, we identify 55 selective sweeps that have occurred during domestication. In-depth analyses of the domestication sweeps and genome-wide patterns reveal that Oryza sativa japonica rice was first domesticated from a specific population of O. rufipogon around the middle area of the Pearl River in southern China, and that Oryza sativa indica rice was subsequently developed from crosses between japonica rice and local wild rice as the initial cultivars spread into South East and South Asia. The domestication-associated traits are analysed through high-resolution genetic mapping. This study provides an important resource for rice breeding and an effective genomics approach for crop domestication research.Supplementary informationThe online version of this article (doi:10.1038/nature11532) contains supplementary material, which is available to authorized users.

Interdomain Disulfide Bridge in the Rice Granule Bound Starch Synthase I Catalytic Domain as Elucidated by X-Ray Structure Analysis

The catalytic domain of rice (Oryza sativa japonica) granule bound starch synthase I (OsGBSSI-CD) was overexpressed and the three-dimensional structures of the ligand-free and ADP-bound forms were determined. The structures were similar to those reported for bacterial and archaeal glycogen synthases, which belong to glycosyltransferase family 5. They had Rossmann fold N- and C-domains connected by canonical two-hinge peptides, and an interdomain disulfide bond that appears to be conserved in the Poaceae plant family. The presence of three covalent linkages might explain why both OsGBSSI-CD structures adopted only the closed domain arrangement.

In silico assessment: Suggested homology of chickpea (Cicer arietinum L.) legumin and prediction of ACE-inhibitory peptides from chickpea proteins using BLAST and BIOPEP analyses

Three protein sequences, chickpea legumin α- and β-subunits [Cicer arietinum] (NCBI accession number: gi|6273402), oat 12S seed storage globulin 1 (NCBI accession number: gi|134918) and rice glutelin precursor [Oryza sativa (japonica cultivar-group)] (NCBI accession number: gi|62546207) were chosen for sequence alignments using BLAST analysis. The sequence alignments gave approximately 30% similarity of AA sequences with chickpea legumin vs. oat 12S globulin 1 and chickpea legumin vs. rice glutelin precursor; the oat 12S globulin 1 and rice glutelin precursor exhibited relatively high sequence homology of 63%. In silico, BIOPEP results showed that the chickpea legumin and provicilin precursor demonstrated either di- or tri-peptides with a total of 177 and 133 potential angiotensin I-converting enzyme (ACE) inhibitory peptides, respectively. Ficain and proteinase K were the proposed proteases that could theoretically release greater numbers of predicted ACE-inhibitory peptides (34 and 35, respectively) from chickpea legumin and provicilin precursor; in addition, the simulation of human gastrointestinal digestion using a combination of pepsin, trypsin and chymotrypsin A could liberate a sum of 23 predicted ACE-inhibitory peptides from these two proteins.

Estimation of Sequencing Error Rates Present in Genome Databases

ABSTRACTThe quality of next-generation sequencing data is a major problem in today's bioinformatics. The validation of sequences, either by re-sequencing or pure statistical error evaluation, is the tool needed to ensure the correct results of all following research done with the data.Estimating the error rates in genome databases gives an idea about the level of inherited errors in genome sequences. It is important as these kinds of errors have cumulative effect on every following step of analysis of the sequences. Here we present a way to define the error level in a genome, using two different databases: National Center of Biotechnology Information (NCBI) (as a verified one) and Resources for Plant Comparative Genomics (PlantGDB) as reference. Based on the most conservative regions in every genome—donor/acceptor splice sites (the canonical forms are the dinucleotides GT or GC and AG), we applied statistical methods to derive the NCBI error level for Oryza sativa (japonica cultivar) genome.

Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm

A high-density haplotype map recently enabled a genome-wide association study (GWAS) in a population of indica subspecies of Chinese rice landraces. Here we extend this methodology to a larger and more diverse sample of 950 worldwide rice varieties, including the Oryza sativa indica and Oryza sativa japonica subspecies, to perform an additional GWAS. We identified a total of 32 new loci associated with flowering time and with ten grain-related traits, indicating that the larger sample increased the power to detect trait-associated variants using GWAS. To characterize various alleles and complex genetic variation, we developed an analytical framework for haplotype-based de novo assembly of the low-coverage sequencing data in rice. We identified candidate genes for 18 associated loci through detailed annotation. This study shows that the integrated approach of sequence-based GWAS and functional genome annotation has the potential to match complex traits to their causal polymorphisms in rice.

The Checkered Prehistory of Rice Movement Southwards as a Domesticated Cereal—from the Yangzi to the Equator

AbstractThis paper discusses the origins ofOryza sativa japonicarice cultivation in the Yangzi region of China and asks how and with which migrating human populations it spread south to reach Taiwan by 3,000 BC and Southeast Asia by 2,000 BC. The perspective adopted is that the spread of rice was driven mainly by demographic expansion, associated with a spread of languages and archaeological material culture. Environmental barriers also played major roles in establishing a “pause, adapt, spread, pause again” mode of movement, such barriers relating to availability of rainfall and alluvial land, latitude (photoperiodism) and climatic seasonality, and the prior presences of other populations, in some cases with vegetative gardening systems that did not involve rice or other cereals. Contingency also played its part in rice history, as we can see with the inability of this crop to spread into Oceania in part due to the route followed by Neolithic colonizers.

Transcriptome map of plant mitochondria reveals islands of unexpected transcribed regions

BackgroundPlant mitochondria contain a relatively large amount of genetic information, suggesting that their functional regulation may not be as straightforward as that of metazoans. We used a genomic tiling array to draw a transcriptomic atlas of Oryza sativa japonica (rice) mitochondria, which was predicted to be approximately 490-kb long.ResultsWhereas statistical analysis verified the transcription of all previously known functional genes such as the ones related to oxidative phosphorylation, a similar extent of RNA expression was frequently observed in the inter-genic regions where none of the previously annotated genes are located. The newly identified open reading frames (ORFs) predicted in these transcribed inter-genic regions were generally not conserved among flowering plant species, suggesting that these ORFs did not play a role in mitochondrial principal functions. We also identified two partial fragments of retrotransposon sequences as being transcribed in rice mitochondria.ConclusionThe present study indicated the previously unexpected complexity of plant mitochondrial RNA metabolism. Our transcriptomic data (Oryza sativa Mitochondrial rna Expression Server: OsMES) is publicly accessible at [http://bioinf.mind.meiji.ac.jp/cgi-bin/gbrowse/OsMes/#search].

An Son and the Neolithic of Southern Vietnam

Between 4500 and 3500 years ago, partially intrusive Neolithic populations in the riverine basins of mainland Southeast Asia began to form mounded settlements and to develop economies based on rice cultivation, fishing, hunting, and the domestication of animals, especially pigs and dogs. A number of these sites have been excavated in recent years and they are often large mounds that can attain several meters in depth, comprising successive layers of alluvial soil brought in periodically to serve as living floors. The site of An Son is of this type and lies in a small valley immediately north of the Mekong Delta in southern Vietnam. Excavated on five occasions since 1978, and most recently in 2009, it was occupied from the late third into the late second millennium b.c . An Son has produced evidence that attests the domestication of pigs and dogs in all layers apart (perhaps) from the most basal one, which was not investigated in 2009, together with the growing of rice of the subspecies Oryza sativa japonica , of Chinese Neolithic origin. The oldest pottery has simple incised and punctate zoned decoration with parallels in central Thailand, especially in the basal phases at Nong Nor and Khok Phanom Di. From its middle and later occupation phases (1800–1200 b.c .), An Son has produced a number of supine extended burials with finely decorated pottery grave goods that carry some unique forms, especially vessels with wavy or serrated rims. The An Son burials represent a Neolithic population that expressed a mixture of both indigenous Hoabinhian and more northerly (probably Neolithic southern Chinese) cranial and dental phenotypes, perhaps representing a likely ancestral population for some of the modern Austroasiatic-speaking populations of mainland Southeast Asia.

Anti-inflammatory effects of peptide fragments of H2A histone and Oryza Sativa Japonica protein

Anti-inflammatory drugs are often of limited use due to low efficacy and toxic effects. The present study describes the anti-inflammatory effects of a novel nonapeptide termed IIIM1, using the mouse hind paw edema as an experimental model of inflammation. Multiple prophylactic injections of IIIM1 resulted in a significant reduction in carrageenan-induced foot pad swelling, both in mice and rats. A single prophylactic treatment of the peptide caused the maximal effect at 7–9 days between the initial peptide treatment and the subsequent carrageenan injection. A reduced inflammatory reaction was observed in transgenic mice constitutively expressing the peptide. A marked decrease in oxidative burst was observed in activated peritoneal macrophages obtained from peptide-treated mice. Furthermore, the sera of IIIM1-treated mice caused a significant decrease in the oxidative burst of macrophages. In addition, the reduction of hind paw swelling in mice injected with the sera of IIIM1-treated mice strongly suggests the presence of a circulating inducible factor responsible for the anti-inflammatory effect of the peptide. Previous LC/MS/MS analysis revealed the presence of a new peptide, termed RA1, in the sera of IIIM1-treated mice. RA1 was identified as a fragment of the Oryza Sativa Japonica protein. The anti-inflammatory effect of RA1 as evidenced by the reduction in carrageenan-induced hind paw swelling corresponded with the decrease in the oxidative burst of macrophages treated in vitro with this peptide. In conclusion, both IIIM1 and RA1 represent potential agents for the efficient treatment of inflammatory diseases that are currently incurable using presently available drugs.

In silico analysis of cis-acting regulatory elements in 5′ regulatory regions of sucrose transporter gene families in rice ( Oryza sativa Japonica) and Arabidopsis thaliana

The regulation of gene expression involves a multifarious regulatory system. Each gene contains a unique combination of cis-acting regulatory sequence elements in the 5′ regulatory region that determines its temporal and spatial expression. Cis-acting regulatory elements are essential transcriptional gene regulatory units; they control many biological processes and stress responses. Thus a full understanding of the transcriptional gene regulation system will depend on successful functional analyses of cis-acting elements. Cis-acting regulatory elements present within the 5′ regulatory region of the sucrose transporter gene families in rice ( Oryza sativa Japonica cultivar-group) and Arabidopsis thaliana, were identified using a bioinformatics approach. The possible cis-acting regulatory elements were predicted by scanning 1.5 kbp of 5′ regulatory regions of the sucrose transporter genes translational start sites, using Plant CARE, PLACE and Genomatix Matinspector professional databases. Several cis-acting regulatory elements that are associated with plant development, plant hormonal regulation and stress response were identified, and were present in varying frequencies within the 1.5 kbp of 5′ regulatory region, among which are; A-box, RY, CAT, Pyrimidine-box, Sucrose-box, ABRE, ARF, ERE, GARE, Me-JA, ARE, DRE, GA-motif, GATA, GT-1, MYC, MYB, W-box, and I-box. This result reveals the probable cis-acting regulatory elements that possibly are involved in the expression and regulation of sucrose transporter gene families in rice and Arabidopsis thaliana during cellular development or environmental stress conditions.

Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq

The functional complexity of the rice transcriptome is not yet fully elucidated, despite many studies having reported the use of DNA microarrays. Next-generation DNA sequencing technologies provide a powerful approach for mapping and quantifying the transcriptome, termed RNA sequencing (RNA-seq). In this study, we applied RNA-seq to globally sample transcripts of the cultivated rice Oryza sativa indica and japonica subspecies for resolving the whole-genome transcription profiles. We identified 15,708 novel transcriptional active regions (nTARs), of which 51.7% have no homolog to public protein data and >63% are putative single-exon transcripts, which are highly different from protein-coding genes (<20%). We found that approximately 48% of rice genes show alternative splicing patterns, a percentage considerably higher than previous estimations. On the basis of the available rice gene models, 83.1% (46,472 genes) of the current rice gene models were validated by RNA-seq, and 6228 genes were identified to be extended at the 5' and/or 3' ends by at least 50 bp. Comparative transcriptome analysis demonstrated that 3464 genes exhibited differential expression patterns. The ratio of SNPs with nonsynonymous/synonymous mutations was nearly 1:1.06. In total, we interrogated and compared transcriptomes of the two rice subspecies to reveal the overall transcriptional landscape at maximal resolution.

Genetic diversity and evolutionary relationships in genus Oryza revealed by using highly variable regions of chloroplast DNA

We studied the phylogeny of the genus Oryza using chloroplast DNA sequences. To identify regions containing sufficient variation for elucidating the relationship of closely related species with fine resolution and high reliability, we first compared the complete chloroplast sequences of Oryza sativa japonica, O. sativa indica, and O. nivara, and identified regions containing many variant sites. Nucleotide sequences of the variant regions were newly determined in 19 Oryza species including 58 cultivated and wild strains. An in silico pre-analysis of the whole chloroplast genome and subsequent nucleotide sequencing of the regions with the greatest number of variant sites, which were disclosed to be hot spots by the in silico pre-analysis, enabled us to examine genetic diversity in the genus Oryza with excellent resolution. Based on phylogenetic trees constructed using highly diverged regions in the chloroplast genome, we discuss the maternal relationships among Oryza species.

Amelioration of experimental autoimmune encephalitis by novel peptides: Involvement of T regulatory cells

The purpose of the present study was to develop a peptide for treatment of multiple sclerosis (MS). We have tested the effect of a novel anti-inflammatory peptide (KGHYAERVG, termed IIIM1) on experimental autoimmune encephalitis (EAE), an animal model of MS. Our findings demonstrate significant reduction in neurological score following oral administration of IIIM1. Structural studies revealed that the entire peptide is required for activity. The peptide caused significant reduction in IL17, interferon γ, IL23 and IL12 production by isolated splenocytes and concomitant elevation of anti-inflammatory cytokines. IIIM1 elevated T regulatory cells (Tregs, CD4 +CD25 +FoxP3 +) in brain and spleen of EAE mice. Similar proliferative effect was observed in isolated human and mouse Tregs in vitro. Stimulation of Tregs by IIIM1 caused production of a new peptide termed RA1 present in Oryza Sativa Japonica group. This Japanese rice peptide ameliorated neurological symptoms in the EAE model. Similar beneficial effect was observed upon oral administration of an extract of Japanese rice. In conclusion, oral treatment with IIIM1 ameliorates EAE symptoms via stimulation of Tregs to proliferate and produce RA1 which reduces EAE symptoms. RA1 might be involved in the relatively low prevalence of MS in Japan and other Japanese rice-eating populations.

The link between multiple sclerosis, T regulatory cells and Japanese rice (96.1)

Abstract The purpose of the present study was to develop a peptide for treatment of multiple sclerosis (MS). We have tested the effect of a novel antiinflammatory peptide (KGHYAERVG, termed IIIM1) on experimental autoimmune encephalitis (EAE), an animal model of MS. Our findings demonstrate significant reduction in neurological score following oral administration of IIIM1, as compared to the control groups received the vehicle (saline). Structural studies revealed that the entire peptide is required for activity. The peptide caused significant reduction in IL17, interferon gamma and IL12 production by isolated splenocytes and concomitant elevation of antiinflammatory cytokines. IIIM1 elevated T regulatory cells (Tregs, CD4+CD25+FoxP3+) in brain and spleen of EAE mice. Similar proliferative effect was observed in isolated human and mouse Tregs in vitro. Stimulation of Tregs by IIIM1 caused production of a new peptide termed RA1 present in Oryza Sativa Japonica group. This Japanese rice peptide ameliorated neurological symptoms in the EAE model. Similar beneficial effect was observed upon oral administration of an extract of Japanese rice. In conclusion, oral treatment with IIIM1 ameliorates EAE symptoms via stimulation of Tregs to proliferate and produce RA1 which reduces EAE symptoms. These findings may explain the relatively low prevalence of MS in Japan and other Japanese rice-eating populations. (This work was supported in part by The Israel Science Foundation grant 747/05).

Systematic identification of X1-homologous genes reveals a family involved in stress responses in rice

X1-homologous genes (XHS) encode plant-specific proteins containing three major domains (XH, XS, zf-XS), but their functions are largely unknown. We report the systematic identification and characterization of XHS genes in the rice genome. Eleven putative XHS protein sequences (OXHS1-11) were identified in the sequenced genome of Oryza sativa japonica cv. Nipponbare, and these sequences, along with other plant XHS homologues, were classified into five subgroups based on phylogenetic analysis. Distinct diversification of the XHS proteins occurred between monocotyledon and dicotyledon plants. The OXHS family has diverse exon-intron structures and organizations of putative domains and motifs. The OXHS proteins showed no transactivation activity, and no interaction between the XH domain and the XS domain in yeast. Four representative OXHS proteins were targeted to cytoplasm, which contradicts the previous speculation that XHS proteins are putative transcription factors. All the OXHS genes are predominantly expressed in floral organs, and some are expressed in a wide range of tissues or organs in indica rice Minghui 63. Nine OXHS genes are responsive to at least one of the abiotic stresses including drought, salt, cold, and abscisic acid treatment. Over-expression of one stress-responsive gene OXHS2 in rice resulted in reduced tolerance to salt and drought stresses. These results suggest that the OXHS family may be functionally diversified and some members of this family may play important roles in regulating stress tolerance in rice.

Characterization of allergenic epitopes of Ory s1 protein from Oryza sativa and its homologs.

Vaccination is the most effective technique suggested now days for allergy treatment. Recombinant-based approaches are mostly focused on genetic modification of allergens to produce molecules with reduced allergenic activity and conserved antigenicity. The molecules developed for vaccination in allergy possess significantly reduced allergenicity in terms of IgE binding, and therefore will not lead to anaphylactic reactions upon injection. This approach is probably feasible with every peptide allergen with known amino acid sequence. In this study an in silico approach was used to investigate allergenic protein sequences. Motif analysis of these sequences reveals the allergenic epitopes in the amino acid sequences. Physicochemical analysis of protein sequences shows that the homolog allergens of Ory s1 are highly correlated with the aromaticity, GRAVY and cysteine content. Moreover, phylogenetic analysis of Ory s1 with other sequences reveals that Oryza sativa japonica and Zea mays are close homologs, whilst Lolium perenne and Dactylis glomerata are found to be remote homologs. The multiple sequence alignment reveals of Ory s1 with all its homologs in this study reveals the high conservation of residues in DPBB_1 domain (amino acid residue positions 86- 164) and was found distinctly in all the sequences. These findings support the proposal that allergenic epitopes encompass conserved residues. The consensus allergenic was found to be mainly composed of hydrophobic residues. The functional sites of allergenic proteins reported in this study shall be attenuated to develop hypoallergenic vaccine. The sequence comparison strategy adopted in this study would pave way effective evolutionary analysis of these allergens.

Matrix Frequency Analysis of Oryza Sativa (japonica cultivar-group) Complete Genomes

The genome sequence information is essential to understand the function of extensive arrangements of genes. It is significant to combine all sequence information in a precise database to provide an efficient manner of sequence similarity search. The complete genome analysis, which is one of the essential steps to know their characteristics, is very important. Complete genome analysis is depends on matrix frequency of sequence residue calculation and CGR analysis. In this study, we select rice as the specimen for complete genome analysis. Rice is one of the most essential cereal crops providing food for more than half of the world’s population. Oryza sativa (japonica cultivar-group) species is an important cereal and model monocot. We have generated a matrix frequency for genetic code analysis, which helps in the study of complete genome residues. Here we report the duplets and triplets codon for genetic code analysis of O. sativa chromosomes. We illustrate a new method of Chaos Game Representation, which produces the objects possessing self-similar structure. As per our findings, the average matrix frequency of stop codons is similar to the matrix frequency of start codon. This average is seems to be similar in the complete genome sequences of every Oryza sativa (japonica cultivar-group) chromosomes.