ABSTRACT The rice species _Oryza sativa_ is considered to be a model plant because of its small genome size, extensive genetic map, relative ease of transformation and synteny with other

cereal crops1,2,3,4. Here we report the essentially complete sequence of chromosome 1, the longest chromosome in the rice genome. We summarize characteristics of the chromosome structure and

the biological insight gained from the sequence. The analysis of 43.3 megabases (Mb) of non-overlapping sequence reveals 6,756 protein coding genes, of which 3,161 show homology to proteins

of _Arabidopsis thaliana_, another model plant. About 30% (2,073) of the genes have been functionally categorized. Rice chromosome 1 is (G + C)-rich, especially in its coding regions, and

OF _NICOTIANA BENTHAMIANA_ Article Open access 16 April 2024 AN ANNOTATED NEAR-COMPLETE SEQUENCE ASSEMBLY OF THE _MAGNAPORTHE ORYZAE_ 70-15 REFERENCE GENOME Article Open access 07 May 2025

MAIN Rice has been studied extensively by molecular genetics and constitutes one of the best characterized crop plants with a fine genetic map of 3,267 markers

(http://rgp.dna.affrc.go.jp/publicdata/geneticmap2000/index.html)1, a yeast artificial chromosome (YAC) physical map with 80.8% coverage2, sequences for about 10,000 unique expressed

sequence tags (ESTs)3, and a transcriptional map indicating the placement of 6,591 unique ESTs2. The Rice Genome Research Program (RGP) in Japan launched its rice genome sequencing project

in 1998. It is a partner of the International Rice Genome Sequencing Project (IRGSP), which involves ten countries in Asia, North America, South America and Europe that are working towards

the immediate release of high-quality sequence data to the public domain4. The draft sequences of the two main subspecies of rice, _japonica_ and _indica_, have been reported5,6. Both

studies were based on whole-genome shotgun sequencing rather than on the clone-by-clone approach of the IRGSP. Although the release of the draft sequence is of immense scientific value, many

challenges in rice genomics demand the availability of a complete, accurate, map-based rice genome sequence. We determined the sequence of chromosome 1 from 390 overlapping phage

(P1)-derived artificial chromosome (PAC) and bacterial artificial chromosome (BAC) clones and assembled it into nine contigs (Fig. 1). The longest contig is 14.4 Mb and spans positions 106.2

centimorgans (cM) to 157.1 cM on the molecular genetic map. Among the eight remaining gaps, gap 4, located at 73.4 cM, corresponds to a portion of the centromeric region and is estimated to

be about 1,400 kilobases (kb) by the pachytene fluorescence _in situ_ hybridization (FISH) method7. PAC/BAC clones adjacent to this gap contain copies of the rice centromere-specific

sequence RCS2 (ref. 8). Two PAC clones, P0402A09 and P0020E09, are localized to the most distal ends of the short arm and the long arm, and their map positions have been verified by

pachytene FISH using pAtT4 (ref. 9), a telomeric clone of _Arabidopsis_ (Supplementary Fig. 1). This indicates that our physical map extends to within less than 50 kb of the telomeres.

Integration of the PAC/BAC physical mapping with the results from fibre FISH gives a total length of 45.7 Mb for chromosome 1, corresponding to 181.8 cM on the genetic map, excluding the

telomeres. Statistics for the nucleotide sequence of rice chromosome 1 are summarized in Table 1. The non-overlapping sequence covers 43,276,883 nucleotides. In this sequence, 6,756 genes

were either identified or predicted. Thus, the average gene density of chromosome 1 is about one gene per 6.4 kb. If this distribution is assumed to be similar throughout the whole genome,

then the total number of genes in the rice genome (400 Mb) is roughly 62,500. This number is 2.5 times larger than the gene total of _Arabidopsis_10. But this difference might easily be the

result of an overestimate of rice genes, because it assumes that there is a uniform distribution of genes along the chromosomes. Cytogenetic analysis has indicated clear differences in the

content of heterochromatin in each of the 12 rice chromosomes, and chromosome 1 shows the least amount of heterochromatic material11. The average exon size is comparable to that of

_Arabidopsis_, but the average intron size is about 3.6 times larger. This means that, although the longer introns engender larger gene sizes in rice, the average transcriptome size is

similar in both species. The G + C content of coding and noncoding regions in rice is higher than in _Arabidopsis_—the rice coding regions are especially (G + C)-rich. This characteristic is

reflected by the biased usage of G/C at the third position of codons within predicted genes (Supplementary Table 1). Buoyant density experiments have shown that rice genes are localized in

(G + C)-rich islands that occupy 24% of the genome12. When we plotted the average G + C values against chromosomal position in chromosome 1, however, we did not detect any CpG islands,

indicating a neutral nucleotide distribution. The ratios of physical to genetic distance on the short and the long arms are 214 kb cM-1 (_r_2 = 0.983) and 288 kb cM-1 (_r_2 = 0.976),

respectively, suggesting that the rate of recombination differs along the two arms of the chromosome. We compared our finished sequence (493,729 bp from the distal end of the short

chromosome arm) with 127,550 _indica_ sequence contigs assembled from the whole-genome shotgun sequences of the Beijing Genomics Institute (BGI, http://btn.genomics.org.cn/rice/) using the

_japonica_ sequence as a query for basic BLASTN (basic local alignment search tool) analysis (Fig. 2). We could detect the corresponding _indica_ sequence in about 78% of the whole region.

But there were 65 gaps in the aligned contigs, and a total of 110,389 bases (22%) of _japonica_ sequence could not be identified in the _indica_ assembly. This may partly reflect the

sequence difference between the two subspecies, although some artefacts in the whole-genome shotgun assembly cannot be ruled out. Among the 96 predicted genes in this region of the completed

_japonica_ sequence, 55 genes are intact, 33 genes are partially predicted and 8 genes are not predicted in the corresponding _indica_ draft sequence. Relative identities near the repeat

(retrotransposon-like) regions are lower than in the other regions, indicating a misassembly in the sequence. Direct comparison with the _japonica_ draft sequence could not be made because

the sequence data are not in the public domain. But previously, 4,467 genes were predicted from a set of 99 BAC contigs assigned to chromosome 1 (ref. 6). It is likely that an estimated

2,835–4,211 gaps (either 63 gaps per megabase or 10% of 42,109 total gaps) for this chromosome prevented an accurate prediction of the number of genes. Not surprisingly, only half of the

genes predicted contain complete coding regions. In addition, no basis was provided for the assignment of genes to chromosome6. We used an automated annotation system, RiceGAAS13, to

characterize the gene composition of chromosome 1 (Supplementary Fig. 2, http://RiceGAAS.dna.affrc.go.jp/chromosome1/). The distribution of genes along both arms of the chromosome indicates

higher density (18–19 genes per 100 kb) in distal as compared with proximal regions (10–12 genes per 100 kb). This was verified by experimental results obtained by mapping 977 expressed

sequence tags on to chromosome 1 (ref. 2). Among the 6,756 predicted genes, 2,073 (31%) were functionally characterized by homology to known proteins using BLASTP, whereas 69% of the

predicted genes corresponded to proteins with no known function (Table 2). The protein signature search program InterPro detected protein domains in 3,660 (54%) of the total predicted genes

(see http://RiceGAAS.dna.affrc.go.jp/chromosome1/). In particular, 1,170 (33%) of 3,600 hypothetical proteins showed domain homology, suggesting that these proteins may correspond to newly

identified proteins in rice. BLASTN analysis was done using the cereal EST entries from the EST database at the National Institute for Biotechnology Information (NCBI). Exon regions from all

predicted genes were used as queries, and 546,723 unclustered ESTs from wheat, maize, barley and sorghum were searched using a threshold probability value of 10-5. A total of 2,985

predicted genes, including 756 hypothetical proteins, have cereal homologues. Thus, among the 6,756 predicted genes, 4,803 (71%) show some evidence of homology to a domain, a functional

site, a cereal EST or a protein. The predicted proteins found on chromosome 1 were categorized into gene families by BLASTP, using a threshold probability score of 10-20 over more than 50%

of the length of the gene. The most abundant gene family was the serine/threonine receptor kinase family with 132 members distributed along the chromosome (Fig. 3a). A cluster of this gene

family was observed at the distal end of the short arm, although some members of the cluster seemed to be pseudogenes. The highest number of tandem repeats detected at a single site was a

cluster of ten copies of the hypothetical gene family located on the short arm of chromosome 1. These results are summarized in Fig. 3b, which shows a dot matrix plot of chromosome 1,

indicating the predicted genes with significant homology to a given gene. On this plot, which disregards self-homology, a clear diagonal line was obtained, indicating that a significant

number of genes are duplicated and arrayed in tandem. To determine whether any of the proteins on rice chromosome 1 are not present in _Arabidopsis_, the 6,756 predicted proteins were

queried in BLASTP searches against all the _Arabidopsis_ proteins in the Munich Information Center for Protein Sequence (MIPS) database using a threshold probability score of 10-5. Among

3,161 positive queries, 824 showed strong similarities (probability value less than 10-100) to proteins found in _Arabidopsis_, whereas 3,595 sequences (53%) did not have positive BLASTP

hits with predicted _Arabidopsis_ proteins at a probability threshold of 10-5. Only 27 of these sequences had homology to known proteins and among them, only Bowman–Birk trypsin inhibitor

and cytochrome _f_ (chloroplast) were clearly found in rice chromosome 1. This suggests that almost all of the known proteins found in rice chromosome 1 are also found in _Arabidopsis_.

Among the hypothetical proteins, 3,051 genes have no counterpart in _Arabidopsis_ and 442 (15%) genes have grass orthologues. Analysis of the draft sequence also showed that half of the

predicted genes have no homologues in Arabidopsis5,6. Although many of these hypothetical genes could be artefacts resulting from prediction errors, functional characterization of these

genes in the future may identify grass-specific or even rice-specific genes. We also observed rice chloroplast genes in sequential order on the chromosomal DNA. For example, at 149.1 cM we

identified 3,564 bp of sequence that matched the rice chloroplast sequence with only a 3-bp difference. This sequence contains three genes14, PSII cytochrome _b_559, cytochrome _f_ and the

chloroplast envelope membrane protein ORF230. We also detected 85 putative transfer RNA genes using tRNAscan SE15. Analysis of the retrotransposable elements and DNA intermediate

transposons, including miniature inverted-repeats transposable elements (MITEs)16, using RepeatMasker is given in Table 1 and summarized in Supplementary Fig. 3. MITEs have a tendency to be

dispersed along the chromosome, whereas the retrotransposons and other autonomous type DNA-mediated transposable elements are clustered in the pericentromeric region. Among retroelements,

Ty3/_Gypsy_-type elements are the most frequent (2,157), followed by Ty1/_Copia_-type elements (384). The sum of the lengths of these three repetitive elements is 6.0 Mb, corresponding to

13% of chromosome 1. There are at least three compelling reasons for obtaining finished high-quality sequence for the complete rice genome: first, the ability to determine gene function is

highly dependent on having accurate sequences; second, as a model plant for the cereal grasses, the complete rice sequence will directly affect what can be accomplished with the other cereal

grasses; and last, the identification of genes responsible for agronomic traits of economic importance requires precise map-based genomic sequence. Chromosome 1 contains many biologically

important genes. More than 20 gene loci have been identified by genetic analysis, including genes controlling dwarfing and fertility. One of these genes, _sd1_ has been cloned and shown to

encode one of the enzymes in gibberellic acid synthesis17. The complete genomic sequence of chromosome 1 has yielded several findings that would be observed only using a clone-by-clone

sequencing strategy. Gene families comprising active and inactive members and sets of tandemly repeated genes seem to be common features of chromosome 1. This redundancy may account for the

unexpectedly large number of predicted genes on this chromosome. The intergenic repetitive fraction of the genome is not well understood and is frequently described as ‘junk’. Repetitive

sequences are usually removed or separated from other sequences before whole-genome shotgun assembly because they can cause global misassembly. But we know that functional genes are found in

repetitive sequences and that transposable elements embedded in the repetitive sequences can restructure genomes, can control gene action and are likely to be involved in generating some of

the allelic variation that has been selected in plants. In addition, high-quality finished sequence provides the only real opportunity to study gene regulation, because most of the

essential regulatory sequences fall outside the transcribed regions and our analysis of a restricted region of the genome showed that 43% of the genes predicted from whole-genome shotgun

sequence methods were incomplete. Our results and those from the sequencing of rice chromosome 4 (ref. 18) show clearly the importance of the finished sequence. The IRGSP has an immediate

goal of sequencing the rice genome to a minimum standard of the high-throughput genomic sequence (HTG) phase 2 level by the end of 2002 and is committed to a long-term goal of obtaining

finished high-quality sequence for the whole genome. METHODS CHROMOSOME SEQUENCING We sequenced the whole chromosome 1 of _Oryza sativa_ ssp. _japonica_, variety Nipponbare, from 390

overlapping PAC/BAC clones. Initially, we constructed a sequence-ready physical map using the RGP _Sau_3AI PAC and _Mbo_I BAC libraries19. We also used _Hin_dIII or _Eco_RI BAC libraries

constructed by Clemson University Genomics Institute (CUGI), and BAC clones with draft sequence data provided by Monsanto for gap filling in particular. We carried out shotgun sequencing of

RGP and CUGI PAC/BAC clones to obtain sequence data with tenfold overlap. For Monsanto BAC clones20, we complemented the available draft sequence (fivefold redundancy) with an additional

fivefold overlap sequence (http://rgp.dna.affrc.go.jp/genomicdata/seqstrategy/newstrategy.html). After the initial assembly of sequence data, stretches of poor or ambiguous quality and

apparent gap regions were identified for further sequencing to obtain greater than 99.99% sequence accuracy. But despite extensive efforts to improve the sequence quality and to fill the

gaps, 4 of the 390 PAC/BAC clones sequenced are still at phase 1 (GenBank, http://www.ncbi.nlm.nih.gov/HTGS/) because the consensus sequence could not be ordered correctly owing to numerous

repeats. The remainder comprises 16 phase 2 and 370 phase 3 clones. The nine contigs for chromosome 1 representing the non-overlapping segments of continuous sequence were conjoined by

inserting into the gap regions nucleotides that were calculated on the basis of the results of FISH experiments. All of the sequence information of chromosome 1 has been submitted to the DNA

Data Bank of Japan (DDBJ, http://www.ddbj.nig.ac.jp/) with the accession number BA000010 (Con Division). GENE PREDICTION AND FUNCTIONAL CLASSIFICATION We carried out gene prediction using

our in-house automated gene prediction system RiceGAAS13. The algorithm for gene domain prediction in RiceGAAS was designed by combining several prediction programs including GENSCAN21 for

maize, GENSCAN21 for _Arabidopsis_, RiceHMM (http://rgp.dna.affrc.go.jp/RiceHMM/index.html) and the exon-finding program MZEF (http://argon.cshl.org/genefinder/), with homology search

results from BLASTN and BLASTX (http://www.ncbi.nlm.nih.gov/BLAST/). These results were merged and integrated for gene prediction. Domain search was done using InterPro

(http://www.ebi.ac.uk/interpro/scan.html), and repeats were identified using RepeatMasker (http://ftp.genome.washington.edu/cgi-bin/RepeatMasker). The predicted proteins were used to query

the nonredundant protein database using BLASTP and categorized according to functional categories defined for _Arabidopsis_ by MIPS

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and their sequence data; R. Wing of Clemson University Genomics Institute and Novartis for the rice Nipponbare BAC library and its fingerprint data, respectively; M. Hattori for technical

assistance; B. Burr and F. Burr for critically reading the manuscript; T. Slezak for comments; and K. Eguchi for encouragement. AUTHOR INFORMATION AUTHORS AND AFFILIATIONS * Rice Genome

Research Program, National Institute of Agrobiological Sciences, and Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, 1-2, Kannondai 2-chome, Tsukuba,

Ibaraki, 305-8602, Japan Takuji Sasaki, Takashi Matsumoto, Kimiko Yamamoto, Katsumi Sakata, Tomoya Baba, Yuichi Katayose, Jianzhong Wu, Yoshiaki Nagamura, Baltazar A. Antonio, Hiroyuki

Kanamori, Satomi Hosokawa, Masatoshi Masukawa, Koji Arikawa, Yoshino Chiden, Mika Hayashi, Masako Okamoto, Tsuyu Ando, Hiroyoshi Aoki, Kohei Arita, Masao Hamada, Chizuko Harada, Saori

Hijishita, Mikiko Honda, Yoko Ichikawa, Atsuko Idonuma, Masumi Iijima, Michiko Ikeda, Maiko Ikeno, Sachie Ito, Tomoko Ito, Yuichi Ito, Yukiyo Ito, Aki Iwabuchi, Kozue Kamiya, Wataru

Karasawa, Satoshi Katagiri, Ari Kikuta, Noriko Kobayashi, Izumi Kono, Kayo Machita, Tomoko Maehara, Hiroshi Mizuno, Tatsumi Mizubayashi, Yoshiyuki Mukai, Hideki Nagasaki, Marina Nakashima, 

Yuko Nakama, Yumi Nakamichi, Mari Nakamura, Nobukazu Namiki, Manami Negishi, Isamu Ohta, Nozomi Ono, Shoko Saji, Kumiko Sakai, Michie Shibata, Takanori Shimokawa, Ayahiko Shomura, Jianyu

Song, Yuka Takazaki, Kimihiro Terasawa, Kumiko Tsuji, Kazunori Waki, Harumi Yamagata, Hiroko Yamane, Shoji Yoshiki, Rie Yoshihara, Kazuko Yukawa, Huisun Zhong & Masahiro Yano * Center

for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, 411-8540, Japan Yoshihito Niimura, Hisakazu Iwama & Takashi Gojobori * Department of

Horticulture, University of Wisconsin-Madison, Wisconsin, 53706, Madison, USA Zhukuan Cheng & Jiming Jiang * Department of Bioinformatics, Tokyo Medical and Dental University, 1-5-45

Yushima, Bunkyo-ku, 113-8510, Tokyo, Japan Toshinori Endo & Hidetaka Ito * Rice Genome Sequencing Project, National Institute of Agricultural Science and Technology, RDA, 249

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T., Yamamoto, K. _et al._ The genome sequence and structure of rice chromosome 1. _Nature_ 420, 312–316 (2002). https://doi.org/10.1038/nature01184 Download citation * Received: 04 April

2002 * Accepted: 19 September 2002 * Issue Date: 21 November 2002 * DOI: https://doi.org/10.1038/nature01184 SHARE THIS ARTICLE Anyone you share the following link with will be able to read

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