International Rice Genome Sequencing Project: the effort to completely sequence the rice genome

Sasaki, Takuji; Burr, Benjamin

doi:10.1016/s1369-5266(99)00047-3

Cited by 405 publications

(233 citation statements)

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“…A map-based, high-quality and completed sequence of the rice genome is essential for extensive scienti®c studies, not only of rice functional genomics but also of The Plant Journal (2003) 36, 720±730 plant comparative genomics, especially among the cereals. To achieve this goal, IRGSP has adopted the clone-by-clone sequencing strategy and adheres to the policy of immediate release of sequence data (Sasaki and Burr, 2000). The genomic sequences of rice chromosomes 1, 4, and 10 have been completed, and this work has led to detailed characterization of the genome, such as the discovery of the presence of many tandemly duplicated genes, as well as the chromosomal distribution of repetitive sequences and the chromosomal integration of organelle DNA sequences (Feng et al, 2002;Sasaki et al, 2002;The Rice Chromosome 10 Sequencing Consortium, 2003).…”

Section: Introductionmentioning

confidence: 99%

Physical maps and recombination frequency of six rice chromosomes

Wu¹,

Mizuno²,

et al. 2003

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These authors contributed equally to this work. SummaryWe constructed physical maps of rice chromosomes 1, 2, and 6±9 with P1-derived arti®cial chromosome (PAC) and bacterial arti®cial chromosome (BAC) clones. These maps, with only 20 gaps, cover more than 97% of the predicted length of the six chromosomes. We submitted a total of 193 Mbp of non-overlapping sequences to public databases. We analyzed the DNA sequences of 1316 genetic markers and six centromere-speci®c repeats to facilitate characterization of chromosomal recombination frequency and of the genomic composition and structure of the centromeric regions. We found marked changes in the relative recombination rate along the length of each chromosome. Chromosomal recombination at the centromere core and surrounding regions on the six chromosomes was completely suppressed. These regions have a total physical length of about 23 Mbp, corresponding to 11.4% of the entire size of the six chromosomes. Chromosome 6 has the longest quiescent region, with about 5.6 Mbp, followed by chromosome 8, with quiescent region about half this size. Repetitive sequences accounted for at least 40% of the total genomic sequence on the partly sequenced centromeric region of chromosome 1. Rice CentO satellite DNA is arrayed in clusters and is closely associated with the presence of Centromeric Retrotransposon of Rice (CRR )-and RIce RetroElement 7 (RIRE7 )-like retroelement sequences. We also detected relatively small coldspot regions outside the centromeric region; their repetitive content and gene density were similar to those of regions with normal recombination rates. Sequence analysis of these regions suggests that either the amount or the organization patterns of repetitive sequences may play a role in the inactivation of recombination.

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Section: Introductionmentioning

confidence: 99%

Physical maps and recombination frequency of six rice chromosomes

Wu¹,

Mizuno²,

et al. 2003

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“…Sequence analysis of the genome has been completed (The Arabidopsis Genome Initiative, 2000). The 430-Mbp rice genome is a model for monocotyledonous plants, and the rice genome project aims to decipher the entire genomic sequence for this species (Sasaki and Burr, 2000). Equally detailed studies are not feasible for many other plant genomes at present, especially given the large genome sizes of most crop plants.…”

Section: Introductionmentioning

confidence: 99%

Comparative Sequence Analysis Reveals Extensive Microcolinearity in the Lateral Suppressor Regions of the Tomato, Arabidopsis, and Capsella Genomes

Rossberg¹,

Theres

Acarkan³

et al. 2001

Plant Cell

114

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A 57-kb region of tomato chromosome 7 harboring five different genes was compared with the sequence of the Arabidopsis genome to search for microsynteny between the genomes of these two species. For all five genes, homologous sequences could be identified in a 30-kb region located on Arabidopsis chromosome 1. Only two inversion events distinguish the arrangement of the five genes in tomato from that in Arabidopsis. Inversions were not detected when the arrangement of the five Arabidopsis genes was compared with the arrangement in the orthologous region of Capsella, a plant closely related to Arabidopsis. These results provide evidence for microcolinearity between closely and distantly related dicotyledonous species. The degree of microcolinearity found can be exploited to localize orthologous genes in Arabidopsis and tomato in an unambiguous way. INTRODUCTIONArabidopsis, a small crucifer, has been adopted as a model in plant genome analysis. The small genome size of 125 Mbp and a low number of repetitive elements facilitated the assembly of comprehensive molecular marker and clone contig maps for the five Arabidopsis chromosomes (reviewed in Schmidt, 1998). Sequence analysis of the genome has been completed (The Arabidopsis Genome Initiative, 2000). The 430-Mbp rice genome is a model for monocotyledonous plants, and the rice genome project aims to decipher the entire genomic sequence for this species (Sasaki and Burr, 2000). Equally detailed studies are not feasible for many other plant genomes at present, especially given the large genome sizes of most crop plants. It needs to be established if and how information generated on the Arabidopsis and rice genomes can be used for the study of other plant genomes.Comparative genetic mapping experiments yielded evidence for the conservation of gene repertoire and colinear chromosome segments for related species. An extensive conservation of marker order was found for the 12 tomato and potato chromosomes, and five chromosomal inversions could explain differences in marker organization (Tanksley et al., 1992). For the Poaceae family, a remarkable degree of genome conservation could be established even between species that diverged as long as 60 million years ago and that differ considerably in genome size (reviewed in Gale and Devos, 1998). Comparing the genetic maps of Arabidopsis and different Brassica species also has revealed many colinear chromosome segments for species belonging to the Brassicaceae family (reviewed in Schmidt, 2000). The results of the first microsynteny studies using sequencelevel resolution in the Poaceae (Chen et al., 1997;Messing and Llaca, 1998;Tikhonov et al., 1999) and Brassicaceae families (Grant et al., 1998;Acarkan et al., 2000) support the view that genome colinearity can be observed at the level of genes.Few attempts to analyze genome colinearity between more distantly related species have been reported (Paterson et al., 1996;Devos et al., 1999;van Dodeweerd et al., 1999;Ku et al., 2000). The low degree of sequence homology in distantl...

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“…Rice benefits from having the smallest genome of the major cereals, dense genetic maps and relative ease of genetic transformation 3 . The discovery of extensive genome colinearity among the Poaceae 4 has established rice as the model organism for the cereal grasses.…”

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The map-based sequence of the rice genome

Matsumoto¹,

Wu²,

Kanamori³

et al. 2005

Nature

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Rice, one of the world's most important food plants, has important syntenic relationships with the other cereal species and is a model plant for the grasses. Here we present a map-based, finished quality sequence that covers 95% of the 389 Mb genome, including virtually all of the euchromatin and two complete centromeres. A total of 37,544 nontransposable-element-related protein-coding genes were identified, of which 71% had a putative homologue in Arabidopsis. In a reciprocal analysis, 90% of the Arabidopsis proteins had a putative homologue in the predicted rice proteome. Twenty-nine per cent of the 37,544 predicted genes appear in clustered gene families. The number and classes of transposable elements found in the rice genome are consistent with the expansion of syntenic regions in the maize and sorghum genomes. We find evidence for widespread and recurrent gene transfer from the organelles to the nuclear chromosomes. The map-based sequence has proven useful for the identification of genes underlying agronomic traits. The additional single-nucleotide polymorphisms and simple sequence repeats identified in our study should accelerate improvements in rice production.

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International Rice Genome Sequencing Project: the effort to completely sequence the rice genome

Cited by 405 publications

References 15 publications

Physical maps and recombination frequency of six rice chromosomes

Physical maps and recombination frequency of six rice chromosomes

Comparative Sequence Analysis Reveals Extensive Microcolinearity in the Lateral Suppressor Regions of the Tomato, Arabidopsis, and Capsella Genomes

The map-based sequence of the rice genome

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