A physical map with yeast artificial chromosome (YAC) clones covering 63% of the 12 rice chromosomes

Saji, Shoko; Umehara, Yosuke; Antonio, Baltazar A.; Yamane, Hiroko; Tanoue, Hiroshi; Baba, Tomoya; Aoki, Hiroyoshi; Ishige, Naoko; Wu, Jianzhong; Koike, Kayo; Matsumoto, Takashi; Sasaki, Takuji

doi:10.1139/g00-076

Cited by 34 publications

(25 citation statements)

References 24 publications

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“…1; Table 1). Therefore, on the basis of an estimated 36.8 Mb of the rice chromosome 4 (Saji et al 2001), the physical map constructed here has a 94% chromosomal coverage and is the most covered chromosome 4 map obtained so far. and 10) were eventually identified (their locations on the chromosome 4) by FISH analysis (data not shown).…”

Section: Resultsmentioning

confidence: 94%

A Fine Physical Map of the Rice Chromosome 4

Zhao¹,

Zhang²,

Cheng³

et al. 2002

Genome Res.

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As part of an international effort to completely sequence the rice genome, we have produced a fine bacterial artificial chromosome (BAC)-based physical map of the Oryza sativa japonica Nipponbare chromosome 4 through an integration of 114 sequenced BAC clones from a taxonomically related subspecies O. sativa indica Guangluai 4 and 182 RFLP and 407 expressed sequence tag (EST) markers with the fingerprinted data of the Nipponbare genome. The map consists of 11 contigs with a total length of 34.5 Mb covering 94% of the estimated chromosome size (36.8 Mb). BAC clones corresponding to telomeres, as well as to the centromere position, were determined by BAC-pachytene chromosome fluorescence in situ hybridization (FISH). This gave rise to an estimated length ratio of 5.13 for the long arm and 2.9 for the short arm (on the basis of the physical map), which indicates that the short arm is a highly condensed one. The FISH analysis and physical mapping also showed that the short arm and the pericentromeric region of the long arm are rich in heterochromatin, which occupied 45% of the chromosome, indicating that this chromosome is likely very difficult to sequence. To our knowledge, this map provides the first example of a rapid and reliable physical mapping on the basis of the integration of the data from two taxonomically related subspecies

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Section: Resultsmentioning

confidence: 94%

A Fine Physical Map of the Rice Chromosome 4

Zhao¹,

Zhang²,

Cheng³

et al. 2002

Genome Res.

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“…Nipponbare, and adopted a hierarchical cloneby-clone method using bacterial and P1 artificial chromosome clones (BACs and PACs, respectively). This strategy used a high-density genetic map 16 , expressed-sequence tags (ESTs) 17 , yeast artificial chromosome (YAC)-and BAC-based physical maps [18][19][20] , BAC-end sequences 21 and two draft sequences 22,23 . A total of 3,401 BAC/PAC clones (Table 1) were sequenced to approximately tenfold sequence coverage, assembled, ordered and finished to a sequence quality of less than one error per 10,000 bases.…”

Section: The International Rice Genome Sequencing Projectmentioning

confidence: 99%

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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“…Theoretically, the substitutions in nupDNAs consist of two types according to their a The sizes of chromosomes 1, 4, and 10 are according to Sasaki et al (2002), Feng et al (2002, and Rice Chromosome 10 Sequencing Consortium (2003), respectively. The sizes of the other chromosomes are according to Saji et al (2001). The rice chloroplast genome was divided into 100-bp segments.…”

Section: Nucleotide Substitution Profiles Reveal That Nupdnas Were Rementioning

confidence: 99%

The Rice Nuclear Genome Continuously Integrates, Shuffles, and Eliminates the Chloroplast Genome to Cause Chloroplast–Nuclear DNA Flux

et al. 2005

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Plastid DNA fragments are often found in the plant nuclear genome, and DNA transfer from plastids to the nucleus is ongoing. However, successful gene transfer is rare. What happens to compensate for this? To address this question, we analyzed nuclear-localized plastid DNA (nupDNA) fragments throughout the rice (Oryza sativa ssp japonica) genome, with respect to their age, size, structure, and integration sites on chromosomes. The divergence of nupDNA sequences from the sequence of the present plastid genome strongly suggests that plastid DNA has been transferred repeatedly to the nucleus in rice. Age distribution profiles of the nupDNA population, together with the size and structural characteristics of each fragment, revealed that once plastid DNAs are integrated into the nuclear genome, they are rapidly fragmented and vigorously shuffled, and surprisingly, 80% of them are eliminated from the nuclear genome within a million years. Large nupDNA fragments preferentially localize to the pericentromeric region of the chromosomes, where integration and elimination frequencies are markedly higher. These data indicate that the plant nuclear genome is in equilibrium between frequent integration and rapid elimination of the chloroplast genome and that the pericentromeric regions play a significant role in facilitating the chloroplast-nuclear DNA flux.

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A physical map with yeast artificial chromosome (YAC) clones covering 63% of the 12 rice chromosomes

Cited by 34 publications

References 24 publications

A Fine Physical Map of the Rice Chromosome 4

A Fine Physical Map of the Rice Chromosome 4

The map-based sequence of the rice genome

The Rice Nuclear Genome Continuously Integrates, Shuffles, and Eliminates the Chloroplast Genome to Cause Chloroplast–Nuclear DNA Flux

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