Genome sequencing of a 239-kb region of rice chromosome 10L reveals a high frequency of gene duplication and a large chloroplast DNA insertion

Abstract. In this study we describe a 239-kb region on the long arm of rice chromosome 10 that contains a high density (71%) of locally duplicated genes, including 24 copies of a glutathione S-transferase gene. Intriguingly, embedded within this cluster is a large insertion (~33 kb) of rice (Oryza sativa) chloroplast DNA that is derived from two separate regions of the chloroplast genome. We used DNA fiber-based fluorescence in situ hybridization (fiber-FISH) analyses of O. sativa spp. japonica nuclei to confirm that the insertion of organellar DNA was not a cloning artifact. The sequence of the chloroplast insertion is nearly identical (99.7% identity) to the corresponding regions in the published rice chloroplast genome sequence, suggesting that the transfer event occurred recently. PCR amplification and sequence analysis in two subspecies of rice, O. sativa spp. japonica and spp. indica, indicates that the transfer event predated the divergence of these two subspecies. The chloroplast insertion is flanked by a 2.1-kb perfect direct repeat that is unique to this location in the rice genome.

[1]  G. F. Barry.  The use of the Monsanto draft rice genome sequence in research. , 2001, Plant physiology.

[2]  S. Eddy,et al.  tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. , 1997, Nucleic acids research.

[3]  K. Struhl,et al.  Current Protocols in Molecular Biology (New York: Greene Publishing Associates and Wiley-Interscience). Host-Range Shuttle System for Gene Insertion into the Chromosomes of Gram-negative Bacteria. , 1988 .

[4]  Daniel Lee,et al.  The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species , 2001, Nucleic Acids Res..

[5]  B. Burr,et al.  International Rice Genome Sequencing Project: the effort to completely sequence the rice genome. , 2000, Current opinion in plant biology.

[6]  A. Oliphant,et al.  A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). , 2002, Science.

[7]  H. Goodman,et al.  Application of fiber-FISH in physical mapping of Arabidopsis thaliana. , 1998, Genome.

[8]  M. Ayliffe,et al.  Plastid DNA sequence homologies in the tobacco nuclear genome , 1992, Molecular and General Genetics MGG.

[9]  Owen White,et al.  TIGR Assembler: A New Tool for Assembling Large Shotgun Sequencing Projects , 1995 .

[10]  B F Lang,et al.  Mitochondrial genome evolution and the origin of eukaryotes. , 1999, Annual review of genetics.

[11]  W. Martin,et al.  How many genes in Arabidopsis come from cyanobacteria? An estimate from 386 protein phylogenies. , 2001, Trends in genetics : TIG.

[12]  D. Ward,et al.  Metaphase and interphase fluorescence in situ hybridization mapping of the rice genome with bacterial artificial chromosomes. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[13]  Fan Yang,et al.  TIGRFAMs: a protein family resource for the functional identification of proteins , 2001, Nucleic Acids Res..

[14]  J. Palmer,et al.  Evolutionary transfer of the chloroplast tufA gene to the nucleus , 1990, Nature.

[15]  Huanming Yang,et al.  A draft sequence of the rice (Oryza sativa ssp.indica) genome , 2001, Chinese Science Bulletin.

[16]  S. Jackson,et al.  Cytogenomic Analyses Reveal the Structural Plasticity of the Chloroplast Genome in Higher Plants , 2001, Plant Cell.

[17]  Y. Nakamura,et al.  Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions (supplement). , 1996, DNA research : an international journal for rapid publication of reports on genes and genomes.

[18]  Huanming Yang,et al.  A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. indica) , 2002, Science.

[19]  T. Sicheritz-Pontén,et al.  The genome sequence of Rickettsia prowazekii and the origin of mitochondria , 1998, Nature.

[20]  S. Goff,et al.  Rice as a model for cereal genomics. , 1999, Current opinion in plant biology.

[21]  Y. Nakamura,et al.  Complete structure of the chloroplast genome of Arabidopsis thaliana. , 1999, DNA research : an international journal for rapid publication of reports on genes and genomes.

[22]  C D Town,et al.  Complex mtDNA constitutes an approximate 620-kb insertion on Arabidopsis thaliana chromosome 2: Implication of potential sequencing errors caused by large-unit repeats , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[23]  J. Blanchard,et al.  Pervasive migration of organellar DNA to the nucleus in plants , 1995, Journal of Molecular Evolution.

[24]  Lars S. Jermiin,et al.  Many Parallel Losses of infA from Chloroplast DNA during Angiosperm Evolution with Multiple Independent Transfers to the Nucleus , 2001, Plant Cell.

[25]  Eugen C. Buehler,et al.  Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana , 1999, Nature.

[26]  S. Salzberg,et al.  Complete Genome Sequence of a Virulent Isolate of Streptococcus pneumoniae , 2001, Science.

[27]  M. Lynch,et al.  Organellar genes: why do they end up in the nucleus? , 2000, Trends in genetics : TIG.

[28]  S. Jackson,et al.  Digital mapping of bacterial artificial chromosomes by fluorescence in situ hybridization. , 1999, The Plant journal : for cell and molecular biology.

[29]  Sean R. Eddy,et al.  Pfam: multiple sequence alignments and HMM-profiles of protein domains , 1998, Nucleic Acids Res..

[30]  The Arabidopsis Genome Initiative.  Analysis of the genome sequence of the flowering plant Arabidopsis thaliana , 2000, Nature.

[31]  M. Hasegawa,et al.  Gene transfer to the nucleus and the evolution of chloroplasts , 1998, Nature.

[32]  A. Brennicke,et al.  The mitochondrial genome of Arabidopsis thaliana contains 57 genes in 366,924 nucleotides , 1997, Nature Genetics.

[33]  J. Callis,et al.  Recent stable insertion of mitochondrial DNA into an Arabidopsis polyubiquitin gene by nonhomologous recombination. , 1993, The Plant cell.

[34]  Herrmann,et al.  Gene transfer from organelles to the nucleus: how much, what happens, and Why? , 1998, Plant Physiology.

[35]  Sayaka,et al.  Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions. , 1996, DNA research : an international journal for rapid publication of reports on genes and genomes.