Sequencing and assembly of low copy and genic regions of isolated Triticum aestivum chromosome arm 7DS.

The genome of bread wheat (Triticum aestivum) is predicted to be greater than 16 Gbp in size and consist predominantly of repetitive elements, making the sequencing and assembly of this genome a major challenge. We have reduced genome sequence complexity by isolating chromosome arm 7DS and applied second-generation technology and appropriate algorithmic analysis to sequence and assemble low copy and genic regions of this chromosome arm. The assembly represents approximately 40% of the chromosome arm and all known 7DS genes. Comparison of the 7DS assembly with the sequenced genomes of rice (Oryza sativa) and Brachypodium distachyon identified large regions of conservation. The syntenic relationship between wheat, B. distachyon and O. sativa, along with available genetic mapping data, has been used to produce an annotated draft 7DS syntenic build, which is publicly available at http://www.wheatgenome.info. Our results suggest that the sequencing of isolated chromosome arms can provide valuable information of the gene content of wheat and is a step towards whole-genome sequencing and variation discovery in this important crop.

[1]  TJHSST Senior,et al.  Greedy Algorithm , 2013 .

[2]  D. Edwards,et al.  Targeted identification of genomic regions using TAGdb , 2010, Plant Methods.

[3]  Hikmet Budak,et al.  Megabase Level Sequencing Reveals Contrasted Organization and Evolution Patterns of the Wheat Gene and Transposable Element Spaces[W] , 2010, Plant Cell.

[4]  J. Doležel,et al.  Development of Chromosome-Specific BAC Resources for Genomics of Bread Wheat , 2010, Cytogenetic and Genome Research.

[5]  Dawei Li,et al.  The sequence and de novo assembly of the giant panda genome , 2010, Nature.

[6]  Sai Guna Ranjan Gurazada,et al.  Genome sequencing and analysis of the model grass Brachypodium distachyon , 2010, Nature.

[7]  Asan,et al.  The genome of the cucumber, Cucumis sativus L. , 2009, Nature Genetics.

[8]  Dawn H. Nagel,et al.  The B73 Maize Genome: Complexity, Diversity, and Dynamics , 2009, Science.

[9]  David Edwards,et al.  De novo sequencing of plant genomes using second-generation technologies , 2009, Briefings Bioinform..

[10]  M T Clegg,et al.  Genome comparisons reveal a dominant mechanism of chromosome number reduction in grasses and accelerated genome evolution in Triticeae , 2009, Proceedings of the National Academy of Sciences.

[11]  Uwe Scholz,et al.  Gene Content and Virtual Gene Order of Barley Chromosome 1H1[C][W][OA] , 2009, Plant Physiology.

[12]  Lincoln Stein,et al.  CMap 1.01: a comparative mapping application for the Internet , 2009, Bioinform..

[13]  Roger G. Chui,et al.  Visualizing and sharing results in bioinformatics projects: GBrowse and GenBank exports , 2009, BMC Bioinformatics.

[14]  David Edwards,et al.  Discovering genetic polymorphisms in next-generation sequencing data. , 2009, Plant biotechnology journal.

[15]  S. Grimmond,et al.  Genome sequencing approaches and successes. , 2009, Methods in molecular biology.

[16]  K. Edwards Welcome to the first issue of the seventh volume of the Plant Biotechnology Journal.. , 2009, Plant biotechnology journal.

[17]  Pascal Condamine,et al.  Coupling amplified DNA from flow-sorted chromosomes to high-density SNP mapping in barley , 2008, BMC Genomics.

[18]  E. Birney,et al.  Velvet: algorithms for de novo short read assembly using de Bruijn graphs. , 2008, Genome research.

[19]  Peter B. McGarvey,et al.  UniRef: comprehensive and non-redundant UniProt reference clusters , 2007, Bioinform..

[20]  John A. Hamilton,et al.  The TIGR Rice Genome Annotation Resource: improvements and new features , 2006, Nucleic Acids Res..

[21]  Jan Bartoš,et al.  Chromosome-based genomics in the cereals , 2007, Chromosome Research.

[22]  J. Doležel,et al.  Advanced resources for plant genomics: a BAC library specific for the short arm of wheat chromosome 1B. , 2006, The Plant journal : for cell and molecular biology.

[23]  O. Anderson,et al.  GrainGenes 2.0. An Improved Resource for the Small-Grains Community1 , 2005, Plant Physiology.

[24]  Takuji Sasaki,et al.  The map-based sequence of the rice genome , 2005, Nature.

[25]  Miftahudin,et al.  A Chromosome Bin Map of 2148 Expressed Sequence Tag Loci of Wheat Homoeologous Group 7 , 2004, Genetics.

[26]  J. Dvorak,et al.  Structural evolution of wheat chromosomes 4A, 5A, and 7B and its impact on recombination , 1995, Theoretical and Applied Genetics.

[27]  J. Macas,et al.  Flow cytogenetics and plant genome mapping , 2004, Chromosome Research.

[28]  Junhua Peng,et al.  Comparative DNA sequence analysis of wheat and rice genomes. , 2003, Genome research.

[29]  Gerard R. Lazo,et al.  GrainGenes, the genome database for small-grain crops , 2003, Nucleic Acids Res..

[30]  J. Doležel,et al.  Flow karyotyping and chromosome sorting in bread wheat (Triticum aestivum L.) , 2002, Theoretical and Applied Genetics.

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

[32]  J. Doležel,et al.  Flow sorting of mitotic chromosomes in common wheat (Triticum aestivum L.). , 2000, Genetics.

[33]  Lukas Wagner,et al.  A Greedy Algorithm for Aligning DNA Sequences , 2000, J. Comput. Biol..

[34]  J. Bennetzen,et al.  Do Plants Have a One-Way Ticket to Genomic Obesity? , 1997, The Plant cell.

[35]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[36]  J. S. Heslop-Harrison,et al.  Nuclear dna amounts in angiosperms. , 1976, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[37]  L. Beadle,et al.  Society for Experimental Biology , 1947, Nature.