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Paul J Berkman,
Adam Skarshewski,
Sahana Manoli,
Michał T Lorenc,
Jiri Stiller, Lars Smits,
Kaitao Lai,
Emma Campbell,
Marie Kubaláková,
Hana Simková,
Jacqueline Batley,
Jaroslav Doležel,
Pilar Hernandez,
David Edwards
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Paul J. Berkman,
Adam Skarshewski,
Sahana Manoli,
Michał T. Lorenc,
Jiri Stiller, Lars Smits,
Kaitao Lai,
Emma Campbell,
Marie Kubaláková,
Hana Šimková,
Jacqueline Batley,
Jaroslav Doležel,
Pilar Hernandez,
David Edwards
[show abstract]
[hide abstract]
ABSTRACT: Complex Triticeae genomes pose a challenge to genome sequencing efforts due to their size and repetitive nature. Genome sequencing
can reveal details of conservation and rearrangements between related genomes. We have applied Illumina second generation
sequencing technology to sequence and assemble the low copy and unique regions of Triticum aestivum chromosome arm 7BS, followed by the construction of a syntenic build based on gene order in Brachypodium. We have delimited the position of a previously reported translocation between 7BS and 4AL with a resolution of one or a
few genes and report approximately 13% genes from 7BS having been translocated to 4AL. An additional 13 genes are found on
7BS which appear to have originated from 4AL. The gene content of the 7DS and 7BS syntenic builds indicate a total of ~77,000
genes in wheat. Within wheat syntenic regions, 7BS and 7DS share 740 genes and a common gene conservation rate of ~39% of
the genes from the corresponding regions in Brachypodium, as well as a common rate of colinearity with Brachypodium of ~60%. Comparison of wheat homoeologues revealed ~84% of genes previously identified in 7DS have a homoeologue on 7BS or
4AL. The conservation rates we have identified among wheat homoeologues and with Brachypodium provide a benchmark of homoeologous gene conservation levels for future comparative genomic analysis. The syntenic build
of 7BS is publicly available at http://www.wheatgenome.info.
Theoretical and Applied Genetics 05/2012; 124(3):423-432. · 3.30 Impact Factor
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[show abstract]
[hide abstract]
ABSTRACT: Bread wheat (Triticum aestivum) is one of the most important crop plants, globally providing staple food for a large proportion of the human population. However, improvement of this crop has been limited due to its large and complex genome. Advances in genomics are supporting wheat crop improvement. We provide a variety of web-based systems hosting wheat genome and genomic data to support wheat research and crop improvement. WheatGenome.info is an integrated database resource which includes multiple web-based applications. These include a GBrowse2-based wheat genome viewer with BLAST search portal, TAGdb for searching wheat second-generation genome sequence data, wheat autoSNPdb, links to wheat genetic maps using CMap and CMap3D, and a wheat genome Wiki to allow interaction between diverse wheat genome sequencing activities. This system includes links to a variety of wheat genome resources hosted at other research organizations. This integrated database aims to accelerate wheat genome research and is freely accessible via the web interface at http://www.wheatgenome.info/.
Plant and Cell Physiology 02/2012; 53(2):e2. · 4.70 Impact Factor
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Paul J Berkman,
Adam Skarshewski,
Sahana Manoli,
Michał T Lorenc,
Jiri Stiller, Lars Smits,
Kaitao Lai,
Emma Campbell,
Marie Kubaláková,
Hana Simková,
Jacqueline Batley,
Jaroslav Doležel,
Pilar Hernandez,
David Edwards
[show abstract]
[hide abstract]
ABSTRACT: Complex Triticeae genomes pose a challenge to genome sequencing efforts due to their size and repetitive nature. Genome sequencing can reveal details of conservation and rearrangements between related genomes. We have applied Illumina second generation sequencing technology to sequence and assemble the low copy and unique regions of Triticum aestivum chromosome arm 7BS, followed by the construction of a syntenic build based on gene order in Brachypodium. We have delimited the position of a previously reported translocation between 7BS and 4AL with a resolution of one or a few genes and report approximately 13% genes from 7BS having been translocated to 4AL. An additional 13 genes are found on 7BS which appear to have originated from 4AL. The gene content of the 7DS and 7BS syntenic builds indicate a total of ~77,000 genes in wheat. Within wheat syntenic regions, 7BS and 7DS share 740 genes and a common gene conservation rate of ~39% of the genes from the corresponding regions in Brachypodium, as well as a common rate of colinearity with Brachypodium of ~60%. Comparison of wheat homoeologues revealed ~84% of genes previously identified in 7DS have a homoeologue on 7BS or 4AL. The conservation rates we have identified among wheat homoeologues and with Brachypodium provide a benchmark of homoeologous gene conservation levels for future comparative genomic analysis. The syntenic build of 7BS is publicly available at http://www.wheatgenome.info.
Theoretical and Applied Genetics 02/2012; 124(3):423-32. · 3.30 Impact Factor
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Paul J Berkman,
Adam Skarshewski,
Michał T Lorenc,
Kaitao Lai,
Chris Duran,
Edmund Y S Ling,
Jiri Stiller, Lars Smits,
Michael Imelfort,
Sahana Manoli,
Megan McKenzie,
Marie Kubaláková,
Hana Šimková,
Jacqueline Batley,
Delphine Fleury,
Jaroslav Doležel,
David Edwards
[show abstract]
[hide abstract]
ABSTRACT: 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.
Plant Biotechnology Journal 02/2011; 9(7):768-75. · 5.44 Impact Factor
