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  Haplotype divergence in Beta vulgaris and microsynteny with sequenced plant genomes

Dohm, J. C., Lange, C., Reinhardt, R., & Himmelbauer, H. (2009). Haplotype divergence in Beta vulgaris and microsynteny with sequenced plant genomes. Plant Journal, 57(1), 14-26. doi:10.1111/j.1365-313X.2008.03665.x.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-7E3F-0 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-7E40-A
Genre: Journal Article

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 Creators:
Dohm, Juliane C.1, Author              
Lange, Cornelia1, Author              
Reinhardt, Richard2, Author              
Himmelbauer, Heinz1, Author              
Affiliations:
1Dept. of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433550              
2High Throughput Technologies, Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433552              

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Free keywords: Comparative plant genomics, Haplotype divergence, Microsynteny, Transposable elements, Genomic sequencing, Repeat detection
 Abstract: We characterized two overlapping sugar beet (Beta vulgaris) bacterial artificial chromosome (BAC) clones representing different haplotypes. A total of 254 kbp of the genomic sequence was determined, of which the two BACs share 92 kbp. Eleven of 15 genes discovered in the sequenced interval locate to the overlap region. The haplotypes differ in exons by 1% (nucleotide level) and in non-coding regions by 9% (6% mismatches, 3% gaps; alignable regions only). Large indels or high sequence divergence comprised 11% of either sequence. Of such indels, 68 and 45%, respectively, could be attributed to haplotype-specific integration of transposable elements. We identified novel repeat candidates by comparing the two BAC sequences to a set of genomic sugar beet sequences. Synteny was found with Arabidopsis chromosome 1 (At1), At2 and At4, Medicago chromosome 7, Vitis chromosome 15 and paralogous regions on poplar chromosomes II and XIV.

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Language(s): eng - English
 Dates: 2009-01-01
 Publication Status: Published in print
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Method: -
 Identifiers: eDoc: 407390
DOI: 10.1111/j.1365-313X.2008.03665.x
 Degree: -

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Title: Plant Journal
Source Genre: Journal
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Pages: - Volume / Issue: 57 (1) Sequence Number: - Start / End Page: 14 - 26 Identifier: ISSN: 0960-7412