Literature DB >> 18764921

Haplotype divergence in Beta vulgaris and microsynteny with sequenced plant genomes.

Juliane C Dohm1, Cornelia Lange, Richard Reinhardt, Heinz Himmelbauer.   

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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Year:  2008        PMID： 18764921     DOI： 10.1111/j.1365-313X.2008.03665.x

Source DB:  PubMed          Journal:  Plant J        ISSN： 0960-7412            Impact factor:   6.417


  10 in total

1.  Epigenetic profiling of heterochromatic satellite DNA.

Authors:  Falk Zakrzewski; Bernd Weisshaar; Jörg Fuchs; Ekaterina Bannack; André E Minoche; Juliane C Dohm; Heinz Himmelbauer; Thomas Schmidt
Journal:  Chromosoma       Date:  2011-05-19       Impact factor: 4.316

2.  The genome of the recently domesticated crop plant sugar beet (Beta vulgaris).

Authors:  Juliane C Dohm; André E Minoche; Daniela Holtgräwe; Salvador Capella-Gutiérrez; Falk Zakrzewski; Hakim Tafer; Oliver Rupp; Thomas Rosleff Sörensen; Ralf Stracke; Richard Reinhardt; Alexander Goesmann; Thomas Kraft; Britta Schulz; Peter F Stadler; Thomas Schmidt; Toni Gabaldón; Hans Lehrach; Bernd Weisshaar; Heinz Himmelbauer
Journal:  Nature       Date:  2013-12-18       Impact factor: 49.962

3.  The Y-segment of novel cold dehydrin genes is conserved and codons in the PR-10 genes are under positive selection in Oxytropis (Fabaceae) from contrasting climates.

Authors:  Annie Archambault; Martina V Strömvik
Journal:  Mol Genet Genomics       Date:  2011-12-20       Impact factor: 3.291

4.  High-throughput identification of genetic markers using representational oligonucleotide microarray analysis.

Authors:  Cornelia Lange; Lukas Mittermayr; Juliane C Dohm; Daniela Holtgräwe; Bernd Weisshaar; Heinz Himmelbauer
Journal:  Theor Appl Genet       Date:  2010-04-09       Impact factor: 5.699

5.  Mechanisms of haplotype divergence at the RGA08 nucleotide-binding leucine-rich repeat gene locus in wild banana (Musa balbisiana).

Authors:  Franc-Christophe Baurens; Stéphanie Bocs; Mathieu Rouard; Takashi Matsumoto; Robert N G Miller; Marguerite Rodier-Goud; Didier MBéguié-A-MBéguié; Nabila Yahiaoui
Journal:  BMC Plant Biol       Date:  2010-07-16       Impact factor: 4.215

6.  MicroSyn: a user friendly tool for detection of microsynteny in a gene family.

Authors:  Bin Cai; Xiaohan Yang; Gerald A Tuskan; Zong-Ming Cheng
Journal:  BMC Bioinformatics       Date:  2011-03-18       Impact factor: 3.169

7.  Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and genome analyzer systems.

Authors:  André E Minoche; Juliane C Dohm; Heinz Himmelbauer
Journal:  Genome Biol       Date:  2011-11-08       Impact factor: 13.583

8.  Genomic distances reveal relationships of wild and cultivated beets.

Authors:  Felix L Wascher; Nancy Stralis-Pavese; J Mitchell McGrath; Britta Schulz; Heinz Himmelbauer; Juliane C Dohm
Journal:  Nat Commun       Date:  2022-04-19       Impact factor: 17.694

9.  Exploiting single-molecule transcript sequencing for eukaryotic gene prediction.

Authors:  André E Minoche; Juliane C Dohm; Jessica Schneider; Daniela Holtgräwe; Prisca Viehöver; Magda Montfort; Thomas Rosleff Sörensen; Bernd Weisshaar; Heinz Himmelbauer
Journal:  Genome Biol       Date:  2015-09-02       Impact factor: 13.583

10.  Reliable in silico identification of sequence polymorphisms and their application for extending the genetic map of sugar beet (Beta vulgaris).

Authors:  Daniela Holtgräwe; Thomas Rosleff Sörensen; Prisca Viehöver; Jessica Schneider; Britta Schulz; Dietrich Borchardt; Thomas Kraft; Heinz Himmelbauer; Bernd Weisshaar
Journal:  PLoS One       Date:  2014-10-10       Impact factor: 3.240
  10 in total

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