Soybean bacterial artificial chromosome contigs anchored with RFLPs

Insights into genome duplication and gene clustering

Joann Mudge, Huihuang D Yan, Roxanne L. Denny, Dana K. Howe, Dariush Danesh, Laura F. Marek, Ernie Retzel, Randy C. Shoemaker, Nevin D. Young

Research output: Contribution to journalArticle

18 Citations (Scopus)

Abstract

Surveying the soybean genome with 683 bacterial artificial chromosome (BAC) contiguous groups (contigs) anchored by restriction fragment length polymorphisms (RFLPs) enabled us to explore microsyntenic relationships among duplicated regions and also to examine the physical organization of hypomethylated (and presumably gene-rich) genomic regions. Numerous cases where nonhomologous RFLPs hybridized to common BAC clones indicated that RFLPs were physically clustered in soybean, apparently in less than 25% of the genome. By extension, we speculate that most of the genes are clustered in less than 275 M of the soybean genome. Approximately 40%-45% of this generich portion is associated with the RFLP-anchored contigs described in this study. Similarities in genome organization among BAC contigs from duplicate genomic regions were also examined. Homoeologous BAC contigs often exhibited extensive microsynteny. Furthermore, paralogs recovered from duplicate contigs shared 86%-100% sequence identity.

Original languageEnglish (US)
Pages (from-to)361-372
Number of pages12
JournalGenome
Volume47
Issue number2
StatePublished - Apr 2004
Externally publishedYes

Fingerprint

Bacterial Artificial Chromosomes
bacterial artificial chromosomes
Gene Duplication
Soybeans
Restriction Fragment Length Polymorphisms
Cluster Analysis
restriction fragment length polymorphism
Genome
soybeans
genome
genes
genomics
Genes
Clone Cells
clones

Keywords

  • Bacterial artifical chromosome
  • Gene distribution
  • Genome duplication
  • Glycine max
  • Restriction fragment length polymorphism

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biotechnology
  • Genetics
  • Genetics(clinical)

Cite this

Mudge, J., Yan, H. D., Denny, R. L., Howe, D. K., Danesh, D., Marek, L. F., ... Young, N. D. (2004). Soybean bacterial artificial chromosome contigs anchored with RFLPs: Insights into genome duplication and gene clustering. Genome, 47(2), 361-372.

Soybean bacterial artificial chromosome contigs anchored with RFLPs : Insights into genome duplication and gene clustering. / Mudge, Joann; Yan, Huihuang D; Denny, Roxanne L.; Howe, Dana K.; Danesh, Dariush; Marek, Laura F.; Retzel, Ernie; Shoemaker, Randy C.; Young, Nevin D.

In: Genome, Vol. 47, No. 2, 04.2004, p. 361-372.

Research output: Contribution to journalArticle

Mudge, J, Yan, HD, Denny, RL, Howe, DK, Danesh, D, Marek, LF, Retzel, E, Shoemaker, RC & Young, ND 2004, 'Soybean bacterial artificial chromosome contigs anchored with RFLPs: Insights into genome duplication and gene clustering', Genome, vol. 47, no. 2, pp. 361-372.
Mudge, Joann ; Yan, Huihuang D ; Denny, Roxanne L. ; Howe, Dana K. ; Danesh, Dariush ; Marek, Laura F. ; Retzel, Ernie ; Shoemaker, Randy C. ; Young, Nevin D. / Soybean bacterial artificial chromosome contigs anchored with RFLPs : Insights into genome duplication and gene clustering. In: Genome. 2004 ; Vol. 47, No. 2. pp. 361-372.
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