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Related Experiment Videos

Patterned sequence in the transcriptome of vascular plants.

Charles F Crane1

  • 1Agricultural Research Service, United States Department of Agriculture, and Department of Botany and Plant Pathology, Purdue University, 915 W. State St, West Lafayette, Indiana 47907-2054, USA. ccrane@purdue.edu

BMC Genomics
|June 19, 2007
PubMed
Summary
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Microsatellites and minisatellites in plant ESTs evolve rapidly, with longer motifs showing distinct GC content and protein-coding associations. Shorter motifs remain valuable genetic markers.

Area of Science:

  • Genomics
  • Molecular Evolution
  • Bioinformatics

Background:

  • Microsatellites (1-6 nt repeats) and minisatellites (>7 nt repeats) are crucial genetic markers.
  • Vast expressed sequence tag (EST) data allows comparative analysis of these repeats across plant taxa.

Purpose of the Study:

  • To compare microsatellite and minisatellite properties using plant EST data.
  • To evaluate the evolutionary dynamics of these repeats in vascular plants.

Main Methods:

  • Developed a custom pipeline to identify repeats (1-250 nt) in over 6.7 million plant ESTs.
  • Analyzed motif length, GC content, protein-coding association, and phylogenetic correlation.
  • Identified PCR primers for polymorphic loci.

Main Results:

Related Experiment Videos

  • Identified microsatellite and minisatellite motifs in 88 plant genera.
  • Found motifs with lengths divisible by three were more GC-rich.
  • 80-85% of minisatellites were protein repeats; 15-20% linked to repetitive elements.
  • Microsatellite frequencies showed low phylogenetic correlation; grasses showed increased GC content.
  • Microsatellites were less frequent in genera with large genomes.

Conclusions:

  • Repeat loci evolve faster than flanking sequences, though EST library specificity is a factor.
  • In-frame motifs are more abundant and GC-rich; most minisatellites are in translated sequences.
  • Motifs of 4-6 nucleotides are as polymorphic as 2-3 nt motifs and useful genetic markers.