Applying Small-Scale DNA Signatures as an Aid in Assembling Soybean Chromosome Sequences. (1st August 2010)

• Record Type: Journal Article
• Authors: Peto, Myron; Grant, David M.; Shoemaker, Randy C.; Cannon, Steven B.
• Other Names: Makalowska Izabela Academic Editor.
• Is Part Of: Advances in bioinformatics. Volume 2010(2010)
• Publication Date: 2010-08-01
• Subjects: Bioinformatics -- Periodicals; Bioinformatics; Computational Biology -- Periodicals; Periodicals; 570.285
• DOI: 10.1155/2010/976792
• Languages: English
• ISSNs: 1687-8027

Abstract

Abstract : Previous work has established a genomic signature based on relative counts of the 16 possible dinucleotides. Until now, it has been generally accepted that the dinucleotide signature is characteristic of a genome and is relatively homogeneous across a genome. However, we found some local regions of the soybean genome with a signature differing widely from that of the rest of the genome. Those regions were mostly centromeric and pericentromeric, and enriched for repetitive sequences. We found that DNA binding energy also presented large-scale patterns across soybean chromosomes. These two patterns were helpful during assembly and quality control of soybean whole genome shotgun scaffold sequences into chromosome pseudomolecules.