Applying Small-Scale DNA Signatures as an Aid in Assembling Soybean Chromosome Sequences.pdfVIP

Hindawi Publishing Corporation Advances in Bioinformatics Volume 2010, Article ID 976792, 7 pages doi:10.1155/2010/976792 Research Article Applying Small-Scale DNA Signatures as an Aid in Assembling Soybean Chromosome Sequences Myron Peto, David M. Grant, Randy C. Shoemaker, and Steven B. Cannon USDA-ARS-CICGR Unit and Department of Agronomy, Iowa State University, Ames, IA 50011, USA Correspondence should be addressed to Steven B. Cannon, steven.cannon@ Received 19 November 2009; Accepted 28 June 2010 Academic Editor: Izabela Makalowska Copyright © 2010 Myron Peto et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 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. 1. Introduction sequence overlap and (2) construction of chromosome pseudomolecules by placing and orienting the scaffolds using The soybean (Glycine max (