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

Authors: Peto, Myron; Grant, David; Shoemaker, Randy; Cannon, Steven

Submitted to: Advances in Bioinformatics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/10/2010
Publication Date: 8/18/2010
Citation: Peto, M.F., Grant, D.M., Shoemaker, R.C., Cannon, S.B. 2010. Applying small-scale DNA signatures as an aid in assembling soybean chromosome sequences. Advances in Bioinformatics. DOI:10.1155/2010/976792.

Interpretive Summary: 'Shotgun sequencing' of an organism's hereditary material results in many millions of short DNA sequences comprised of combinations of four component parts of DNA. Assembling the DNA sequence of a whole-genome shotgun sequence is difficult, especially for a complicated genome such as soybean's. Many errors are possible. Many lines of evidence are required to gain confidence that the assembly agreed upon is correct. In this paper, the authors discovered that the component parts of soybean DNA create large-scale patterns across soybean chromosomes. They used these patterns as an aid in assembling the soybean genome shotgun sequences. The demonstration that the patterns created by comparing two of the component parts side by side along the span of a chromosome can be used to help assemble shotgun sequence is a novel and creative use of an old concept (nucleotide 'signatures'). This information is important to genome evolutionary geneticists and to scientists carrying out genome sequence assembly.

Technical Abstract: Previous work has established a genomic signature, based on relative counts of the 16 possible dinucleotides. This signature has been used as a means of detecting genes that have undergone recent horizontal transfer events, as additional evidence supporting or contradicting evolutionary relationship, and even as a tool to suggest that double stranded DNA is of opposite rather than similar polarity. 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 repetitive. We found that DNA binding energy also presented large-scale patterns across soybean chromosomes. These gradients were helpful during assembly and quality control of soybean whole genome shotgun scaffold sequences into pseudomolecule chromosome sequences.