Applying Small-scale DNA Signatures As an Aid in Assembling Soybean Chromosome Sequences

Overview

Journal Adv Bioinformatics

Specialty Biology

Date 2010 Sep 10

PMID 20827309

Authors

Myron Peto

David M Grant

Randy C Shoemaker

Steven B Cannon

Affiliations

Soon will be listed here.

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.

References

Schmutz J, Cannon S, Schlueter J, Ma J, Mitros T, Nelson W . Genome sequence of the palaeopolyploid soybean. Nature. 2010; 463(7278):178-83. DOI: 10.1038/nature08670. View

Breslauer K, Frank R, Blocker H, Marky L . Predicting DNA duplex stability from the base sequence. Proc Natl Acad Sci U S A. 1986; 83(11):3746-50. PMC: 323600. DOI: 10.1073/pnas.83.11.3746. View

Rice P, Longden I, Bleasby A . EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000; 16(6):276-7. DOI: 10.1016/s0168-9525(00)02024-2. View

Gill N, Findley S, Walling J, Hans C, Ma J, Doyle J . Molecular and chromosomal evidence for allopolyploidy in soybean. Plant Physiol. 2009; 151(3):1167-74. PMC: 2773056. DOI: 10.1104/pp.109.137935. View

Du J, Tian Z, Hans C, Laten H, Cannon S, Jackson S . Evolutionary conservation, diversity and specificity of LTR-retrotransposons in flowering plants: insights from genome-wide analysis and multi-specific comparison. Plant J. 2010; 63(4):584-98. DOI: 10.1111/j.1365-313X.2010.04263.x. View

Karlin S, Burge C . Dinucleotide relative abundance extremes: a genomic signature. Trends Genet. 1995; 11(7):283-90. DOI: 10.1016/s0168-9525(00)89076-9. View

Burge C, Campbell A, Karlin S . Over- and under-representation of short oligonucleotides in DNA sequences. Proc Natl Acad Sci U S A. 1992; 89(4):1358-62. PMC: 48449. DOI: 10.1073/pnas.89.4.1358. View

Tuskan G, Difazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U . The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science. 2006; 313(5793):1596-604. DOI: 10.1126/science.1128691. View

Karlin S . Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial genomes. Trends Microbiol. 2001; 9(7):335-43. DOI: 10.1016/s0966-842x(01)02079-0. View

10.

Anderson L, Salameh N, Bass H, Harper L, Cande W, Weber G . Integrating genetic linkage maps with pachytene chromosome structure in maize. Genetics. 2004; 166(4):1923-33. PMC: 1470829. DOI: 10.1534/genetics.166.4.1923. View

11.

Nelson W, Soderlund C . Integrating sequence with FPC fingerprint maps. Nucleic Acids Res. 2009; 37(5):e36. PMC: 2655663. DOI: 10.1093/nar/gkp034. View

12.

Hyten D, Cannon S, Song Q, Weeks N, Fickus E, Shoemaker R . High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence. BMC Genomics. 2010; 11:38. PMC: 2817691. DOI: 10.1186/1471-2164-11-38. View

13.

Benham C, Bi C . The analysis of stress-induced duplex destabilization in long genomic DNA sequences. J Comput Biol. 2004; 11(4):519-43. DOI: 10.1089/cmb.2004.11.519. View

14.

Jaillon O, Aury J, Noel B, Policriti A, Clepet C, Casagrande A . The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature. 2007; 449(7161):463-7. DOI: 10.1038/nature06148. View

15.

. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature. 2000; 408(6814):796-815. DOI: 10.1038/35048692. View

16.

Josse J, Kaiser A, Kornberg A . Enzymatic synthesis of deoxyribonucleic acid. VIII. Frequencies of nearest neighbor base sequences in deoxyribonucleic acid. J Biol Chem. 1961; 236:864-75. View

17.

Karlin S, Brocchieri L, Trent J, Blaisdell B, Mrazek J . Heterogeneity of genome and proteome content in bacteria, archaea, and eukaryotes. Theor Popul Biol. 2002; 61(4):367-90. DOI: 10.1006/tpbi.2002.1606. View

18.

Karlin S, Mrazek J . Compositional differences within and between eukaryotic genomes. Proc Natl Acad Sci U S A. 1997; 94(19):10227-32. PMC: 23344. DOI: 10.1073/pnas.94.19.10227. View

19.

Collyn F, Guy L, Marceau M, Simonet M, Roten C . Describing ancient horizontal gene transfers at the nucleotide and gene levels by comparative pathogenicity island genometrics. Bioinformatics. 2005; 22(9):1072-9. DOI: 10.1093/bioinformatics/bti793. View

20.

Kibbe W . OligoCalc: an online oligonucleotide properties calculator. Nucleic Acids Res. 2007; 35(Web Server issue):W43-6. PMC: 1933198. DOI: 10.1093/nar/gkm234. View