title: Gene duplication and paleopolyploidy in soybean and the implications for whole genome sequencing.
abstract: BACKGROUND
  Soybean, Glycine max (L.) Merr., is a well documented paleopolyploid. What remains relatively under characterized is the level of sequence identity in retained homeologous regions of the genome. Recently, the Department of Energy Joint Genome Institute and United States Department of Agriculture jointly announced the sequencing of the soybean genome. One of the initial concerns is to what extent sequence identity in homeologous regions would have on whole genome shotgun sequence assembly.
  
  
  RESULTS
  Seventeen BACs representing approximately 2.03 Mb were sequenced as representative potential homeologous regions from the soybean genome. Genetic mapping of each BAC shows that 11 of the 20 chromosomes are represented. Sequence comparisons between homeologous BACs shows that the soybean genome is a mosaic of retained paleopolyploid regions. Some regions appear to be highly conserved while other regions have diverged significantly. Large-scale "batch" reassembly of all 17 BACs combined showed that even the most homeologous BACs with upwards of 95% sequence identity resolve into their respective homeologous sequences. Potential assembly errors were generated by tandemly duplicated pentatricopeptide repeat containing genes and long simple sequence repeats. Analysis of a whole-genome shotgun assembly of 80,000 randomly chosen JGI-DOE sequence traces reveals some new soybean-specific repeat sequences.
  
  
  CONCLUSIONS
  This analysis investigated both the structure of the paleopolyploid soybean genome and the potential effects retained homeology will have on assembling the whole genome shotgun sequence. Based upon these results, homeologous regions similar to those characterized here will not cause major assembly issues.
authors: 1Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA. acissej@purdue.edu
authors: Jessica A
authors: JA
authors: Schlueter
authors: Jer-Young
authors: JY
authors: Lin
authors: Shannon D
authors: SD
authors: Schlueter
authors: Iryna F
authors: IF
authors: Vasylenko-Sanders
authors: Shweta
authors: S
authors: Deshpande
authors: Jing
authors: J
authors: Yi
authors: Majesta
authors: M
authors: O'Bleness
authors: Bruce A
authors: BA
authors: Roe
authors: Rex T
authors: RT
authors: Nelson
authors: Brian E
authors: BE
authors: Scheffler
authors: Scott A
authors: SA
authors: Jackson
authors: Randy C
authors: RC
authors: Shoemaker
mesh_terms: D001483:Base Sequence / Q000235:genetics; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics; D032461:Chromosomes, Plant / Q000235:genetics; D019143:Evolution, Molecular; D020131:Genes, Duplicate / Q000235:genetics*; D005819:Genetic Markers; D018745:Genome, Plant / Q000235:genetics*; D018895:Microsatellite Repeats; D010802:Phylogeny; D020161:Physical Chromosome Mapping / Q000379:methods*; D011110:Polymorphism, Genetic / Q000235:genetics; D011123:Polyploidy; D012091:Repetitive Sequences, Nucleic Acid; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D013025:Glycine max / Q000235:genetics*; D013045:Species Specificity; D026801:Synteny / Q000235:genetics
chemical_list: D005819:Genetic Markers