Gene duplication and paleopolyploidy in soybean and the implications for whole genome sequencing-3

<p><b>Copyright information:</b></p><p>Taken from "Gene duplication and paleopolyploidy in soybean and the implications for whole genome sequencing"</p><p>http://www.biomedcentral.com/1471-2164/8/330</p><p>BMC Genomics 2007;8():330-330.</p><p>Published online 19 Sep 2007</p><p>PMCID:PMC2077340.</p><p></p>me shotgun trace files. BAC corresponds to any contig that showed greatest identity to already assembled soybean BAC sequence. Mdh refers to a previously sequenced region of soybean containing repetitive sequence. No hit means that there was no blast-based match to the nonredundant database. Other was a best match to a sequence (BAC or genomic) from another organism that was not characterized. Satellite refers to known Sb92 or Str120 centromeric repeat sequences. The rest of the categories are as described in the figure legend

Gene duplication and paleopolyploidy in soybean and the implications for whole genome sequencing-2

<p><b>Copyright information:</b></p><p>Taken from "Gene duplication and paleopolyploidy in soybean and the implications for whole genome sequencing"</p><p>http://www.biomedcentral.com/1471-2164/8/330</p><p>BMC Genomics 2007;8():330-330.</p><p>Published online 19 Sep 2007</p><p>PMCID:PMC2077340.</p><p></p>e11. Predicted gene structures are shown as green boxes and arrows, with the boxes representing exons and lines being introns. Black tick marks on a gene show the start position of a repeated PPR domains within the gene. The blue boxes show the repetitive sequences identified by Vmatch. Orange gene alignments reflect the realignment of predicted gene structures back to the genomics sequence

Gene duplication and paleopolyploidy in soybean and the implications for whole genome sequencing-1

<p><b>Copyright information:</b></p><p>Taken from "Gene duplication and paleopolyploidy in soybean and the implications for whole genome sequencing"</p><p>http://www.biomedcentral.com/1471-2164/8/330</p><p>BMC Genomics 2007;8():330-330.</p><p>Published online 19 Sep 2007</p><p>PMCID:PMC2077340.</p><p></p>Consed. Grey boxes represent the assembled contigs and are scaled in base pairs across each contig. Contig numbers are shown in pink boxes and are arbitrarily assigned by Phred/Phrap during sequence assembly. The blue and green boxes above each assembly show the predicted gene positions for gmw1-15k6 and gmw1-105h23, respectively. The green line-plot above each contig shows the average clone pair consistency. Sequence matches within and between contigs were determined with Cross-Match as part of Consed. Black lines within and between contigs show sequence matches that are in reverse orientation, while the orange lines show sequence matches in the same orientation. The bars between sequence matches correspond to the length of the match. Purple peak-shaped lines between contigs show clone pairs that span a gap. Below each contig is a purple line containing either blue (gmw1-15k6) or green (gmw1-105h23) tick marks; these are the tags that distinguish between traces from each BAC

SyMAP view of unedited physical maps of chromosome 1 from eight diploid species aligned to the ssp

chromosome 1 RefSeq. The numbers in the small rectangles on the left are contig numbers of OMAP phase I physical maps. Beige bars on the right represent the RefSeq (IRGSP V.4 assembly) and the red crosses on the beige bars represent the CentO position of [18]. Purple lines represent BESs aligned to the RefSeq. The order of the species from the left to right is; [AA], [AA], [AA], [BB]; [CC], [EE]; [FF], [GG].<p><b>Copyright information:</b></p><p>Taken from "Construction, alignment and analysis of twelve framework physical maps that represent the ten genome types of the genus "</p><p>http://genomebiology.com/2008/9/2/R45</p><p>Genome Biology 2008;9(2):R45-R45.</p><p>Published online 28 Feb 2008</p><p>PMCID:PMC2374706.</p><p></p