Transposable element distribution, abundance and role in genome size variation in the genus -1

<p><b>Copyright information:</b></p><p>Taken from "Transposable element distribution, abundance and role in genome size variation in the genus "</p><p>http://www.biomedcentral.com/1471-2148/7/152</p><p>BMC Evolutionary Biology 2007;7():152-152.</p><p>Published online 29 Aug 2007</p><p>PMCID:PMC2041954.</p><p></p>netic tree using the neighbor-joining method. Bootstrap values were calculated for 1000 replicates; only those with values greater than 50 are proposed B) distribution of the domains isolated in different species. Bar colors are the same of those used in the circles marking, on the neighbor-joining tree sequences from different species

Transposable element distribution, abundance and role in genome size variation in the genus -6

<p><b>Copyright information:</b></p><p>Taken from "Transposable element distribution, abundance and role in genome size variation in the genus "</p><p>http://www.biomedcentral.com/1471-2148/7/152</p><p>BMC Evolutionary Biology 2007;7():152-152.</p><p>Published online 29 Aug 2007</p><p>PMCID:PMC2041954.</p><p></p>(2006) [9] and normalized to 1 Mbp. The confidence intervals, displayed as error bars, were calculated assuming a Poisson distribution of repeats in the genome. The mean length used in calculation for different repeats were as follows: Ty3-elements: 12 Kbp; Ty1-elements: 5.5 Kbp; others LTR-RTs not classified (LTR-retrotransposons): 8.75 Kbp; LINEs: 3.5 kbp; helitrons (complete autonomous): 12.8 Kbp; CACTA: 15.2 Kbp; hAT: 3.6 Kbp *In this case all the calculations are based on a rough estimate of the genome size of this species: the real value is unknown, we therefore used the value estimated for [HHJJ; 1283 Mbp], which is also an allotetraploid species and shares the HH genome type with

Transposable element distribution, abundance and role in genome size variation in the genus -2

<p><b>Copyright information:</b></p><p>Taken from "Transposable element distribution, abundance and role in genome size variation in the genus "</p><p>http://www.biomedcentral.com/1471-2148/7/152</p><p>BMC Evolutionary Biology 2007;7():152-152.</p><p>Published online 29 Aug 2007</p><p>PMCID:PMC2041954.</p><p></p>netic tree using the neighbor-joining method. Bootstrap values were calculated for 1000 replicates; only those with values greater than 50 are proposed B) distribution of the domains isolated in different species. Bar colors are the same of those used in the circles marking, on the neighbor-joining tree sequences from different species

Transposable element distribution, abundance and role in genome size variation in the genus -5

<p><b>Copyright information:</b></p><p>Taken from "Transposable element distribution, abundance and role in genome size variation in the genus "</p><p>http://www.biomedcentral.com/1471-2148/7/152</p><p>BMC Evolutionary Biology 2007;7():152-152.</p><p>Published online 29 Aug 2007</p><p>PMCID:PMC2041954.</p><p></p>e using the neighbor-joining method. Bootstrap values were calculated for 1000 replicates; only those with values greater than 50 are proposed B) distribution of the domains isolated in different species. Bar colors are the same of those used in the circles marking, on the neighbor-joining tree sequences from different species

Additional file 1: Figures S1. of DNA methylation changes facilitated evolution of genes derived from Mutator-like transposable elements

a) shows the phylogenetic tree of 10 Oryza and 1 Leersia species. Based on the presence and absence of MULEs on the phylogenetic tree, we inferred the origination time points of the MULEs measured with divergence time of the 11 species. We listed the origination time index on the phylogenetic tree as 1-9, e.g. “1” represents MULEs originated after each species diverged, “4” represents MULEs originated before Asian rice diverged but after Asian rice split from the rest of Oryza species, 9 represents MULEs originated before the AA and BB genome rice diverged. Then for each of the 9 Oryza 2 species, we grouped their MULEs based on its origination time index. b) We categorized MULEs based on their origination time points (shown in ‘a’) inferred from presence and absence of MULEs in the phylogenetic tree of Oryza species, and drew the density distribution of the amplification time of MULEs, which were estimated based on the sequence divergence of MULEs and their most similar paralogs, in each origination time point category for 9 species, respectively. Figure S2. Methylation level distribution of parental sequences of MULE-derived genes and randomly selected non-TE genic-regions in across the O. nivara genome. Figure S3. Methylation level of MULE-derived putative genes a) in O. sativa ssp. japonica genome; b) the genes derived from MULEs overlapped between Ferguson et al. and us.; c) in O. nivara genome. Figure S4. Analysis of methylation levels of genic-MULEs with the overlapped data set of Ferguson et al. and us. a) Methylation level of MULE internal sequences; b) Methylation level of entire MULEs and flanking regions. Figure S5. Analysis of TE-coverage and TIR similarity of genic-MULEs with the overlapped data set of Ferguson et al and us. Figure S6. Analysis of methylation levels of genic-MULEs in O. nivara genome. a) Methylation level of MULE internal sequences; b) Methylation level of entire MULEs and flanking regions. Figure S7. Analysis of TE-coverage of genic-MULEs in O. nivara genome. Figure S8. The Marey’s and recombination rate map of O. sativa ssp. japonica genome. The Blue line is based on LOESS function and the red line is based on cubic splines. (DOCX 3.19 mb

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