Global repeat discovery and estimation of genomic copy number in a large, complex genome using a high-throughput 454 sequence survey-1

<p><b>Copyright information:</b></p><p>Taken from "Global repeat discovery and estimation of genomic copy number in a large, complex genome using a high-throughput 454 sequence survey"</p><p>http://www.biomedcentral.com/1471-2164/8/132</p><p>BMC Genomics 2007;8():132-132.</p><p>Published online 24 May 2007</p><p>PMCID:PMC1894642.</p><p></p>nces of soybean DNA, and estimation of copy number. Copy number was estimated according to the number of sequence survey reads aligning to each 1 kb window of the BACs. The alignment represents the superposition of identical or closely related sequences on the BAC sequence, in order to visualize the individual reads showing regions present in many copies per genome. The BAC sequences were: A) The euchromatic BAC described by Clough .(20); B) the euchromatic BAC GM_WBb0098N11; C) the BAC GM_WBb0078A23 from a heterochromatic regio

Global repeat discovery and estimation of genomic copy number in a large, complex genome using a high-throughput 454 sequence survey-0

<p><b>Copyright information:</b></p><p>Taken from "Global repeat discovery and estimation of genomic copy number in a large, complex genome using a high-throughput 454 sequence survey"</p><p>http://www.biomedcentral.com/1471-2164/8/132</p><p>BMC Genomics 2007;8():132-132.</p><p>Published online 24 May 2007</p><p>PMCID:PMC1894642.</p><p></p>abases and the top significant (1E-6) hit recorded. Percentages represent the percentage of reads with hits to sequences from a particular organism with respect to all reads with hits to the TIGR repeats. B) Distribution of hits to plant repeat databases, by class of repetitive element Raw reads from the genomic sequence survey were matched to the combined plant repeat databases as for (A), and the class of repetitive element for the top hit was used to show the relative abundance of different classes of repetitive elements. This gives an estimate of the relative frequency of these families in the soybean genome. Retrotransposons and rDNA are the most common classes of repeat. See Additional File for common repeat sequences not included in the TIGR database

Global repeat discovery and estimation of genomic copy number in a large, complex genome using a high-throughput 454 sequence survey-2

<p><b>Copyright information:</b></p><p>Taken from "Global repeat discovery and estimation of genomic copy number in a large, complex genome using a high-throughput 454 sequence survey"</p><p>http://www.biomedcentral.com/1471-2164/8/132</p><p>BMC Genomics 2007;8():132-132.</p><p>Published online 24 May 2007</p><p>PMCID:PMC1894642.</p><p></p>T with e < 1E-6). The total number of sequences matching at 95% or higher identity is 37% of total EST clones. Note that few sequences match at 100% identity due to the error rate of the 454 pyrosequencing used for this study.B) Coding fragments discovered within the short reads (with e values to the GenBank protein (nr) database < 1E-6), and their closest protein-level sequence hit by taxonomy of the source organism of the database sequence

Size distribution and genome mapping of the small RNAs.

<p>(A) Percentage of small RNA reads from each genotype by size. (B) Percentages of small RNA reads (abundance) mapped to the reference genome. CC: ColXCol; LL: LerXLer; CL: ColXLer; LC: LerXCol. The numbers on the X-axis differentiate the biological replicates. Two technical replicates were included for each biological replicate. (C) Percentage of small RNA reads mapped to different genomic components. The mean percentage across all libraries was plotted. (D) Average abundance of small RNA mapped to individual genomic features. The abundance of small RNA mapped to each genomic feature was first normalized to the total genome-mapped reads in each library and then to the length of the genomic feature (reads per kilobase per million, RPKM). The error bars represent the standard error of the mean.</p

Annotation of differentially expressed small RNA clusters.

<p>(A) Size distribution of small RNAs in the differentially expressed clusters and (B) relationship between the genomic origins and the hybrid inheritance patterns of the differentially expressed clusters identified in set I (analysis considering both reciprocal hybrids). 500 bp gene: within 500 bp upstream or downstream of a protein coding gene; 500 bp TE: within 500 bp upstream or downstream of a transposable element; LP: low parent; HP: high parent; MP: mid-parent (additive); BLP: below low parent.</p

d/a plots showing the dominant/additive hybrid inheritance patterns relative to parents.

<p>(A) Diagram demonstrating the calculation of d/a value and parental d/a′ value. d/a = 1 indicates the hybrid small RNA level is similar to the high parent while d/a = −1 indicates the hybrid small RNA level is similar to the low parent. d/a = 0 means the hybrid small RNA level is the same as the mid-parent value. In parental d/a′ plots, d/a′ = 1 indicates hybrid small RNA level is similar to the male parent while d/a′ = −1 indicates the hybrid small RNA level is similar to the female parent. d/a′ = 0 means the hybrid small RNAlevel is the same as the mid-parent value. (B) d/a plot of the DE clusters in set I (analysis considering both reciprocal hybrids as a single dataset). (C) Parental d/a′ plot of the DE clusters identified in set II (analysis considering the hybrid with the Landsberg line as female only). (D) parental d/a′ plot of the DE clusters identified in set III (analysis considering the hybrid with the Columbia line as female only).</p

Numbers of differentially expressed (DE) clusters with different small RNA expression patterns.

a<p>Differentially expressed.</p>b<p>Low parent like.</p>c<p>High parent like.</p>d<p>Above high parent.</p>e<p>Below low parent.</p

Gene Ontology (GO) terms identified in the genes associated with low-parent like small RNA level and between LP and MP small RNA level.

<p>The GO terms are represented by circles, visualized in a semantic similarity-based scatter plot, where similar GO terms are close to each other, using software ReviGO. The area of the circle is proportional to the significance of the over-representation of the GO term (-log10 p-value). The color of the circles represents the statistical significance of the over-representation of the GO term, as shown in the legend. The GO term annotations are in Supplemental <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0047043#pone.0047043.s011" target="_blank">Table S2</a>.</p

Approach and results of hybrid inheritance pattern fitting.

<p>(A) Diagram showing how a differentially expressed small RNA cluster (DE cluster) was categorized as one of the seven patterns: Mid-parent like (Additive), high parent like (HP), low parent like (LP), above high parent (AHP), below low parent (BLP), between mid-parent and HP, and between mid-parent and LP. Significance cutoff for t-tests was 0.05. (B) Numbers of additive and non-additive DE clusters identified when (i) both LerXCol and ColXLer were combined as the hybrid group (ii) only considering LerXCol as the hybrid and (iii) only considering ColXLer as the hybrid. (C) Percentages of different patterns in the non-additive DE clusters identified in set I (analysis considering both reciprocal hybrids). (D) Small RNA levels of DE clusters identified in set I (analysis considering both reciprocal hybrids), grouped by their hybrid inheritance pattern. Each row represents the normalized expression level (cluster count) of a DE cluster. The columns represent individual biological replicates of the four genotypes. MP: mid-parent; HP: high parent; LP: low parent; BLP: below low parent.</p

Heterotic phenotypes.

<p>A. Example picture showing one plant of each of the four genotypes at 52 days after planting (DAP). B. Rosette area of the inbreds and hybrids measured as the green leafy area from horizontal plane photographs of plants at 52DAP. C. Rosette sizes of the inbred and hybrid plants, measured as the sum of the lengths of the longest leaf and second longest leaf on 52DAP. D. Number of leaves of the hybrids and inbreds on 52DAP (leaf length>0.5 cM). E. Bolting time of the four genotypes was measured. In all panels, 30–40 individual plants of each of the four genotypes (inbred parents LerXLer, ColXCol and hybrids LerXCol, ColXLer) were measured (except for bolting time where data from 5–7 plants are shown). Error bars represent the 95% confidence interval.</p