Repetitive DNA in the pea (L.) genome: comprehensive characterization using 454 sequencing and comparison to soybean and -3

<p><b>Copyright information:</b></p><p>Taken from "Repetitive DNA in the pea (L.) genome: comprehensive characterization using 454 sequencing and comparison to soybean and "</p><p>http://www.biomedcentral.com/1471-2164/8/427</p><p>BMC Genomics 2007;8():427-427.</p><p>Published online 21 Nov 2007</p><p>PMCID:PMC2206039.</p><p></p>ilarity to sequences from the other species. The contribution of various repeat families is displayed in different colors as indicated on the legend. . Repeat families conserved between pea and soybean (), soybean and (), and pea and (). Dots on the scatter plots represent 454 reads from one species with similarity to sequences from the other species. Positions of the dots along the axes correspond to the number of significant hits obtained for each 454 read and to their average similarity expressed as BLAST bit score. Repeat families are displayed in the same colors as on panel A; rDNA and unidentified sequences were omitted from panels C and D

Repetitive DNA in the pea (L.) genome: comprehensive characterization using 454 sequencing and comparison to soybean and -5

<p><b>Copyright information:</b></p><p>Taken from "Repetitive DNA in the pea (L.) genome: comprehensive characterization using 454 sequencing and comparison to soybean and "</p><p>http://www.biomedcentral.com/1471-2164/8/427</p><p>BMC Genomics 2007;8():427-427.</p><p>Published online 21 Nov 2007</p><p>PMCID:PMC2206039.</p><p></p>TTAGG)(), and (TTAGG)(). Preparations on panels were simultaneously hybridized to PisTR-B probe (green) to discriminate individual chromosome types [20]. Chromosomes were counterstained with DAPI (blue)

Repetitive DNA in the pea (L.) genome: comprehensive characterization using 454 sequencing and comparison to soybean and -2

<p><b>Copyright information:</b></p><p>Taken from "Repetitive DNA in the pea (L.) genome: comprehensive characterization using 454 sequencing and comparison to soybean and "</p><p>http://www.biomedcentral.com/1471-2164/8/427</p><p>BMC Genomics 2007;8():427-427.</p><p>Published online 21 Nov 2007</p><p>PMCID:PMC2206039.</p><p></p>n their best BLAST hits (Additional files and ). Ogre retrotransposons were further classified into several subfamilies as shown in the Additional file

Repetitive DNA in the pea (L.) genome: comprehensive characterization using 454 sequencing and comparison to soybean and -1

<p><b>Copyright information:</b></p><p>Taken from "Repetitive DNA in the pea (L.) genome: comprehensive characterization using 454 sequencing and comparison to soybean and "</p><p>http://www.biomedcentral.com/1471-2164/8/427</p><p>BMC Genomics 2007;8():427-427.</p><p>Published online 21 Nov 2007</p><p>PMCID:PMC2206039.</p><p></p>TTAGG)(), and (TTAGG)(). Preparations on panels were simultaneously hybridized to PisTR-B probe (green) to discriminate individual chromosome types [20]. Chromosomes were counterstained with DAPI (blue)

Repetitive DNA in the pea (L.) genome: comprehensive characterization using 454 sequencing and comparison to soybean and -0

<p><b>Copyright information:</b></p><p>Taken from "Repetitive DNA in the pea (L.) genome: comprehensive characterization using 454 sequencing and comparison to soybean and "</p><p>http://www.biomedcentral.com/1471-2164/8/427</p><p>BMC Genomics 2007;8():427-427.</p><p>Published online 21 Nov 2007</p><p>PMCID:PMC2206039.</p><p></p>S) was reconstructed as a single contig (CL2Contig6). The graph shows the read depth (number of assembled reads) along the contig sequence. () Reconstruction of the Ty3/gypsy retroelement Peabody, including most of its long terminal repeat (LTR) sequence and complete polyprotein-coding region (gag-pol). () A novel Ty1/copia element Ps-copia-1/751, reconstructed from ten overlapping contigs. The region devoid of stop codons encoding gag-pol was identified in frame +3. Yellow bars depict length and relative positions of the overlapping contigs, stop codons are represented by red vertical lines

Repetitive DNA in the pea (L.) genome: comprehensive characterization using 454 sequencing and comparison to soybean and -4

<p><b>Copyright information:</b></p><p>Taken from "Repetitive DNA in the pea (L.) genome: comprehensive characterization using 454 sequencing and comparison to soybean and "</p><p>http://www.biomedcentral.com/1471-2164/8/427</p><p>BMC Genomics 2007;8():427-427.</p><p>Published online 21 Nov 2007</p><p>PMCID:PMC2206039.</p><p></p>S) was reconstructed as a single contig (CL2Contig6). The graph shows the read depth (number of assembled reads) along the contig sequence. () Reconstruction of the Ty3/gypsy retroelement Peabody, including most of its long terminal repeat (LTR) sequence and complete polyprotein-coding region (gag-pol). () A novel Ty1/copia element Ps-copia-1/751, reconstructed from ten overlapping contigs. The region devoid of stop codons encoding gag-pol was identified in frame +3. Yellow bars depict length and relative positions of the overlapping contigs, stop codons are represented by red vertical lines

Genome proportions of repetitive sequences.

<p>Genome proportions of repetitive sequences.</p

Comparative analysis of Musaceae species based on the cluster composition.

<p>(A) Sequence composition of the largest clusters is shown. The size of the rectangle is proportional to the number of reads in a cluster for each species. Bar plot in the top row shows the size of the clusters as number of reads. Color of the rectangles correspond to the type of the repeat. Upper lines label groups of clusters discussed in the text. The percentage of reads included in the group is shown in parentheses. (B) The presence of mobile element protein domains in the contig assembled from sequences within the cluster. Only clusters that were annotated are shown. (C–E) Validation of clustering results by Southern blot. Genomic DNA from 15 species was probed with sequences derived from clusters CL16, CL51. and CL30. The lanes contain DNA from 1/<i>M. acuminata</i> ssp. <i>zebrina</i> (ITC 0728), 2/<i>M. acuminata</i> ssp. <i>malaccensis</i> (ITC 0250), 3/<i>M. acuminata</i> ssp. <i>burmannicoides</i> (ITC 0249), 4/<i>M. ornata</i> (ITC 0637), 5/<i>M. mannii</i> (ITC 1411), 6/<i>M. ornata</i> (ITC 0528), 7/<i>M. balbisiana</i> (ITC 1120), 8/<i>M. balbisiana</i> (‘Pisang Klutuk Wulung’), 9/<i>M. balbisiana</i> (ITC 0247), 10/<i>M. peekelii</i> (ITC 0917), 11/<i>M. maclayi</i> (ITC 0614), 12/<i>M. textilis</i> (ITC 0539), 13/<i>M. beccarii</i> (ITC 1070), 14/<i>E. ventricosum</i> (ITC 1387), and 15/<i>E. gilletii</i> (ITC 1389).</p

Comparison of genomic abundance of analyzed reads in all six species.

<p>(A–O) Scatter plots show pairwise comparisons of all analyzed sequences between pairs of species. Each spot corresponds to one sequence read. For each sequence read, the number of similarity hits in each species is displayed (this number is proportional to genomic representation of a particular sequence). Red diagonal line marks the position of sequences with equiproportional genomic representations. Sequences with differential genomic representation between species deviate from diagonal. The 45S rDNA sequences are shown in red. (P) Graph summarizing the number of identified read similarities between and within genomes. Width of the lines connecting nodes of the graph correspond to the number of identified similarity hits between sequence reads from different species (straight lines) and within the same species (loops).</p

Evolutionary relationship between species of Musaceae family.

<p>Phylogeny estimated from ITS data using BioNJ. Six genomes selected for repeat analysis are highlighted.</p