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

Sequence diversity of the two parts of CL18-like satellite sequences.

<p>Consensus sequences of both parts of CL18-like satellite were reconstructed from all analyzed accessions and are displayed as sequence logo (A: CL18-part1; C: CL18-part2). Neighbor-Joining trees constructed from a Jukes-Cantor distance matrix and rooted to the midpoint show diversity of reconstructed parts of CL18-like satellite units obtained from all studied species (B: CL18-part1; D: CL18-part2).</p

List of <i>Musa</i> accessions and their genome sizes.

a<p>Genome constitution as described in MGIS database (<a href="http://www.crop-diversity.org/banana/#AvailableITCAccessions" target="_blank">http://www.crop-diversity.org/banana/#AvailableITCAccessions</a>).</p>b<p>1 pg = 0.978×10⁹ bp <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054808#pone.0054808-Doleel2" target="_blank">[34]</a>.</p>c<p>The study in which DNA content was estimated.</p>*<p>Estimated in the present work.</p

Analysis of 100-Pahang assembly using Profrep.

<p>Genomic sequence Chr9:20,150,000–20,250,000 together with repeat annotation was obtained from the Banana Genome Hub (<a href="http://banana-genome.cirad.fr/" target="_blank">http://banana-genome.cirad.fr/</a>) and analyzed using the Profrep tool against our Musaceae repetitive sequence databases. (A) Six tracks show the numbers of similarity hits against reads from six Musaceae genomes as calculated by Profrep. (B) Annotation of genomic region based on our <i>M. acuminata</i> repeat annotation and Profrep analysis. (C) Annotation of repeats in the DH-Pahang genome obtained from the Banana Genome Hub.</p

Idiograms of three diploid <i>Musa</i> accessions.

<p>(A) <i>M. acuminata</i> ‘DH Pahang’ ITC 1511; (B) <i>M. balbisiana</i> ‘Pisang Klutuk Wulung’; (C) <i>M. schizocarpa</i> ITC 0560.</p

Southern hybridization of genomic DNA isolated from nineteen <i>Musa</i> accessions.

<p>Samples of genomic DNA corresponding to 1×10⁷ copies of monoploid (1C_x) nuclear genomes were digested using <i>Dra</i>I restriction enzyme and hybridized with probes for CL18-like satellite (A) and CL33-like satellite (B) at hybridization stringency of 85%.</p

Diversity of CL33-like satellite sequence.

<p>Consensus sequence of CL33-like satellite was reconstructed from all obtained sequence units of all analyzed accessions and is displayed as sequence logo (A). Neighbor-Joining tree constructed from a Jukes-Cantor distance matrix and rooted to the midpoint shows diversity of individual types of CL33-like repetitive units obtained from all studied accessions (B).</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

Sequenced species.

<p>Sequenced species.</p