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

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

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

Sequenced species.

<p>Sequenced species.</p

Variability of sequences within cluster CL18.

<p>(A) Sequence reads are represented by nodes of the graph and reads with identity of at least 90% with minimal overlap of 110 nt are connected by lines. Graph layout was calculated using the 3D version of the Fruchterman and Reingold algorithm <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0098918#pone.0098918-Fruchterman1" target="_blank">[55]</a> from which a 2D projection is shown. Reads are colored based on their similarity to conserved coding domains of LTR retrotransposons. Reads from LTR regions are colored by light blue. (B) Nodes of the graph are colored based on their species of origin. The six identical graphs show reads derived from each species in red; remaining reads are gray to highlight species-specific parts of the graphs. The parts of the graphs that represent the most variable sequence regions in CRM CL18 element, which can differentiate between species, are labeled by black arrows. (C) Maximum-likelihood tree based on nucleotide alignment of sequences covering the reverse transcriptase protein domain of CRM CL18. Sequence read names are colored based on the species of origin.</p

Pea has two variants of the CenH3 that fully colocalize in centromeres of all chromosomes.

<p>A: Alignment of protein sequences of the pea CenH3 histones. Red line above the alignment marks a putative centromere targeting domain (CATD). Dotted lines above and below the alignment show the peptide sequences which were used as antigens to produce antibody to CenH3-1 and CenH3-2, respectively. Secondary structure of the histone fold domain is depicted below the alignment. B–C: Direct visualization of fusion proteins of CenH3-1 or CenH3-2 with YFP revealed 14 foci in the interphase nucleus, corresponding to the number of chromosomes in diploid cells. D: Fusion protein of canonical H3 with YFP is localized in whole nucleus. ELISA assays of the two CenH3 antibodies revealed low level of cross-reaction of the CenH3-1 antibody to the peptide designed from the CenH3-2 (data not shown). As we could not determine if the cross-reactivity was sufficient to produce signal after detection <i>in situ</i>, the colocalization experiments were performed using highly-specific antibodies to YFP and CenH3-2 in hairy root lines expressing CenH3-1_YFP. E–J: Detection of CenH3-1_YFP (red) and CenH3-2 (green) revealed full colocalization of the two proteins both in interphase nucleus (E–G) and metaphase chromosomes (H–J). K–M: Fully overlapping signals were observed also using simultaneous detection of CenH3 proteins with antibodies to CenH3-1 (red) and CenH3-2 (green) as shown on the example of chromosome 3 possessing three distinct domains containing CenH3. This indicates that either of the two antibodies was capable of detecting all functional centromere domains and that the gaps between individual domains lack CenH3 of any type. Bar = 5 µm.</p

Characterization of satellite DNA families identified in the pea.

<p>Characterization of satellite DNA families identified in the pea.</p

Organization and DNA sequence composition of CenH3-containing domains in chromosome 3.

<p>A–B: Primary constriction of chromosome 3 contains three functional centromere domains as defined by the presence of CenH3-1. Correlative fluorescence and scanning electron microscopy images of the same chromosome using FluoroNanogold showed that the three domains recognized with fluorescence (A, red signals) are composed of multiple foci from markers (bright spots) near the surface of the primary constriction (B, backscattered electron micrograph). C: Secondary electron micrograph image of the same chromosome. The primary constriction exhibits few chromomeres and a typical longitudinal orientation of fibrillar substructures, to which the CenH3 domains roughly correspond. The arrows mark the CenH3-1 containing regions. D–F: Detection of three different families of satellite DNA by FISH (green) combined with immunodection of CenH3-1 (red). Each of the functional centromere domains is composed of different family of satellite DNA; the domain closest to the long arm is composed of PisTR-B (D), the middle one of TR-1 (E) and the one closest to the short arm of TR-18 (F). Chromosomes were counterstained with DAPI (blue). Bar = 2 µm (A and D–F) or 0.2 µm (B–C).</p