Table 1.
Description of the results of the alignments on PN40024 for the different sequenced clones by 454 methodology and for PN115 available sequences.
Table 2.
Coverage of clones genomes.
Figure 1.
Read alignment on chromosome 1.
To test the random distribution of reads, three runs were sequentially aligned. The first 454 run was aligned (red line) on chromosome 1. Then both first and second runs were aligned together (blue line), and finally all three runs (green line) were aligned on the chromosome. The insufficiently covered region around 13 Mb in chromosome 1 corresponds to the centromere.
Table 3.
Composition of 454 reads aligned with the reference genome.
Figure 2.
Results from polymorphism call. A) Number of polymorphisms detected between, each pair of clones; Numbers of SSR, SNP, indel and mobile element polymorphisms between each pair of clones in regions of 6.00 fold genome coverage only covering 4.5 Mb of genome. B) Map of polymorphism between clone PN115 and clones PN386, PN583, PN777. All types of polymorphisms (SNPs, indels, mobile elements) detected between PN115 and partially 454-sequenced (6.00 fold genome coverage ) clones (green, blue, red for PN386, PN583, PN777 respectively). SNPs, indels and mobile elements are represented by crosses, squares, and diamonds respectively.
Figure 3.
Number of SSR, SNP, indel and mobile element polymorphisms with PN115 per Mb of genome sequence for each clone.
In red PN386, in blue PN583 and in green PN777.
Figure 4.
Tree of all registered Pinot clones based on S-SAP data with 4 mobile elements.
S-SAP performed with Gret-1, Copia-10, Gypsy-19 and Cauliv-1 mobile elements. All analyzed clones have a specific pattern for these elements. 60 Pinot clones (PN = Pinot noir (40) ; PM = Pinot meunier (15) ; PG = Pinot gris (3) ; PB = Pinot blanc (2)) and 4 Cabernet-Sauvignon clones were analyzed.
Table 4.
Distribution of consensus LTRs from clones sequenced by 454 methodology.
Table 5.
Sequencing statistics of the raw data.
Figure 5.
Gret-1 tree from the consensus sequence detected in LTR.
The consensus region used to build the tree for Gret-1 mobile element is indicated by the dashed line. On the tree, the group of similar sequences (circled in red) suggests recent activity of Gret-1.
Figure 6.
Summary of the alignment method used in the present study.
Alignment was accomplished in three successive steps: i) The first alignment used Mosaik with default parameters for 454 GS-FLX: 95% alignment homology in the sequences; ii) Reads not aligned in the first step and that were not paralogs were then filtered with RepeatMasker software. Reads with less than 90% homology with repeat elements were aligned by Mosaik with default parameters. iii) For reads not aligned in the second step, a third alignment was performed using a gap parameter fixed at a minimum (0.1 gap open and extensive penalties).