L'Athlète : journal hebdomadaire de tous les sports

18 novembre 19261926/11/18 (N496)-1926/11/18.Appartient à l’ensemble documentaire : Aquit

Comparison of <i>de novo</i> predicted repeated elements between the European pear, Chinese pear and apple genomes. na: not available from [18].

<p>Comparison of <i>de novo</i> predicted repeated elements between the European pear, Chinese pear and apple genomes. na: not available from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0092644#pone.0092644-Wu1" target="_blank">[18]</a>.</p

Gene prediction summary for <i>Pyrus communis</i> and comparison with <i>P. bretschneideri</i>, <i>Fragaria vesca</i> and <i>Malus</i>×<i>domestica</i>.

<p>Gene predictions were performed using Augustus for European pear and GeneMark-ES for strawberry. The apple gene models were estimated as the total number of gene predictions minus an estimation of duplications generated by contig overlaps. The redundancy was filtered out using similarity among predictions and positional considerations.</p

Basic statistics on the <i>Pyrus communis</i> ‘Bartlett’ genome sequence.

<p>Figures are given in bp.</p><p>*: the assumed genome size of pear is 600 Mb.</p

Phylogenetic tree of six rosids, four malvids, and three asterids constructed with 83 euKaryote Orthologous Genes (KOGs).

<p>Bootstrap values are listed on each branch. Nodes represent speciation events and branch length represents the degree of evolutional changes over time. The unit for the scale bar at the bottom is nucleotide substitutions per site. The high bootstrap values strongly support that the species in Rosaceae cluster together to the exclusion of any other, and that the European pear and Chinese pear separation event happened after apple speciation.</p

Classification of repeated elements in European pear based on the ‘Rosaceae’ clade from RepBase.

<p>Classification of repeated elements in European pear based on the ‘Rosaceae’ clade from RepBase.</p

Protein-protein comparison between European pear and 12 other species: Chinese pear, apple, grape, strawberry, papaya, sweet orange, clementine, kiwifruit, tomato, potato, poplar and <i>Arabidopsis</i>.

<p>The figure shows every possible combination of species included in this proteome ortholog analysis, using concentric circles. Each ring represents a single plant species and is depicted in a unique colour. For the 13 species shown, there are hence a total of 2¹³–1 combination cases, from 556 ortholog groups found in European pear only, 682 clades in Chinese pear only, to 5393 clusters present in all thirteen species. For each combination, the number of ortholog groups discovered is labelled outside the outermost ring and the number of proteins for a species inside a coloured, circular cell that represents the particular species. As the angular width of the cells for each case is drawn proportional to its number of groups, there is no labelling where the angular width is too small. A complete list of all combination cases with detected ortholog genes is provided in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0092644#pone.0092644.s005" target="_blank">Table S4</a>.</p

Anchoring of the <i>Pyrus communis</i> ‘Bartlett’ assembly v1.0 genome sequence.

<p>Anchoring of the <i>Pyrus communis</i> ‘Bartlett’ assembly v1.0 genome sequence.</p

Additional file 4: of A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants

BLASTP comparison of manually edited gene models to the revised ‘Hongyang’ gene models. List of best reciprocal BLASTp matches between the revised Actinidia chinensis ‘Hongyang’ genes [18]and the Red5 gene set (XLSX 436 kb

Additional file 3: of A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants

Comparison of predicted paired end distance to genome.Heatmaps of alignment distance scores for the alignment of the read pairs from the 9Kb long-insert mate-paired-end (LIMP) library to each of the 29 chromosomes within the Red5 whole genome assembly and. Individual chromosome plots were prepared using hagfish_blockplot from the software program ‘hagfish’ ( https://github.com/mfiers/hagfish/ ). Individual images were cropped for height (not length) then cut and pasted into a table format for easier viewing. Each image depicted the entire length of the chromosome but all images are of standard length irrespective of chromosome length. Green regions indicate mate pairs aligning to the whole genome sequence within the expected distance of the library. Black indicates regions without mate pair alignment. Pinkish-red indicates regions where the distance between mated paired end reads is shorter (assembly compression relative to physical genome) or longer (assembly expansion relative to physical genome). (PPTX 432 kb