第768回千葉医学会例会・第3回磯野外科例会 83.

List of the sequences used in the analyses. (XLSX 67 kb

Xanthomonas citri - 44 strain PhyML phylogeny SYM model

A maximum likelihood phylogenetic tree constructed with PhyML from the genome alignment of 44 strains of Xanthomonas citri. Regions of recombination were removed from the alignment as well as gap-containing columns and +/- 20bp from a gap-containing column. The evolutionary model used was SYM, as chosen with jModeltest 2.1.7

Xanthomonas citri - 36 strain concatenated genome alignment (gaps +/- 20nt removed) FASTA format, Contains recombination

A FASTA format multiple sequence alignment used for phylogenetic reconstruction. The alignment was constructed by concatenating blocks from a whole genome multiple alignment using the IAPAR 306 strain to order blocks. Gap-containing columns and 20 nt surrounding gap-containing columns were removed. The alignment contains regions of recombination and the distibution of A pathotype strains is reduced to only those containing recombination event 16

Xanthomonas citri - 36 strain PhyML phylogeny GTR model, Reduced A-strain distribution, Contains recombination

A maximum likelihood phylogenetic tree constructed with PhyML from the genome alignment of 36 strains of Xanthomonas citri. The alignment contains regions of recombination and the distibution of A pathotype strains is reduced to only those containing recombination Event 16. The evolutionary model used was GTR

Xanthomonas citri - 44 strain Mugsy genome alignment

A multiple genome alignment of 44 strains of Xanthomonas citri output from the Mugsy genome alignment softwar

Xanthomonas citri - 44 strain concatenated genome alignment (recombination, gaps +/- 20nt removed) FASTA format

A FASTA format multiple sequence alignment used for phylogenetic reconstruction. The alignment was constructed by concatenating blocks from a whole genome multiple alignment using the IAPAR 306 strain to order blocks. Regions of recombination detected using RDP were removed, as were gap-containing columns and 20 nt surrounding gap-containing columns

Bipartite food webs of predator-prey interactions on (A) bare soil, and (B) cover cropped banana plantation.

<p>For each web, lower bars represent relative abundance of consumed prey, and upper bars represent relative abundance of positive ground-dwelling predators, each drawn at different scale. The width of links between ground-dwelling predators and prey represents the frequency of consumption. Numbers in grey indicate unlinked taxa. Visualization was performed with the R package “bipartite” <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0093740#pone.0093740-Dormann1" target="_blank">[50]</a>. 1: <i>Anopheles claviger.</i> 2: <i>Anopheles nimbus.</i> 3: <i>Baetis rhodani.</i> 4: <i>Blatella germanica.</i> 5: <i>Calliphora vomitoria.</i> 6: <i>Carabidae</i> spp. 7: <i>Codophila varia</i>. 8: <i>Coridius chinensis</i>. <i>9</i>: <i>Cosmopolites sordidus</i>. 10: Diptera. 11: <i>Drosophila anceps</i>. 12: <i>Drosophila melanica</i>. 13: <i>Drosophila montana</i>. 14: <i>Gryllus</i>. 15: Hemiptera. 16: <i>Jalysus spinosus</i>. 17: <i>Nebria chinensis</i>. 18: <i>Neoneides muticus</i>. 19: <i>Nezara viridula</i>. 20: Oniscidae. 21: <i>Ophyra spinigera</i>. 22: <i>Periplaneta americana</i>. 23: <i>Podisus serieventris</i>. 24: <i>Polytus mellerborgi</i>. 25: <i>Resseliella yagoi</i>. 26: <i>Sarcophila</i>. 27: <i>Scolopendra</i>. 28: <i>Scolopendra mutilans</i>. 29: <i>Stephensioniella sterrei</i>. 30: Lycosidae. 31: <i>Camponotus sexguttatus</i>. 32: <i>Euborellia caraibea</i>. 33: <i>Odontomachus baurii</i>. 34: Scolopendridae. 35: <i>Solenopsis geminata</i>. 36: Staphilinidae. 37: <i>Wasmannia auropunctata.</i></p

Additional file 6: of Comparative genomics of 43 strains of Xanthomonas citri pv. citri reveals the evolutionary events giving rise to pathotypes with different host ranges

Pathotype-specific significantly enriched or depleted ( P <0.05) COG categories for missing genes, SNP-containing genes or genes within zones of recombination. (XLSX 12 kb

Frequency of taxa identified corresponding to each taxon analysed with the mini-COI barcodes.

<p>Generated by 454 pyrosequencing, the table displays the taxonomic rank, the frequencies of samples and the corresponding sample size in brackets, and the number of sequences corresponding to taxa identified by barcoding and belonging to the same order of the taxa analysed. A frequency of 100% means that all samples of the taxa analysed had at least two sequences of the taxa identified by barcoding (BLAST+ with E-value = 10⁻²⁰, FASTA with 85% similarity threshold, and Nearest Neighbour algorithm for the final identification).</p

Diet changes of ground-dwelling predators between bare soil plot and cover cropped plot.

<p>The bar charts display the difference of frequencies of consumption for each prey calculated between the two plots, with the bare soil plot as a reference. The significance of the difference of frequencies of consumption observed between plots was assessed with a Fisher’s exact test. (***: <i>p</i>-value<0.0001; **: <i>p</i>-value<0.001; *: <i>p</i>-value<0.01). Black crosses above bar charts indicate that the prey was not detected in both treatments.</p