Additional file 9: Figure S8. of Comprehensive repeatome annotation reveals strong potential impact of repetitive elements on tomato ripening

The age of the genes specific to each genomic region. Counting genes considering their phylogenetic origin and comparing that repartition to that expected give us an information about gene age repartition in the three compartments. Statistical analyzes (chi-square tests) were conducted to validate the observations and are represented by the P-value on this graphic. (TIF 130 kb

Petasites fragrans Presl

原著和名: ニホヒクヮントウ科名: キク科 = Compositae採集地: 千葉県 船橋市三山2-2-1 東邦大学 (下総 東邦大学)採集日: 1972/3/1採集者: 萩庭丈壽整理番号: JH007510国立科学博物館整理番号: TNS-VS-95751

Wolbachia wsp gene sequence accession numbers used in phylogenetic analysis.

<p>Wolbachia wsp gene sequence accession numbers used in phylogenetic analysis.</p

Comparison of genome properties for <i>Wolbachia</i> endosymbiont of <i>Diaphorina citri</i> (wDi) with the complete genome sequences for four Wolbachia strains^a.

<p>Comparison of genome properties for <i>Wolbachia</i> endosymbiont of <i>Diaphorina citri</i> (wDi) with the complete genome sequences for four Wolbachia strains^{<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0050067#nt103" target="_blank">a</a>}.</p

Maximum Parsimony tree for <i>Wolbachia</i> Wsp sequences highlighting the placement of Florida (blue arrow) and Chinese isolates (red arrows) in different sub-clades of supergroup B.

<p>Maximum Parsimony tree for <i>Wolbachia</i> Wsp sequences highlighting the placement of Florida (blue arrow) and Chinese isolates (red arrows) in different sub-clades of supergroup B.</p

Endosymbionts identified in <i>D. citri</i> and <i>B. cockerelli</i> isolates by rDNA sequencing and evidence for sequences derived from these candidates in the <i>D. citri</i> metagenome.

<p>Endosymbionts identified in <i>D. citri</i> and <i>B. cockerelli</i> isolates by rDNA sequencing and evidence for sequences derived from these candidates in the <i>D. citri</i> metagenome.</p

Identification of core genome for Wolbachia strains with complete genome sequences using OrthoMCL^a.

<p>Identification of core genome for Wolbachia strains with complete genome sequences using OrthoMCL^{<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0050067#nt104" target="_blank">a</a>}.</p

Maximum Parsimony tree for <i>Wolbachia</i> FtsZ sequences supporting placement of <i>Wolbachia</i> endosymbiont of <i>Diaphorina citri</i> (wDi) in supergroup B.

<p>Chinese strains are indicated with red arrows and the Florida strain with a blue arrow.</p

Table_1_Differential gene expression of Asian citrus psyllids infected with ‘Ca. Liberibacter asiaticus’ reveals hyper-susceptibility to invasion by instar fourth-fifth and teneral adult stages.xlsx

The bacterial pathogen Candidatus Liberibacter asiaticus (CLas) is the causal agent of citrus greening disease. This unusual plant pathogenic bacterium also infects its psyllid host, the Asian citrus psyllid (ACP). To investigate gene expression profiles with a focus on genes involved in infection and circulation within the psyllid host of CLas, RNA-seq libraries were constructed from CLas-infected and CLas-free ACP representing the five different developmental stages, namely, nymphal instars 1-2, 3, and 4-5, and teneral and mature adults. The Gbp paired-end reads (296) representing the transcriptional landscape of ACP across all life stages and the official gene set (OGSv3) were annotated based on the chromosomal-length v3 reference genome and used for de novo transcript discovery resulting in 25,410 genes with 124,177 isoforms. Differential expression analysis across all ACP developmental stages revealed instar-specific responses to CLas infection, with greater overall responses by nymphal instars, compared to mature adults. More genes were over-or under-expressed in the 4-5th nymphal instars and young (teneral) adults than in instars 1-3, or mature adults, indicating that late immature instars and young maturing adults were highly responsive to CLas infection. Genes identified with potential for direct or indirect involvement in the ACP-CLas circulative, propagative transmission pathway were predominantly responsive during early invasion and infection processes and included canonical cytoskeletal remodeling and endo-exocytosis pathway genes. Genes with predicted functions in defense, development, and immunity exhibited the greatest responsiveness to CLas infection. These results shed new light on ACP-CLas interactions essential for pathogenesis of the psyllid host, some that share striking similarities with effector protein-animal host mechanisms reported for other culturable and/or fastidious bacterial- or viral- host pathosystems.</p

Workflow used to identify regions of reference genomes illuminated by sequence reads from the <i>Diaphorina citri</i> metagenome data set.

<p>Workflow used to identify regions of reference genomes illuminated by sequence reads from the <i>Diaphorina citri</i> metagenome data set.</p