Summary of ‘omics data available for filarial parasites.

<p>Genomic, transcriptomic, proteomic and secretomic datasets of human and animal filarial parasites presently accessible for analyses.</p

Defining <i>Brugia malayi</i> and <i>Wolbachia</i> symbiosis by stage-specific dual RNA-seq

<div><p>Background</p><p>Filarial nematodes currently infect up to 54 million people worldwide, with millions more at risk for infection, representing the leading cause of disability in the developing world. <i>Brugia malayi</i> is one of the causative agents of lymphatic filariasis and remains the only human filarial parasite that can be maintained in small laboratory animals. Many filarial nematode species, including <i>B</i>. <i>malayi</i>, carry an obligate endosymbiont, the alpha-proteobacteria <i>Wolbachia</i>, which can be eliminated through antibiotic treatment. Elimination of the endosymbiont interferes with development, reproduction, and survival of the worms within the mamalian host, a clear indicator that the <i>Wolbachia</i> are crucial for survival of the parasite. Little is understood about the mechanism underlying this symbiosis.</p><p>Methodology/ Principle findings</p><p>To better understand the molecular interplay between these two organisms we profiled the transcriptomes of <i>B</i>. <i>malayi</i> and <i>Wolbachia</i> by dual RNA-seq across the life cycle of the parasite. This helped identify functional pathways involved in this essential symbiotic relationship provided by the co-expression of nematode and bacterial genes. We have identified significant stage-specific and gender-specific differential expression in <i>Wolbachia</i> during the nematode’s development. For example, during female worm development we find that <i>Wolbachia</i> upregulate genes involved in ATP production and purine biosynthesis, as well as genes involved in the oxidative stress response.</p><p>Conclusions/ Significance</p><p>This global transcriptional analysis has highlighted specific pathways to which both <i>Wolbachia</i> and <i>B</i>. <i>malayi</i> contribute concurrently over the life cycle of the parasite, paving the way for the development of novel intervention strategies.</p></div

Circos plots of stage-specific <i>Wolbachia</i> gene expression.

<p><i>Wolbachia</i> expression profiles using normalized FPKMs over development of male and female worms from L4 to 120 days post infection (dpi); genomic location is shown around the perimeter, and the black rectangles represent the CDS.</p

Dual RNA-seq sequencing summary.

<p>The table shows the total reads sequenced and mapped in each biological replicate at each developmental stage, L4 to 120 days post infection (dpi) males (M) and females (F), lower case a and b refer to separate biological replicates.</p

Clustering of stages and <i>Wolbachia</i> DE genes.

<p>Hierarchical clustering of <i>Wolbachia</i> DE genes and developmental stages, L4 through 120 days post infection (dpi) male (M) and female (F), based on gene expression in normalized FPKMs. Expression values were scaled prior to clustering using a Z score calculation, with red representing high expression and blue representing low expression. Biological replicates were combined prior to clustering.</p

DE expression of chaperones.

<p>The table shows the differential expression of genes encoding chaperone proteins over the development of the parasite, L4 to 120 days post infection (dpi) males (M) and females (F). The stage at which the gene is up-regulated is listed, and the stage at which it was compared to is in parentheses.</p

The co-expression network for <i>B</i>. <i>malayi</i> and <i>Wolbachia</i>.

<p>The network heatmap plot of network connectivity for <i>B</i>. <i>malayi</i> and <i>Wolbachia</i> calculated using weighted gene correlation network analysis (WGCNA). The black branches show the hierarchical clustering dendrograms, which were assigned to clusters using dynamic tree cutting to identify modules of co-expressed genes, shown as colored bars. High co-expression interconnectedness is indicated by increasingly saturated orange and red coloring. Modules correspond to groups of highly interconnected genes.</p

Heatmap of gene expression of pathways of interest.

<p>Expression, in log FPKMs, is plotted over the development of the nematode, L4 to 120 days post infection (dpi) male (M) and female (F), by pathway for heme, riboflavin, FAD, peptidoglycan, and isoprenoid biosynthesis as well as expression of the main secretion systems in <i>Wolbachia</i> including Sec translocase, Type IV secretion system, and ABC transporters.</p

Clustering of stages based on <i>B</i>. <i>malayi</i> gene expression.

<p>Clustering of <i>B</i>. <i>malayi</i> genes and developmental stages, L4 to 120 days post infection (dpi) Male (M) and Female (F), based on gene expression in normalized FPKMs. Expression was scaled using Z score prior to clustering, with red representing high expression and blue representing low expression. Biological replicates were combined prior to analysis.</p