Lessons from the genomes and transcriptomes of filarial nematodes

Abstract

Human filarial infections are a leading cause of morbidity in the developing world. While a small arsenal of drugs exists to treat these infections, there remains a tremendous need for the development of additional interventions. Recent genome sequences and transcriptome analyses of filarial nematodes have provided novel biological insight and allowed for the prediction of novel drug targets as well as potential vaccine candidates. In this review, we discuss the currently available data, insights gained into the metabolism of these organisms, and how the filaria field can move forward by leveraging these data.

Complete representation of a tapeworm genome reveals chromosomes capped by centromeres, necessitating a dual role in segregation and protection

“…Over the past decade, reference and draft genomes of key fluke and tapeworm species have been produced including the causative agents of schistosomiasis, neurocysticercosis, and hydatid and alveolar echinococcosis [1][2][3][4][5][6]. Subsequently, improved assemblies and annotations have been published [7] and/or released to the public, as have RNA sequences from an increasing number of transcriptomic studies, profiling genome-wide gene expression for different life cycle stages, cell compartments, and experimental conditions [8][9][10][11]. Most recently, the diversity of draft genomes of both flatworm and roundworm helminths has been expanded, enabling broader circumscription of helminth-specific gene families and more informative comparative analyses [12].…”

Prediction pipeline for discovery of regulatory motifs associated with Brugia malayi molting

“…We used RNA-seq to profile transcription at different time points during the molt, collecting samples from the infective L3 (from mosquitoes), L3 Day 6, and L3 Day 9 worms recovered from infected gerbils (NCBI PRJNA557263). We combined this transcriptome data with previously published L4 data (Grote et al 2017) that corresponds to Day 14 post infection of gerbils ( Table 1 ). In total, 2.36 billion reads were generated, with 1.38 billion reads mapping to the B. malayi genome.…”

“…Over the past decade, a few parasitic nematode genomes have been sequenced, including B. malayi (Ghedin et al, 2007), Loa loa (Desjardins et al 2013), and Onchocerca volvulus (Cotton et al 2016). Transcriptomic experiments have helped quantify differentially expressed genes and their biological implications (Bennuru et al, 2016; Choi et al, 2011; Grote et al, 2017; Kariuki, Hearne, & Beerntsen, 2010; Li, Wang, Rush, Mitreva, & Weil, 2012). However, little is known about how these genes are regulated through cis-regulatory motifs.…”

Mining Filarial Genomes for Diagnostic and Therapeutic Targets

“…Following the elucidation of the first filarial genome ( B. malayi ) [12], the draft genomes of the human filarial parasites L. loa [13, 14], W. bancrofti [13], O. volvulus [15] and the non-human filarial parasites Brugia pahangi [16], Dirofilaria immitis [17] and Onchocerca ochengi [15] became available. Recent reviews highlight the advances and insights gained from the comparative analyses of the genomes, transcriptomes and proteomes of these filarial nematodes [18, 19].…”