The genome of Onchocerca volvulus, agent of river blindness

Cotton, James A.; Bennuru, Sasisekhar; Grote, Alexandra; Harsha, Bhavana; Tracey, Alan S.; Beech, Robin N.; Doyle, Stephen R.; Dunn, Matthew; Hotopp, Julie C. Dunning; Holroyd, Nancy; Kikuchi, Taisei; Lambert, Olivia J.; Mhashilkar, Amruta S.; Mutowo, Prudence; Nursimulu, Nirvana; Ribeiro, José M. C.; Rogers, Matthew B.; Stanley, Eleanor; Swapna, Lakshmipuram S.; Tsai, Isheng Jason; Unnasch, Thomas R.; Voronin, Denis; Parkinson, John; Nutman, Thomas B.; Ghedin, Elodie; Berriman, Matthew; Lustigman, Sara

doi:10.1038/nmicrobiol.2016.216

Cited by 121 publications

(188 citation statements)

References 111 publications

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“…The strategy was to use C. elegans as a reference for assigning ancestral chromosomal identity. To test if this was a valid approach, we confirmed that the chromosomal identity for most orthologs has been conserved between C. elegans and C. briggsae (for which the genome is resolved at the chromosomal level [40, 41]) and Haemonchus contortus [42]. H. contortus also has six chromosomes, but is much more distantly related to Caenorhabditis than is Caenorhabditis to Diploscapter , thus serving as an outgroup representative for these comparisons (Figures 1A, S4).…”

Section: Resultsmentioning

confidence: 99%

Genome Architecture and Evolution of a Unichromosomal Asexual Nematode

et al. 2017

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SUMMARY Asexual reproduction in animals, though rare, is the main or exclusive mode of reproduction in some long-lived lineages. The longevity of asexual clades may be correlated with the maintenance of heterozygosity by mechanisms that rearrange genomes and reduce recombination. Asexual species thus provide an opportunity to gain insight into the relationship between molecular changes, genome architecture and cellular processes. Here, we report the genome sequence of the parthenogenetic nematode Diploscapter pachys with only one chromosome pair. We show that this unichromosomal architecture is shared by a long-lived clade of asexual nematodes closely related to the genetic model organism Caenorhabditis elegans. Analysis of the genome assembly reveals that the unitary chromosome arose through fusion of six ancestral chromosomes, with extensive rearrangement among neighboring regions. Typical nematode telomeres and telomeric protection-encoding genes are lacking. Most regions show significant heterozygosity; homozygosity is largely concentrated to one region and attributed to gene conversion. Cell-biological and molecular evidence are consistent with the absence of key features of Meiosis I, including synapsis and recombination. We propose that D. pachys preserves heterozygosity and produces diploid embryos without fertilizationthrough a truncated meiosis. As a prelude to functional studies, we demonstrate that D. pachys is amenable to experimental manipulation by RNA interference.

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Section: Resultsmentioning

confidence: 99%

Genome Architecture and Evolution of a Unichromosomal Asexual Nematode

et al. 2017

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“…The publication of the genome of O. volvulus [108] should assist this search. Means to improve coverage and compliance of CDTI and the discovery of a reliable macrofilaricide are also required, together with continuing research to find a vaccine.…”

Section: Five-year Viewmentioning

confidence: 99%

Factors affecting onchocerciasis transmission: lessons for infection control

Cheke

2017

Expert Review of Anti-infective Therapy

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Introduction: Onchocerca volvulus infects in excess of 15 million people. The vectors are Simulium blackflies, varieties of which differ in their ecologies, behaviour and vectorial abilities. Control of the vectors and mass administrations of ivermectin have succeeded in reducing prevalences with elimination achieved in some foci, particularly in Central and southern America. In Africa, progress towards elimination has been less successful.Areas covered: Even with community directed treatment with ivermectin (CDTI), control has been difficult in African areas with initial prevalences in excess of 55%, especially if only annual treatments are dispensed. This is partly attributable to insufficient coverage, but the appearance of incipiently resistant non-responding parasites and lack of attention to vector biology in modelling and planning outcomes of intervention programmes have also played their parts, with recrudescence now appearing in some treated areas. Expert commentary:The biology of onchocerciasis is complex involving different vectors with differing abilities to transmit parasites, diverse pathologies related to geographical and parasite variations and endosymbionts in both parasite and vector. Modelling to predict epidemiological and control outcomes is addressing this complexity but more attention needs to be given to the vectors' roles to further understanding of where and when control measures will succeed.

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“…Advances in sequencing technologies have enabled the exploration of many new genomes across all domains of life [1–8]. Unfortunately, in most instances correctly aligning even just two genomes at base-pair resolution can be challenging.…”

Section: Introductionmentioning

confidence: 99%

Inferring synteny between genome assemblies: a systematic evaluation

2018

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BackgroundGenome assemblies across all domains of life are being produced routinely. Initial analysis of a new genome usually includes annotation and comparative genomics. Synteny provides a framework in which conservation of homologous genes and gene order is identified between genomes of different species. The availability of human and mouse genomes paved the way for algorithm development in large-scale synteny mapping, which eventually became an integral part of comparative genomics. Synteny analysis is regularly performed on assembled sequences that are fragmented, neglecting the fact that most methods were developed using complete genomes. It is unknown to what extent draft assemblies lead to errors in such analysis.ResultsWe fragmented genome assemblies of model nematodes to various extents and conducted synteny identification and downstream analysis. We first show that synteny between species can be underestimated up to 40% and find disagreements between popular tools that infer synteny blocks. This inconsistency and further demonstration of erroneous gene ontology enrichment tests raise questions about the robustness of previous synteny analysis when gold standard genome sequences remain limited. In addition, assembly scaffolding using a reference guided approach with a closely related species may result in chimeric scaffolds with inflated assembly metrics if a true evolutionary relationship was overlooked. Annotation quality, however, has minimal effect on synteny if the assembled genome is highly contiguous.ConclusionsOur results show that a minimum N50 of 1 Mb is required for robust downstream synteny analysis, which emphasizes the importance of gold standard genomes to the science community, and should be achieved given the current progress in sequencing technology.Electronic supplementary materialThe online version of this article (10.1186/s12859-018-2026-4) contains supplementary material, which is available to authorized users.

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The genome of Onchocerca volvulus, agent of river blindness

Cited by 121 publications

References 111 publications

Genome Architecture and Evolution of a Unichromosomal Asexual Nematode

Genome Architecture and Evolution of a Unichromosomal Asexual Nematode

Factors affecting onchocerciasis transmission: lessons for infection control

Inferring synteny between genome assemblies: a systematic evaluation

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