Rendering the Intractable More Tractable: Tools from <i>Caenorhabditis elegans</i> Ripe for Import into Parasitic Nematodes

Ward, Jordan D.

doi:10.1534/genetics.115.182717

Cited by 49 publications

(60 citation statements)

References 141 publications

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“…Nematodes are useful models in synteny analysis as 1) extensive chromosomal rearrangement is a hallmark of their genome evolution [7, 25, 26, 45, 46] and 2) their genome sequences are highly contiguous and assembled into chromosomes [7, 25, 26, 45]. These two genera were also chosen to investigate the intrinsic species effect as they differ in gene density (Table 1).…”

Section: Resultsmentioning

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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Section: Resultsmentioning

confidence: 99%

Inferring synteny between genome assemblies: a systematic evaluation

2018

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“…Caenorhabditis elegans [49,50]. CRISPR/Cas9 application to the mouse has been discussed by recent protocol and review papers [51-54] so we will not discuss these studies here.…”

Section: Crispr/cas9 In Animal Modelsmentioning

confidence: 99%

Insert, remove or replace: A highly advanced genome editing system using CRISPR/Cas9

Ceasar

Rajan

Prykhozhij

et al. 2016

Biochimica et Biophysica Acta (BBA) - Molecular Cell Research

127

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The clustered, regularly interspaced, short palindromic repeat (CRISPR) and CRISPR associated protein 9 (Cas9) system discovered as an adaptive immunity mechanism in prokaryotes has emerged as the most popular tool for the precise alterations of the genomes of diverse species. CRISPR/Cas9 system has taken the world of genome editing by storm in recent years. Its popularity as a tool for altering genomes is due to the ability of Cas9 protein to cause double-stranded breaks in DNA after binding with short guide RNA molecules, which can be produced with dramatically less effort and expense than required for production of transcription-activator like effector nucleases (TALEN) and zinc-finger nucleases (ZFN). This system has been exploited in many species from prokaryotes to higher animals including human cells as evidenced by the literature showing increasing sophistication and ease of CRISPR/Cas9 as well as increasing species variety where it is applicable. This technology is poised to solve several complex molecular biology problems faced in life science research including cancer research. In this review, we highlight the recent advancements in CRISPR/Cas9 system in editing genomes of prokaryotes, fungi, plants and animals and provide details on software tools available for convenient design of CRISPR/Cas9 targeting plasmids. We also discuss the future prospects of this advanced molecular technology.

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“…The successful application of tools from C. elegans (e.g. transformations and RNAi) [56] in H. bacteriophora coupled with this archive of genetic information is expected to lead to significant advances in the application of molecular genetics to improve the field efficacy of EPNs in biological control.…”

Section: The Genome Of Heterorhabditis Bacteriophoramentioning

confidence: 99%

Genomics of Entomopathogenic Nematodes and Implications for Pest Control

Baiocchi

Dillman

2016

Trends in Parasitology

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Entomopathogenic nematodes (EPNs) have been used in biological control but improvement is needed to realize their full potential for broader application in agriculture. Some improvements have been gained through selective breeding and the isolation of additional species and populations. Having genomic sequences for at least six EPNs opens the possibility of genetic improvement, either by facilitating the selection of candidate genes for hypothesis-driven studies of gene-trait relationships or by genomics-assisted breeding for desirable traits. However, the genomic data will be of limited use without a more mechanistic understanding of the genes underlying traits important for biological control. Additionally, molecular tools are required to fully translate the genomic resources into further functional studies and better biological control.

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Rendering the Intractable More Tractable: Tools from Caenorhabditis elegans Ripe for Import into Parasitic Nematodes

Cited by 49 publications

References 141 publications

Inferring synteny between genome assemblies: a systematic evaluation

Inferring synteny between genome assemblies: a systematic evaluation

Insert, remove or replace: A highly advanced genome editing system using CRISPR/Cas9

Genomics of Entomopathogenic Nematodes and Implications for Pest Control

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