The Pristionchus pacificus genome provides a unique perspective on nematode lifestyle and parasitism

Dieterich, Christoph; Clifton, Sandra W.; Schuster, Lisa N; Chinwalla, Asif T.; Delehaunty, Kimberly D.; Dinkelacker, Iris; Fulton, Lucinda A.; Fulton, Robert S.; Godfrey, Jennifer; Minx, Pat; Mitreva, Makedonka; Roeseler, Waltraud; Tian, Huiyu; Witte, Hanh; Yang, Shiaw-Pyng; Wilson, Richard K.; Sommer, Ralf J.

doi:10.1038/ng.227

Cited by 321 publications

(332 citation statements)

References 38 publications

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“…Analyses of the complete genome of the necromenic nematode Pristionchus pacificus and transcriptomic studies reveal that several functional cellulase genes have been transferred to the ancestor of the Pristionchus genus from bacterial donors [27][28][29]. These cellulase genes are unrelated to the cellulase genes found in plant-parasitic nematodes (see below).…”

Section: Acquisition Of Adaptive Genes By Nematodesmentioning

confidence: 99%

Horizontal gene transfer in the acquisition of novel traits by metazoans

2014

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Horizontal gene transfer is accepted as an important evolutionary force modulating the evolution of prokaryote genomes. However, it is thought that horizontal gene transfer plays only a minor role in metazoan evolution. In this paper, I critically review the rising evidence on horizontally transferred genes and on the acquisition of novel traits in metazoans. In particular, I discuss suspected examples in sponges, cnidarians, rotifers, nematodes, molluscs and arthropods which suggest that horizontal gene transfer in metazoans is not simply a curiosity. In addition, I stress the scarcity of studies in vertebrates and other animal groups and the importance of forthcoming studies to understand the importance and extent of horizontal gene transfer in animals.

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Section: Acquisition Of Adaptive Genes By Nematodesmentioning

confidence: 99%

Horizontal gene transfer in the acquisition of novel traits by metazoans

2014

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“…Pristionchus pacificus and C. elegans are members of different nematode families and are separated for more than 200 myr [5], thus representing distantly related species. They share, by convergent evolution, an androdioecious mode of reproduction by self-fertilizing hermaphrodites and males [6].…”

Section: Introductionmentioning

confidence: 99%

Oxygen-induced social behaviours inPristionchus pacificushave a distinct evolutionary history and genetic regulation fromCaenorhabditis elegans

et al. 2016

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Wild isolates of the nematode Caenorhabditis elegans perform social behaviours, namely clumping and bordering, to avoid hyperoxia under laboratory conditions. In contrast, the laboratory reference strain N2 has acquired a solitary behaviour in the laboratory, related to a gain-of-function variant in the neuropeptide Y-like receptor NPR-1. Here, we study the evolution and natural variation of clumping and bordering behaviours in Pristionchus pacificus nematodes in a natural context, using strains collected from 22 to 2400 metres above sea level on La Réunion Island. Through the analysis of 106 wild isolates, we show that the majority of strains display a solitary behaviour similar to C. elegans N2, whereas social behaviours are predominantly seen in strains that inhabit high-altitude locations. We show experimentally that P. pacificus social strains perform clumping and bordering to avoid hyperoxic conditions in the laboratory, suggesting that social strains may have adapted to or evolved a preference for the lower relative oxygen levels available at high altitude in nature. In contrast to C. elegans, clumping and bordering in P. pacificus do not correlate with locomotive behaviours in response to changes in oxygen conditions. Furthermore, QTL analysis indicates clumping and bordering to represent complex quantitative traits. Thus, clumping and bordering behaviours represent an example of phenotypic convergence with a different evolutionary history and distinct genetic control in both nematode species.

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“…High quality gene predictions for additional nematode genomes have been generated. [7][8][9] The Million Mutation Project provided more than 800,000 novel mutations in C.…”

Section: Introductionmentioning

confidence: 99%

GExplore 1.4: An expanded web interface for queries onCaenorhabditis elegansprotein and gene function

Hutter

Suh

2016

Worm

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Genetic high-throughput experiments often result in hundreds or thousands of genes satisfying certain experimental conditions. Grouping and prioritizing a large number of genes for further analysis can be a time-consuming challenge. In 2009 we developed a web-based user interface, GExplore, to assist with large-scale data-mining related to gene function in Caenorhabditis elegans. The underlying database contained information about Caenorhabditis elegans genes and proteins including domain organization of the proteins, phenotypic descriptions, expression data and Gene Ontology Consortium annotations. These data enable users to quickly obtain an overview of biological and biochemical functions of a large number of genes at once. Since its inception the underlying database has been updated and expanded significantly. Here we describe the current version of GExplore 1.4, documenting the changes since the original release. GExplore 1.4 now contains information about the domain organization of the proteomes of 9 nematode species, can display the location of Caenorhabditis elegans mutations with respect to the domain organization of the proteins, and includes stage-specific RNAseq gene expression data generated by the modENCODE project. The underlying database has been reorganized to facilitate independent updates of the different parts of the database and to allow the addition of novel data sets in the future. The web interface is available under http://genome.sfu.ca/gexplore.

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The Pristionchus pacificus genome provides a unique perspective on nematode lifestyle and parasitism

Cited by 321 publications

References 38 publications

Horizontal gene transfer in the acquisition of novel traits by metazoans

Horizontal gene transfer in the acquisition of novel traits by metazoans

Oxygen-induced social behaviours inPristionchus pacificushave a distinct evolutionary history and genetic regulation fromCaenorhabditis elegans

GExplore 1.4: An expanded web interface for queries onCaenorhabditis elegansprotein and gene function

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