Pristionchus pacificus genomics: from genetics to genome sequence

Dieterich, Christoph; Roeseler, Waltraud; Srinivasan, Jagan

doi:10.1895/wormbook.1.116.1

Cited by 3 publications

(6 citation statements)

References 25 publications

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“…Recombinant inbred lines from two P. pacificus strains (wild-type P. pacificus var. California and the polymorphic Washington strain) were used to generate the linkage map (Srinivasan et al 2002;Dieterich et al 2006). Our assignment matched all of the X chromosome SSCP markers and all but one autosomal marker ( Figure 1E).…”

Section: Resultsmentioning

confidence: 86%

“…(D) Overlap of C. briggsae copy-number assignment with WormBase assignment indicates high accuracy. (E) Overlap of P. pacificus copy-number assignment with previously reported SSCP markers (Srinivasan et al 2002;Dieterich et al 2006) indicates high accuracy. Chromosomal assignments by SSCP are indicated below each bar.…”

Section: Dnaseqmentioning

confidence: 83%

“…More recently, estimates of neutral mutation rates were used to approximate the divergence time between C. elegans and C. briggsae to 40 million years (Cutter 2008). The fifth species, P. pacificus, is estimated to have diverged 300 million years ago (Dieterich et al 2006(Dieterich et al , 2008.…”

Section: Resultsmentioning

confidence: 99%

“…(A) Phylogeny showing the evolutionary relationship of the five nematode species (Kiontke et al 2004(Kiontke et al , 2011. Pristionchus pacificus is estimated to have split from Caenorhabditis 300 million years ago (Dieterich et al 2006). C. briggsae, C. elegans, and P. pacificus are androgynous.…”

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confidence: 99%

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Sex-Biased Gene Expression and Evolution of the X Chromosome in Nematodes

et al. 2014

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Studies of X chromosome evolution in various organisms have indicated that sex-biased genes are nonrandomly distributed between the X and autosomes. Here, to extend these studies to nematodes, we annotated and analyzed X chromosome gene content in four Caenorhabditis species and in Pristionchus pacificus. Our gene expression analyses comparing young adult male and female mRNAseq data indicate that, in general, nematode X chromosomes are enriched for genes with high female-biased expression and depleted of genes with high male-biased expression. Genes with low sex-biased expression do not show the same trend of X chromosome enrichment and depletion. Combined with the observation that highly sex-biased genes are primarily expressed in the gonad, differential distribution of sex-biased genes reflects differences in evolutionary pressures linked to tissue-specific regulation of X chromosome transcription. Our data also indicate that X dosage imbalance between males (XO) and females (XX) is influential in shaping both expression and gene content of the X chromosome. Predicted upregulation of the single male X to match autosomal transcription (Ohno's hypothesis) is supported by our observation that overall transcript levels from the X and autosomes are similar for highly expressed genes. However, comparison of differentially located one-to-one orthologs between C. elegans and P. pacificus indicates lower expression of X-linked orthologs, arguing against X upregulation. These contradicting observations may be reconciled if X upregulation is not a global mechanism but instead acts locally on a subset of tissues and X-linked genes that are dosage sensitive. IN an XY sex-determination system, male and female genomes are identical with the exception of the male-specific Y chromosome, which bears few genes (Charlesworth et al. 2005). This is particularly true when the Y chromosome is thought to be completely lost, as is the case for C. elegans and many other nematodes (Walton 1940). Because gene content is the same, phenotypic differences between males and females, termed "sexual dimorphisms," must be caused by differential gene expression between the two sexes (Connallon and Knowles 2005;Ellegren and Parsch 2007). Throughout the article, such differentially expressed genes are referred to as "sex biased." As males and females have different fitness optima, a trait that is beneficial to one sex can be harmful to the other (termed sexual antagonism) (Rice and Chippindale 2001;Arnqvist 2004;Connallon and Knowles 2005;Ellegren and Parsch 2007;Mank et al. 2008a;Rice 1984). The evolution of sex-biased gene expression is thought to mediate the effects of sexual antagonism and allow for achievement of sex-specific fitness. Previous studies have indicated that anywhere between 30 and 60% of metazoan genes may be sex biased Parisi et al. 2004;Reinke et al. 2004;Yang et al. 2006;Reinius et al. 2008;Small et al. 2009;Innocenti and Morrow 2010;Assis et al. 2012;Reinius et al. 2012;Thomas et al. 2012). Genes with sex-biased exp...

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Section: Resultsmentioning

confidence: 86%

Section: Dnaseqmentioning

confidence: 83%

Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

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Sex-Biased Gene Expression and Evolution of the X Chromosome in Nematodes

et al. 2014

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“…Full tool sets for the isolation and systematic study of mutations in known genes generated by forward and reverse genetics are currently available only for two nematode species other than C. elegans, namely Caenorhabditis briggsae and P. pacificus. For both species, relatively dense genetic maps, which are well anchored in the genome, allow the positional cloning of genes (22,56,90). Mutations in molecularly defined genes have been isolated by polymerase chain reaction (PCR) based screening for small deletions (5,77), and very recently zinc finger nucleases were used for targeted mutagenesis in C. briggsae (B. Meyer, personal communication).…”

Section: Comparative Geneticsmentioning

confidence: 99%

Comparative Genetics and Genomics of Nematodes: Genome Structure, Development, and Lifestyle

Sommer

Streit²

2011

Annu. Rev. Genet.

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Nematodes are found in virtually all habitats on earth. Many of them are parasites of plants and animals, including humans. The free-living nematode, Caenorhabditis elegans, is one of the genetically best-studied model organisms and was the first metazoan whose genome was fully sequenced. In recent years, the draft genome sequences of another six nematodes representing four of the five major clades of nematodes were published. Compared to mammalian genomes, all these genomes are very small. Nevertheless, they contain almost the same number of genes as the human genome. Nematodes are therefore a very attractive system for comparative genetic and genomic studies, with C. elegans as an excellent baseline. Here, we review the efforts that were made to extend genetic analysis to nematodes other than C. elegans, and we compare the seven available nematode genomes. One of the most striking findings is the unexpectedly high incidence of gene acquisition through horizontal gene transfer (HGT).

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Genetics: modes of reproduction and genetic analysis

Streit

2016

Parasitology

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Classical and reverse genetics remain invaluable tools for the scientific investigation of model organisms. Genetic analysis of endoparasites is generally difficult because the sexual adults required for crossing and other manipulations are usually hidden within their host. Strongyloides spp. and Parastrongyloides spp. are notable exceptions to this and their free-living adults offer unique opportunities to manipulate these parasites experimentally. Here I review the modes of inheritance in the two generations of Strongyloides/Parastrongyloides and I discuss the opportunities and the limitations of the currently available methodology for the genetic analysis of these two genera.

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Pristionchus pacificus genomics: from genetics to genome sequence

Cited by 3 publications

References 25 publications

Sex-Biased Gene Expression and Evolution of the X Chromosome in Nematodes

Sex-Biased Gene Expression and Evolution of the X Chromosome in Nematodes

Comparative Genetics and Genomics of Nematodes: Genome Structure, Development, and Lifestyle

Genetics: modes of reproduction and genetic analysis

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