A toolkit for rapid gene mapping in the nematode Caenorhabditis briggsae

Koboldt, Daniel C.; Staisch, Julia; Thillainathan, Bavithra; Haines, Karen; Baird, Scott Everet; Chamberlin, Helen; Haag, Eric S.; Miller, Raymond D.; Gupta, Bhagwati P.

doi:10.1186/1471-2164-11-236

Cited by 44 publications

(70 citation statements)

References 30 publications

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“…Moreover, the deep split of "Kerala" strains from all other C. briggsae lineages approximately 2 million generations ago (∼200 kya), averaging 1.2% silent-site sequence divergence, is an especially striking feature of the evolutionary history of this species. This splitting reinforces a key role for C. briggsae in studying adaptive divergence (Prasad et al 2011) and incipient speciation (Dolgin et al 2008;Ross et al 2011;Baird and Stonesifer 2012), by exploiting available genetic toolkits (Koboldt et al 2010;Ross et al 2011;Frøkjaer-Jensen 2013), and the genomic resource provided here.…”

Section: Wwwgenomeorgsupporting

confidence: 73%

“…These features make C. briggsae a powerful tool for dissecting evolutionary pattern and process in connection with trait divergence in nature, especially in combination with its deep experimental toolkit (Koboldt et al 2010;Ross et al 2011;Frøkjaer-Jensen 2013). Indeed, this species is now an active target of research into the molecular basis of trait variation and adaptation (Baird et al 2005;Prasad et al 2011;Ross et al 2011;Stegeman et al 2013), the evolution of development (Delattre and Félix 2001;Hill et al 2006;Guo et al 2009;Marri and Gupta 2009), and speciation (Woodruff et al 2010;Baird and Stonesifer 2012;Kozlowska et al 2012;Yan et al 2012).…”

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confidence: 99%

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Full-genome evolutionary histories of selfing, splitting, and selection in Caenorhabditis

et al. 2015

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The nematode Caenorhabditis briggsae is a model for comparative developmental evolution with C. elegans. Worldwide collections of C. briggsae have implicated an intriguing history of divergence among genetic groups separated by latitude, or by restricted geography, that is being exploited to dissect the genetic basis to adaptive evolution and reproductive incompatibility; yet, the genomic scope and timing of population divergence is unclear. We performed high-coverage whole-genome sequencing of 37 wild isolates of the nematode C. briggsae and applied a pairwise sequentially Markovian coalescent (PSMC) model to 703 combinations of genomic haplotypes to draw inferences about population history, the genomic scope of natural selection, and to compare with 40 wild isolates of C. elegans. We estimate that a diaspora of at least six distinct C. briggsae lineages separated from one another approximately 200,000 generations ago, including the “Temperate” and “Tropical” phylogeographic groups that dominate most samples worldwide. Moreover, an ancient population split in its history approximately 2 million generations ago, coupled with only rare gene flow among lineage groups, validates this system as a model for incipient speciation. Low versus high recombination regions of the genome give distinct signatures of population size change through time, indicative of widespread effects of selection on highly linked portions of the genome owing to extreme inbreeding by self-fertilization. Analysis of functional mutations indicates that genomic context, owing to selection that acts on long linkage blocks, is a more important driver of population variation than are the functional attributes of the individually encoded genes.

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Section: Wwwgenomeorgsupporting

confidence: 73%

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confidence: 99%

Full-genome evolutionary histories of selfing, splitting, and selection in Caenorhabditis

et al. 2015

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“…As an emerging model for determining the genetic basis of phenotypic variation (Baird et al, 2005;Hillier et al, 2007;Ross et al, 2011;Koboldt et al, 2010), these data further position C. briggsae as a model system for the genetic analysis of complex behavioural traits. We compared genetic backgrounds for the ability to perform thermotaxis and isothermal tracking within and between species by assaying 15 natural isolate strains of C. briggsae alongside two C. elegans strains, and demonstrated that C. briggsae can sense and navigate a thermal landscape in a manner similar to C. elegans.…”

Section: Discussionmentioning

confidence: 86%

“…Caenorhabditis briggsae is morphologically very similar to C. elegans, sharing a common life cycle and similar androdioecious sexual system (Nigon and Dougherty, 1949;Baird, 2001), but C. briggsae exhibits greater molecular differentiation among wild strains that might, in turn, underlie higher phenotypic variation (Cutter et al, 2006). As more genetic tools become available in C. briggsae, it is quickly catching up to C. elegans as a model system in its own right (Koboldt et al, 2010;Ross et al, 2011).…”

Section: Introductionmentioning

confidence: 99%

Temperature-dependent behaviours are genetically variable in the nematode Caenorhabditis briggsae

Stegeman

Mesquita

Ryu

et al. 2012

Journal of Experimental Biology

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SUMMARY Temperature-dependent behaviours inCaenorhabditis elegans, such as thermotaxis and isothermal tracking, are complex behavioural responses that integrate sensation, foraging and learning, and have driven investigations to discover many essential genetic and neural pathways. The ease of manipulation of the Caenorhabditis model system also has encouraged its application to comparative analyses of phenotypic evolution, particularly contrasts of the classic model C. elegans with C. briggsae. And yet few studies have investigated natural genetic variation in behaviour in any nematode. Here we measure thermotaxis and isothermal tracking behaviour in genetically distinct strains of C. briggsae, further motivated by the latitudinal differentiation in C. briggsae that is associated with temperature-dependent fitness differences in this species. We demonstrate that C. briggsae performs thermotaxis and isothermal tracking largely similar to that of C. elegans, with a tendency to prefer its rearing temperature. Comparisons of these behaviours among strains reveal substantial heritable natural variation within each species that corresponds to three general patterns of behavioural response. However, intraspecific genetic differences in thermal behaviour often exceed interspecific differences. These patterns of temperature-dependent behaviour motivate further development of C. briggsae as a model system for dissecting the genetic underpinnings of complex behavioural traits. Supplementary material available online at

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“…When we compared our C. briggsae gene assignments to the current WormBase assignment [based on a high-density recombination map (Hillier et al 2007;Koboldt et al 2010;Ross et al 2011)] we found that we correctly assigned 236 of 236 contigs to autosomes and 27 of 28 contigs to the X chromosome ( Figure 1D). The inconsistent contig, cb25.…”

Section: Resultsmentioning

confidence: 96%

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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A toolkit for rapid gene mapping in the nematode Caenorhabditis briggsae

Cited by 44 publications

References 30 publications

Full-genome evolutionary histories of selfing, splitting, and selection in Caenorhabditis

Full-genome evolutionary histories of selfing, splitting, and selection in Caenorhabditis

Temperature-dependent behaviours are genetically variable in the nematode Caenorhabditis briggsae

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

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