Whole-genome sequencing and variant discovery in C. elegans

Hillier, La Deana W.; Marth, Gábor; Quinlan, Aaron R.; Dooling, David J.; Fewell, Ginger A.; Barnett, Derek W.; Fox, Paul M.; Glasscock, Jarret; Hickenbotham, Matthew T.; Huang, Weichun; Magrini, Vincent; Richt, Ryan; Sander, Sacha N.; Stewart, Donald A.; Strömberg, Michael; Tsung, Eric F.; Wylie, Todd; Schedl, Tim; Wilson, Richard K.; Mardis, Elaine R.

doi:10.1038/nmeth.1179

Cited by 373 publications

(322 citation statements)

References 16 publications

Supporting

Mentioning

305

Contrasting

Order By: Relevance

“…This 44% reduction in polymorphism in the inbred genome is smaller than the 59.4% predicted from four generations of brother-sister mating, indicating that selection favouring heterozygotes had occurred 19 . The polymorphism combining inbred and wild (among four haplotypes) was 2.3%, higher than that in most studied animal genomes 20,21 but comparable to that in known high-polymorphism species 7 . In inbred and wild, we found 3,094 short indels located in coding regions inferred to cause frameshift variants in 2,665 genes, providing an important source for recessive lethal mutations.…”

Section: Polymorphism and Repetitive Sequencesmentioning

confidence: 60%

The oyster genome reveals stress adaptation and complexity of shell formation

Zhang

Fang

Guo³

et al. 2012

Nature

1,925

1,922

View full text Add to dashboard Cite

The Pacific oyster Crassostrea gigas belongs to one of the most species-rich but genomically poorly explored phyla, the Mollusca. Here we report the sequencing and assembly of the oyster genome using short reads and a fosmid-pooling strategy, along with transcriptomes of development and stress response and the proteome of the shell. The oyster genome is highly polymorphic and rich in repetitive sequences, with some transposable elements still actively shaping variation. Transcriptome studies reveal an extensive set of genes responding to environmental stress. The expansion of genes coding for heat shock protein 70 and inhibitors of apoptosis is probably central to the oyster's adaptation to sessile life in the highly stressful intertidal zone. Our analyses also show that shell formation in molluscs is more complex than currently understood and involves extensive participation of cells and their exosomes. The oyster genome sequence fills a void in our understanding of the Lophotrochozoa.Oceans cover approximately 71% of the Earth's surface and harbour most of the phylum diversity of the animal kingdom. Understanding marine biodiversity and its evolution remains a major challenge. The Pacific oyster C. gigas (Thunberg, 1793) is a marine bivalve belonging to the phylum Mollusca, which contains the largest number of described marine animal species 1 . Molluscs have vital roles in the functioning of marine, freshwater and terrestrial ecosystems, and have had major effects on humans, primarily as food sources but also as sources of dyes, decorative pearls and shells, vectors of parasites, and biofouling or destructive agents. Many molluscs are important fishery and aquaculture species, as well as models for studying neurobiology, biomineralization, ocean acidification and adaptation to coastal environments under climate change 2,3 . As the most speciose member of the Lophotrochozoa, phylum Mollusca is central to our understanding of the biology and evolution of this superphylum of protostomes.As sessile marine animals living in estuarine and intertidal regions, oysters must cope with harsh and dynamically changing environments. Abiotic factors such as temperature and salinity fluctuate wildly, and toxic metals and desiccation also pose serious challenges. Filter-feeding oysters face tremendous exposure to microbial pathogens. Oysters do have a notable physical line of defence against predation and desiccation in the formation of thick calcified shells, a key evolutionary innovation making molluscs a successful group. However, acidification of the world's oceans by uptake of anthropogenic carbon dioxide poses a potentially serious threat to this ancient adaptation 4 . Understanding biomineralization and molluscan shell formation is, thus, a major area of interest 5 . Crassostrea gigas is also an interesting model for developmental biology owing to its mosaic development with typical molluscan stages, including trochophore and veliger larvae and metamorphosis.A complete genome sequence of C. gigas would enable a more th...

show abstract

Section: Polymorphism and Repetitive Sequencesmentioning

confidence: 60%

The oyster genome reveals stress adaptation and complexity of shell formation

Zhang

Fang

Guo³

et al. 2012

Nature

1,925

1,922

View full text Add to dashboard Cite

show abstract

“…We use MOSAIK (http://bioinformatics.bc.edu/marthlab/Mosaik) to map the reads to the human reference genome (hg19) with parameters -hs 15 -p 12 -mmp 0.05 -act 26 - mhp 100 -bw 51 as recommended in its documentation. MOSAIK is a widely used reference-guided assembler that hashes the whole reference genome and locate information in the hash table using a 'jump database' [19-21]. Then we use SAMtools (http://samtools.sourceforge.net/) [22] to pileup the reads onto the target regions.…”

Section: Methodsmentioning

confidence: 99%

A unified approach for allele frequency estimation, SNP detection and association studies based on pooled sequencing data using EM algorithms

Chen

Sun

2013

BMC Genomics

View full text Add to dashboard Cite

BackgroundGenome-wide association studies (GWAS) have identified many common polymorphisms associated with complex traits. However, these associated common variants explain only a small fraction of the phenotypic variances, leaving a substantial portion of genetic heritability unexplained. As a result, searches for "missing" heritability are drawing increasing attention, particularly for rare variant studies that often require a large sample size and, thus, extensive sequencing effort. Although the development of next generation sequencing (NGS) technologies has made it possible to sequence a large number of reads economically and efficiently, it is still often cost prohibitive to sequence thousands of individuals that are generally required for association studies. A more efficient and cost-effective design would involve pooling the genetic materials of multiple individuals together and then sequencing the pools, instead of the individuals. This pooled sequencing approach has improved the plausibility of association studies for rare variants, while, at the same time, posed a great challenge to the pooled sequencing data analysis, essentially because individual sample identity is lost, and NGS sequencing errors could be hard to distinguish from low frequency alleles.ResultsA unified approach for estimating minor allele frequency, SNP calling and association studies based on pooled sequencing data using an expectation maximization (EM) algorithm is developed in this paper. This approach makes it possible to study the effects of minor allele frequency, sequencing error rate, number of pools, number of individuals in each pool, and the sequencing depth on the estimation accuracy of minor allele frequencies. We show that the naive method of estimating minor allele frequencies by taking the fraction of observed minor alleles can be significantly biased, especially for rare variants. In contrast, our EM approach can give an unbiased estimate of the minor allele frequency under all scenarios studied in this paper. A SNP calling approach, EM-SNP, for pooled sequencing data based on the EM algorithm is then developed and compared with another recent SNP calling method, SNVer. We show that EM-SNP outperforms SNVer in terms of the fraction of db-SNPs among the called SNPs, as well as transition/transversion (Ti/Tv) ratio. Finally, the EM approach is used to study the association between variants and type I diabetes.ConclusionsThe EM-based approach for the analysis of pooled sequencing data can accurately estimate minor allele frequencies, call SNPs, and find associations between variants and complex traits. This approach is especially useful for studies involving rare variants.

show abstract

“…New theoretical work is also aiming to statistically distinguishing true polymorphisms from sequencing errors (see, for example, Lynch, 2009). GigaBayes (Hillier et al, 2008) and VarScan (Koboldt et al, 2009) represent examples of programs for SNP detection. GigaBayes calculates the probability that a polymorphism represent a true SNP or a sequencing error, for this calculation the program uses a Bayesian approach, taking into account the alignment depth, the base call in each sequence, the base composition in the region and the expected a priori polymorphism rate.…”

Section: Large-scale Identification and Development Of Molecular Markersmentioning

confidence: 99%

Applications of next generation sequencing in molecular ecology of non-model organisms

2010

View full text Add to dashboard Cite

As most biologists are probably aware, technological advances in molecular biology during the last few years have opened up possibilities to rapidly generate large-scale sequencing data from non-model organisms at a reasonable cost. In an era when virtually any study organism can 'go genomic', it is worthwhile to review how this may impact molecular ecology. The first studies to put the next generation sequencing (NGS) to the test in ecologically well-characterized species without previous genome information were published in 2007 and the beginning of 2008. Since then several studies have followed in their footsteps, and a large number are undoubtedly under way. This review focuses on how NGS has been, and can be, applied to ecological, population genetic and conservation genetic studies of non-model species, in which there is no (or very limited) genomic resources. Our aim is to draw attention to the various possibilities that are opening up using the new technologies, but we also highlight some of the pitfalls and drawbacks with these methods. We will try to provide a snapshot of the current state of the art for this rapidly advancing and expanding field of research and give some likely directions for future developments.

show abstract

Whole-genome sequencing and variant discovery in C. elegans

Cited by 373 publications

References 16 publications

The oyster genome reveals stress adaptation and complexity of shell formation

The oyster genome reveals stress adaptation and complexity of shell formation

A unified approach for allele frequency estimation, SNP detection and association studies based on pooled sequencing data using EM algorithms

Applications of next generation sequencing in molecular ecology of non-model organisms

Contact Info

Product

Resources

About