Whole genome sequencing and the transformation of C. elegans forward genetics

Methods ◽  
2014 ◽  
Vol 68 (3) ◽  
pp. 437-440 ◽  
Author(s):  
Patrick J. Hu
2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ho-Yon Hwang ◽  
Jiou Wang

AbstractGenetic mapping is used in forward genetics to narrow the list of candidate mutations and genes corresponding to the mutant phenotype of interest. Even with modern advances in biology such as efficient identification of candidate mutations by whole-genome sequencing, mapping remains critical in pinpointing the responsible mutation. Here we describe a simple, fast, and affordable mapping toolkit that is particularly suitable for mapping in Caenorhabditis elegans. This mapping method uses insertion-deletion polymorphisms or indels that could be easily detected instead of single nucleotide polymorphisms in commonly used Hawaiian CB4856 mapping strain. The materials and methods were optimized so that mapping could be performed using tiny amount of genetic material without growing many large populations of mutants for DNA purification. We performed mapping of previously known and unknown mutations to show strengths and weaknesses of this method and to present examples of completed mapping. For situations where Hawaiian CB4856 is unsuitable, we provide an annotated list of indels as a basis for fast and easy mapping using other wild isolates. Finally, we provide rationale for using this mapping method over other alternatives as a part of a comprehensive strategy also involving whole-genome sequencing and other methods.


2008 ◽  
Vol 5 (2) ◽  
pp. 183-188 ◽  
Author(s):  
LaDeana W Hillier ◽  
Gabor T Marth ◽  
Aaron R Quinlan ◽  
David Dooling ◽  
Ginger Fewell ◽  
...  

PLoS ONE ◽  
2010 ◽  
Vol 5 (11) ◽  
pp. e13922 ◽  
Author(s):  
Katherine P. Weber ◽  
Subhajyoti De ◽  
Iwanka Kozarewa ◽  
Daniel J. Turner ◽  
M. Madan Babu ◽  
...  

BMC Genomics ◽  
2015 ◽  
Vol 16 (1) ◽  
pp. 57 ◽  
Author(s):  
Lisa Schierenbeck ◽  
David Ries ◽  
Kristin Rogge ◽  
Sabrina Grewe ◽  
Bernd Weisshaar ◽  
...  

PLoS ONE ◽  
2008 ◽  
Vol 3 (12) ◽  
pp. e4012 ◽  
Author(s):  
Yufeng Shen ◽  
Sumeet Sarin ◽  
Ye Liu ◽  
Oliver Hobert ◽  
Itsik Pe'er

2021 ◽  
Author(s):  
Donald G. Moerman ◽  
Erica Li-Leger ◽  
Stephane Flibotte ◽  
Ralf Schnabel ◽  
Heinke Holzkamp ◽  
...  

It has been estimated that 15-30% of the ~20,000 genes in C. elegans are essential, yet many of these genes remain to be identified or characterized. With the goal of identifying unknown essential genes, we performed whole genome sequencing on complementation pairs from legacy collections of maternal-effect lethal and sterile mutants. This approach uncovered maternal genes required for embryonic development and genes with putative sperm-specific functions. In total, 58 essential genes were identified on chromosomes III, IV, and V, of which 49 genes are represented by novel alleles in this collection. Of these 49 genes, 19 (40 alleles) were selected for further functional characterization. The terminal phenotypes of embryos were examined, revealing defects in cell division, morphogenesis, and osmotic integrity of the eggshell. Mating assays with wild-type males revealed previously unknown male-expressed genes required for fertilization and embryonic development. The result of this study is a catalogue of mutant alleles in essential genes that will serve as a resource to guide further study toward a more complete understanding of this important model organism. As many genes and developmental pathways in C. elegans are conserved and essential genes are often linked to human disease, uncovering the function of these genes may also provide insight to further our understanding of human biology.


PLoS Genetics ◽  
2013 ◽  
Vol 9 (1) ◽  
pp. e1003219 ◽  
Author(s):  
Katherine R. Bull ◽  
Andrew J. Rimmer ◽  
Owen M. Siggs ◽  
Lisa A. Miosge ◽  
Carla M. Roots ◽  
...  

PLoS ONE ◽  
2010 ◽  
Vol 5 (11) ◽  
pp. e15435 ◽  
Author(s):  
Maria Doitsidou ◽  
Richard J. Poole ◽  
Sumeet Sarin ◽  
Henry Bigelow ◽  
Oliver Hobert

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