scholarly journals Identification of essential genes in Caenorhabditis elegans through whole genome sequencing of legacy mutant collections

2021 ◽  
Author(s):  
Erica Li-Leger ◽  
Richard Feichtinger ◽  
Stephane Flibotte ◽  
Heinke Holzkamp ◽  
Ralf Schnabel ◽  
...  
Keyword(s):  
Embryonic Development ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Functional Characterization ◽  
Model Organism ◽  
Essential Genes ◽  
Whole Genome ◽  
C Elegans ◽  
Novel Alleles ◽  
Unknown Male

Abstract 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 apparent sperm-specific functions. In total, 58 putative essential genes were identified on chromosomes III, IV, and V, of which 52 genes are represented by novel alleles in this collection. Of these 52 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.

scholarly journals Identification of essential genes in Caenorhabditis elegans through whole genome sequencing of legacy mutant collections

2021 ◽  
Author(s):  
Donald G. Moerman ◽  
Erica Li-Leger ◽  
Stephane Flibotte ◽  
Ralf Schnabel ◽  
Heinke Holzkamp ◽  
...  
Keyword(s):  
Embryonic Development ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Functional Characterization ◽  
Model Organism ◽  
Essential Genes ◽  
Whole Genome ◽  
C Elegans ◽  
Novel Alleles ◽  
Unknown Male

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.

Whole-genome sequencing and variant discovery in C. elegans

2008 ◽  
Vol 5 (2) ◽  
pp. 183-188 ◽  
Author(s):  
LaDeana W Hillier ◽  
Gabor T Marth ◽  
Aaron R Quinlan ◽  
David Dooling ◽  
Ginger Fewell ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
C Elegans ◽  
Variant Discovery

scholarly journals Whole Genome Sequencing Highlights Genetic Changes Associated with Laboratory Domestication of C. elegans

PLoS ONE ◽  
2010 ◽  
Vol 5 (11) ◽  
pp. e13922 ◽  
Author(s):  
Katherine P. Weber ◽  
Subhajyoti De ◽  
Iwanka Kozarewa ◽  
Daniel J. Turner ◽  
M. Madan Babu ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Genetic Changes ◽  
C Elegans

scholarly journals Graph-guided assembly for novel HLA allele discovery

2017 ◽  
Author(s):  
Heewook Lee ◽  
Carl Kingsford
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
High Accuracy ◽  
Hla Typing ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Sequencing Data ◽  
Hla Genes ◽  
Guided Assembly ◽  
Novel Alleles

AbstractAccurate typing of human leukocyte antigen (HLA), a histocompatibility test, is important because HLA genes play various roles in immune responses, and have also been shown to be associated with many diseases such as cancer. The current gold standard for HLA typing uses DNA sequencing technology combined with sequence enrichment techniques using specially designed primers or probes, causing it to be slow and labor-intensive. Although there exist enrichment-free computational methods that use various types of sequencing data, hyper-polymorphism found in HLA region of the human genome makes it challenging to type HLA genes with high accuracy from whole genome sequencing data. Furthermore, these methods are database-matching approaches where their output is inherently limited by the completeness of already known types, forcing them to find the best matching known alleles from a database, thereby causing them to be unsuitable for discovery of rare or novel alleles. In order to ensure both high accuracy as well as the ability to type novel alleles, we have developed a graph-guided assembly technique for classical HLA genes, which is capable of assembling phased, full-length haplotype sequences of typing exons given high-coverage (>30-fold) whole genome sequencing data. Our method delivers highly accurate HLA typing, comparable to the current state-of-the-art database-matching methods. We also demonstrate that our method can type novel alleles by experimenting on various data including simulated, Illumina Platinum Genomes, and 1000 Genomes data.

scholarly journals Comparing Platforms for C. elegans Mutant Identification Using High-Throughput Whole-Genome Sequencing

PLoS ONE ◽  
2008 ◽  
Vol 3 (12) ◽  
pp. e4012 ◽  
Author(s):  
Yufeng Shen ◽  
Sumeet Sarin ◽  
Ye Liu ◽  
Oliver Hobert ◽  
Itsik Pe'er
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
High Throughput ◽  
Whole Genome ◽  
C Elegans ◽  
Mutant Identification

Functional characterization of naturally occurring wild soybean mutant (sg-5) lacking astringent saponins using whole genome sequencing approach

Plant Science ◽  
2018 ◽  
Vol 267 ◽  
pp. 148-156 ◽  
Author(s):  
Hafiz Mamoon Rehman ◽  
Muhammad Amjad Nawaz ◽  
Zahid Hussain Shah ◽  
Seung Hwan Yang ◽  
Gyuhwa Chung
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Functional Characterization ◽  
Wild Soybean ◽  
Whole Genome ◽  
Naturally Occurring

scholarly journals A simplified workflow for the analysis of whole-genome sequencing data from Pristionchus pacificus mutant lines

2020 ◽  
Author(s):  
Christian Rödelsperger
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Model Organism ◽  
Model Systems ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Sequencing Data ◽  
Single Nucleotide Variants ◽  
Pristionchus Pacificus ◽  
Mutant Lines

AbstractNematodes are attractive model systems to understand the genetic basis of various biological processes ranging from development to complex behaviors. In particular, mutagenesis experiments combined with whole-genome sequencing has been proven as one of the most effective methods to identify core players of multiple biological pathways. To enable experimentalists to apply such integrative genetic and bioinformatic analysis in the case of the satellite model organism Pristionchus pacificus, I present a simplified workflow for the analysis of whole-genome data from mutant lines and corresponding mapping panels. Individual components are based on well-maintained and widely used software packages and are extended by 50 lines of code for the analysis and visualization of allele frequencies. The effectiveness of this workflow is demonstrated by an application to recently generated data of a P. pacificus mutant line, where it reduced the number of candidate mutations from an initial set of 3,500 single nucleotide variants to ten.

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