Genome-wide variations in a natural isolate of the nematode Caenorhabditis elegans

Abstract

BackgroundIncreasing genetic and phenotypic differences found among natural isolates of C. elegans have encouraged researchers to explore the natural variation of this nematode species.ResultsHere we report on the identification of genomic differences between the reference strain N2 and the Hawaiian strain CB4856, one of the most genetically distant strains from N2. To identify both small- and large-scale genomic variations (GVs), we have sequenced the CB4856 genome using both Roche 454 (~400 bps single reads) and Illumina GA DNA sequencing methods (101 bps paired-end reads). Compared to previously described variants (available in WormBase), our effort uncovered twice as many single nucleotide variants (SNVs) and increased the number of small InDels almost 20-fold. Moreover, we identified and validated large insertions, most of which range from 150 bps to 1.2 kb in length in the CB4856 strain. Identified GVs had a widespread impact on protein-coding sequences, including 585 single-copy genes that have associated severe phenotypes of reduced viability in RNAi and genetics studies. Sixty of these genes are homologs of human genes associated with diseases. Furthermore, our work confirms previously identified GVs associated with differences in behavioural and biological traits between the N2 and CB4856 strains.ConclusionsThe identified GVs provide a rich resource for future studies that aim to explain the genetic basis for other trait differences between the N2 and CB4856 strains.

Comprehensive identification and characterization of conserved small ORFs in animals

“…SNPs were downloaded as gvf files from Ensembl (for human: v75, 1000 Genomes phase 1; for mouse, zebrafish and fly: v77); for C. elegans we took a list of polymorphisms between the Bristol and Hawaii strains from Vergara et al 96 and used liftOver to convert ce9 coordinates to ce6. We removed SNPs on the minus strand, SNPs falling into genomic repeats (using the RepeatMasker track from the UCSC genome browser, March 2015), and (if applicable) rare SNPs with derived allele frequency <1%.…”

All the microbiology nematodes can teach us

“…Moreover, both its genome sequence and structure have been subsequently confirmed (e.g. Gerstein et al 2010;Lamm et al 2011;Vergara et al 2014), and the model nematode subjected to many genetic screens (e.g. Lejeune et al 2012;Roy et al 2014).…”

Inverted repeat structures are associated with essential and highly expressed genes on C. elegans autosome distal arms

“…If repeat-associated dsRNA structures promote gene expression, in theory, expression differences should be observed in identical genes with and without dsRNA elements. Two well-studied and genetically diverse C. elegans strains, Bristol N2 and the Hawaiian strain CB4856, exhibit distinct transposon insertion and deletion patterns (Vergara et al 2014;Laricchia et al 2017) that result in some genes containing dsRNA elements in one strain but not the other. We used mRNA expression data from each strain (Kamkina et al 2016) to compare strain-specific expression of genes in which a palindromic transposon in N2 was deleted in CB4856 (Supplemental Fig.…”