Project description:The standard reference Caenorhabditis elegans strain, N2, has evolved marked behavioral changes in social feeding behavior since its isolation from the wild. We show that the causal, laboratory-derived mutations in two genes, npr-1 and glb-5, confer large fitness advantages in standard laboratory conditions. Using environmental manipulations that suppress social/solitary behavior differences, we show the fitness advantages of the derived alleles remained unchanged, suggesting selection on these alleles acted through pleiotropic traits. Transcriptomics, developmental timing, and food consumption assays showed that N2 animals mature faster, produce more sperm, and consume more food than a strain containing ancestral alleles of these genes regardless of behavioral strategies. Our data suggest that the pleiotropic effects of glb-5 and npr-1 are a consequence of changes to O2 -sensing neurons that regulate both aerotaxis and energy homeostasis. Our results demonstrate how pleiotropy can lead to profound behavioral changes in a popular laboratory model.
Project description:Caenorhabditis elegans was the first multicellular eukaryotic genome sequenced to apparent completion. Although this assembly employed a standard C. elegans strain (N2), it used sequence data from several laboratories, with DNA propagated in bacteria and yeast. Thus, the N2 assembly has many differences from any C. elegans available today. To provide a more accurate C. elegans genome, we performed long-read assembly of VC2010, a modern strain derived from N2. Our VC2010 assembly has 99.98% identity to N2 but with an additional 1.8 Mb including tandem repeat expansions and genome duplications. For 116 structural discrepancies between N2 and VC2010, 97 structures matching VC2010 (84%) were also found in two outgroup strains, implying deficiencies in N2. Over 98% of N2 genes encoded unchanged products in VC2010; moreover, we predicted ?53 new genes in VC2010. The recompleted genome of C. elegans should be a valuable resource for genetics, genomics, and systems biology.
Project description:Caenorhabditis elegans is a nematode widely used in biology and genomics as a model organism. We provide an integrated, quantitative reference map for the transcriptome of whole, wild type Bristol N2 strain C. elegans worms. The map has been obtained by meta-analysis of 110 gene expression profiles available in Gene Expression Omnibus (GEO) repository and integrated using the computational biology tool Transcriptome Mapper (TRAM). Following probe assignment to the relative locus and intra- and inter-sample normalization (in particular using the scaled quantile method), a mean, consensus reference value is provided for 45,932 transcripts, along with standard deviation. Expression values are all mapped in the context of genomic coordinates. The map provides easy access to relationships among expression values of different genes in this standard condition, highlights genomic segments with relatively high over-/under-expression and may serve as a reference to test for gene expression variation for both individual genes and the whole transcriptome in specific biological conditions (e.g. mutated strains or differently grown worms).
Project description:Investigation of whole genome gene expression level changes in early generation Caenorhabditis elegans Bristol N2 prg-1 and Bristol N2 prg-1; daf-2 double mutant, compared to late-generation strains. A seven chip study using total RNA recovered from three separate alleles of Caenorhabditis elegans Bristol N2 prg-1 and four separate allelic combinations of a double mutant strain, Bristol N2 prg-1; daf-2 , in which prg-1 (pk2298) and prg-1 (tm872) are combined with one of three daf-2 alleles (e1368, 1370, m41).
Project description:Background:Aminopeptidases play important roles in various biological processes in nematodes including growth, development and reproduction. Although the aminopeptidases have been shown to regulate reproduction in Caenorhabditis elegans (C. elegans), the role of aminopeptidases in development and aging has not been reported. This study focused on the function of aminopeptidase AlaNyl aminopeptidase 1 (ANP-1) on development in C. elegans. Methods:In the present study, we reported the identification of ANP-1 in C. elegans along with sequence analysis and its functional expression and characterization. The phenotype changes were observed when anp-1 mutated. Then, differential expression genes (DEGs) between wild type strain (N2) and anp-1 deletion strain (RB804) were identified using transcriptome sequencing method. Finally, DEGs were verified by qRT-PCR assay. Results:Our observations suggested that anp-1 mutation induced small body size in the L4/young adult stage of C. elegans, however, there was no difference between N2 and RB804 in adult stage. Moreover, deletion of anp-1 resulted in shortening lifespan and laying fewer eggs. DEGs (184 genes) were observed between N2 groups and RB804 groups by transcriptome sequencing. According to GO annotations and KEGG enrichment analysis, these DEGs play vital roles in development regulation in C. elegans. These data demonstrate ANP-1 participates in development and aging of C. elegans and will considerably contribute to the existing knowledge of aminopeptidase function in C. elegans.