scholarly journals Intron Size Correlates Positively With Recombination Rate in Caenorhabditis elegans

Genetics ◽  
2004 ◽  
Vol 166 (3) ◽  
pp. 1585-1590 ◽  
Author(s):  
Anuphap Prachumwat ◽  
Laura DeVincentis ◽  
Michael F. Palopoli
Keyword(s):  
Caenorhabditis Elegans ◽  
Recombination Rate ◽  
Intron Size

scholarly journals Degradation of the Repetitive Genomic Landscape in a Close Relative of Caenorhabditis elegans

2020 ◽  
Vol 37 (9) ◽  
pp. 2549-2567 ◽  
Author(s):  
Gavin C Woodruff ◽  
Anastasia A Teterina
Keyword(s):  
Caenorhabditis Elegans ◽  
Recombination Rate ◽  
Genomic Organization ◽  
Reproductive Mode ◽  
Repetitive Elements ◽  
Repeat Content ◽  
Genomic Landscape ◽  
Chromosome Position ◽  
Caenorhabditis Species ◽  
Evolutionary Simulations

Abstract The abundance, diversity, and genomic distribution of repetitive elements is highly variable among species. These patterns are thought to be driven in part by reproductive mode and the interaction of selection and recombination, and recombination rates typically vary by chromosomal position. In the nematode Caenorhabditis elegans, repetitive elements are enriched at chromosome arms and depleted on centers, and this mirrors the chromosomal distributions of other genomic features such as recombination rate. How conserved is this genomic landscape of repeats, and what evolutionary forces maintain it? To address this, we compared the genomic organization of repetitive elements across five Caenorhabditis species with chromosome-level assemblies. As previously reported, repeat content is enriched on chromosome arms in most Caenorhabditis species, and no obvious patterns of repeat content associated with reproductive mode were observed. However, the fig-associated C. inopinata has experienced repetitive element expansion and reveals no association of global repeat density with chromosome position. Patterns of repeat superfamily specific distributions reveal this global pattern is driven largely by a few repeat superfamilies that in C. inopinata have expanded in number and have weak associations with chromosome position. Additionally, 15% of predicted protein-coding genes in C. inopinata align to transposon-related proteins. When these are excluded, C. inopinata has no enrichment of genes in chromosome centers, in contrast to its close relatives who all have such clusters. Forward evolutionary simulations reveal that chromosomal heterogeneity in recombination rate alone can generate structured repetitive genomic landscapes when insertions are weakly deleterious, whereas chromosomal heterogeneity in the fitness effects of transposon insertion can promote such landscapes across a variety of evolutionary scenarios. Thus, patterns of gene density along chromosomes likely contribute to global repetitive landscapes in this group, although other historical or genomic factors are needed to explain the idiosyncrasy of genomic organization of various transposable element taxa within C. inopinata. Taken together, these results highlight the power of comparative genomics and evolutionary simulations in testing hypotheses regarding the causes of genome organization.

scholarly journals Meiotic recombination, noncoding DNA and genomic organization in Caenorhabditis elegans.

Genetics ◽  
1995 ◽  
Vol 141 (1) ◽  
pp. 159-179 ◽  
Author(s):  
T M Barnes ◽  
Y Kohara ◽  
A Coulson ◽  
S Hekimi
Keyword(s):  
Caenorhabditis Elegans ◽  
Genetic Map ◽  
Recombination Rate ◽  
Physical Map ◽  
Gene Density ◽  
Cdna Clones ◽  
Recombination Rates ◽  
Noncoding Dna ◽  
Physical Size ◽  
C Elegans

Abstract The genetic map of each Caenorhabditis elegans chromosome has a central gene cluster (less pronounced on the X chromosome) that contains most of the mutationally defined genes. Many linkage group termini also have clusters, though involving fewer loci. We examine the factors shaping the genetic map by analyzing the rate of recombination and gene density across the genome using the positions of cloned genes and random cDNA clones from the physical map. Each chromosome has a central gene-dense region (more diffuse on the X) with discrete boundaries, flanked by gene-poor regions. Only autosomes have reduced rates of recombination in these gene-dense regions. Cluster boundaries appear discrete also by recombination rate, and the boundaries defined by recombination rate and gene density mostly, but not always, coincide. Terminal clusters have greater gene densities than the adjoining arm but similar recombination rates. Thus, unlike in other species, most exchange in C. elegans occurs in gene-poor regions. The recombination rate across each cluster is constant and similar; and cluster size and gene number per chromosome are independent of the physical size of chromosomes. We propose a model of how this genome organization arose.

scholarly journals Transposons but Not Retrotransposons Are Located Preferentially in Regions of High Recombination Rate in Caenorhabditis elegans

Genetics ◽  
2000 ◽  
Vol 156 (4) ◽  
pp. 1661-1669 ◽  
Author(s):  
Laurent Duret ◽  
Gabriel Marais ◽  
Christian Biémont
Keyword(s):  
Caenorhabditis Elegans ◽  
Recombination Rate ◽  
Ltr Retrotransposons ◽  
Coding Region ◽  
Nematode Caenorhabditis Elegans ◽  
Noncoding Regions ◽  
Dna And Rna ◽  
Gene Coding ◽  
Intergenic Dna ◽  
The Difference

Abstract We analyzed the distribution of transposable elements (TEs: transposons, LTR retrotransposons, and non-LTR retrotransposons) in the chromosomes of the nematode Caenorhabditis elegans. The density of transposons (DNA-based elements) along the chromosomes was found to be positively correlated with recombination rate, but this relationship was not observed for LTR or non-LTR retrotransposons (RNA-based elements). Gene (coding region) density is higher in regions of low recombination rate. However, the lower TE density in these regions is not due to the counterselection of TE insertions within exons since the same positive correlation between TE density and recombination rate was found in noncoding regions (both in introns and intergenic DNA). These data are not compatible with a global model of selection acting against TE insertions, for which an accumulation of elements in regions of reduced recombination is expected. We also found no evidence for a stronger selection against TE insertions on the X chromosome compared to the autosomes. The difference in distribution of the DNA and RNA-based elements along the chromosomes in relation to recombination rate can be explained by differences in the transposition processes.

scholarly journals Large genetic diversity and strong positive selection in F-box and GPCR genes among the wild isolates of Caenorhabditis elegans

2020 ◽  
Author(s):  
Fuqiang Ma ◽  
Chun Yin Lau ◽  
Chaogu Zheng
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Caenorhabditis Elegans ◽  
Positive Selection ◽  
Recombination Rate ◽  
Selective Sweep ◽  
Gene Families ◽  
Strong Positive Selection ◽  
High Recombination Rate ◽  
C Elegans

AbstractThe F-box and chemosensory GPCR (csGPCR) gene families are greatly expanded in nematodes, including the model organism Caenorhabditis elegans, compared to insects and vertebrates. However, the intraspecific evolution of these two gene families in nematodes remain unexamined. In this study, we analyzed the genomic sequences of 330 recently sequenced wild isolates of C. elegans using a range of population genetics approaches. We found that F-box and csGPCR genes, especially the Srw family csGPCRs, showed much more diversity than other gene families. Population structure analysis and phylogenetic analysis divided the wild strains into eight non-Hawaiian and three Hawaiian subpopulations. Some Hawaiian strains appeared to be more ancestral than all other strains. F-box and csGPCR genes maintained a great amount of the ancestral variants in the Hawaiian subpopulation and their divergence among the non-Hawaiian subpopulations contributed significantly to population structure. These genes are mostly located at the chromosomal arms and high recombination rate correlates with their large polymorphism. Gene flow might also contribute to their diversity. Moreover, we identified signatures of strong positive selection in the F-box and csGPCR genes in the non-Hawaiian population using both neutrality tests and Extended Haplotype Homozygosity analysis. Accumulation of high frequency derived alleles in these genes were found in non-Hawaiian population, leading to divergence from the ancestral genotype found in Hawaiian strains. In summary, we found that F-box and csGPCR genes harbour a large pool of natural variants, which may be subjected to positive selection during the recent selective sweep in non-Hawaiian population. These variants are mostly mapped to the substrate-recognition domains of F-box proteins and the extracellular regions of csGPCRs, possibly resulting in advantages during adaptation by affecting protein degradation and the sensing of environmental cues, respectively.Significance statementThe small nematode Caenorhabditis elegans has emerged as an important organism in studying the genetic mechanisms of evolution. F-box and chemosensory GPCR are two of the largest gene families in C. elegans, but their intraspecific evolution within C. elegans was not studied before. In this work, using the nonsynonymous SNV data of 330 C. elegans wild isolates, we found that F-box and chemosensory GPCR genes showed larger polymorphisms and stronger positive selection than other genes. The large diversity is likely the result of rapid gene family expansion, high recombination rate, and gene flow. Analysis of subpopulation suggests that positive selection of these genes occurred most strongly in the non-Hawaiian population, which underwent a selective sweep possibly linked to human activities.

The glycomes of Caenorhabditis elegans and other model organisms

2002 ◽  
Vol 69 ◽  
pp. 117-134 ◽  
Author(s):  
Stuart M. Haslam ◽  
David Gems ◽  
Howard R. Morris ◽  
Anne Dell
Keyword(s):  
Caenorhabditis Elegans ◽  
Current Knowledge ◽  
Structural Data ◽  
Model Organisms ◽  
Entire Genome ◽  
C Elegans ◽  
The Face ◽  
Area Of Concern ◽  
Nematode Worm

There is no doubt that the immense amount of information that is being generated by the initial sequencing and secondary interrogation of various genomes will change the face of glycobiological research. However, a major area of concern is that detailed structural knowledge of the ultimate products of genes that are identified as being involved in glycoconjugate biosynthesis is still limited. This is illustrated clearly by the nematode worm Caenorhabditis elegans, which was the first multicellular organism to have its entire genome sequenced. To date, only limited structural data on the glycosylated molecules of this organism have been reported. Our laboratory is addressing this problem by performing detailed MS structural characterization of the N-linked glycans of C. elegans; high-mannose structures dominate, with only minor amounts of complex-type structures. Novel, highly fucosylated truncated structures are also present which are difucosylated on the proximal N-acetylglucosamine of the chitobiose core as well as containing unusual Fucα1–2Gal1–2Man as peripheral structures. The implications of these results in terms of the identification of ligands for genomically predicted lectins and potential glycosyltransferases are discussed in this chapter. Current knowledge on the glycomes of other model organisms such as Dictyostelium discoideum, Saccharomyces cerevisiae and Drosophila melanogaster is also discussed briefly.

A Relationship Between Thermotolerance and Longevity in Caenorhabditis elegans

1998 ◽  
Vol 3 (1) ◽  
pp. 6-10 ◽  
Author(s):  
Glenda A Walker ◽  
David W Walker ◽  
Gordon J Lithgow
Keyword(s):  
Caenorhabditis Elegans
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