Gene-environment and protein-degradation signatures characterize genomic and phenotypic diversity in wild Caenorhabditis elegans populations.


BACKGROUND:Analyzing and understanding the relationship between genotypes and phenotypes is at the heart of genetics. Research on the nematode Caenorhabditis elegans has been instrumental for unraveling genotype-phenotype relations, and has important implications for understanding the biology of mammals, but almost all studies, including forward and reverse genetic screens, are limited by investigations in only one canonical genotype. This hampers the detection and functional analysis of allelic variants, which play a key role in controlling many complex traits. It is therefore essential to explore the full potential of the natural genetic variation and evolutionary context of the genotype-phenotype map in wild C. elegans populations. RESULTS:We used multiple wild C. elegans populations freshly isolated from local sites to investigate gene sequence polymorphisms and a multitude of phenotypes including the transcriptome, fitness, and behavioral traits. The genotype, transcriptome, and a number of fitness traits showed a direct link with the original site of the strains. The separation between the isolation sites was prevalent on all chromosomes, but chromosome V was the largest contributor to this variation. These results were supported by a differential food preference of the wild isolates for naturally co-existing bacterial species. Comparing polymorphic genes between the populations with a set of genes extracted from 19 different studies on gene expression in C. elegans exposed to biotic and abiotic factors, such as bacteria, osmotic pressure, and temperature, revealed a significant enrichment for genes involved in gene-environment interactions and protein degradation. CONCLUSIONS:We found that wild C. elegans populations are characterized by gene-environment signatures, and we have unlocked a wealth of genotype-phenotype relations for the first time. Studying natural isolates provides a treasure trove of evidence compared with that unearthed by the current research in C. elegans, which covers only a diminutive part of the myriad of genotype-phenotype relations that are present in the wild.


BMC Biol


BMC biology


Volkers RJ,Snoek LB,Hubar CJ,Coopman R,Chen W,Yang W,Sterken MG,Schulenburg H,Braeckman BP,Kammenga JE




Has Abstract


2013-08-19 00:00:00










  • Spontaneous focal activation of invariant natural killer T (iNKT) cells in mouse liver and kidney.

    abstract:BACKGROUND:Invariant natural killer T (iNKT) cells differ from other T cells by their hyperactive effector T-cell status, in addition to the expression of NK lineage receptors and semi-invariant T-cell receptors. It is generally agreed that the immune phenotype of iNKT cells is maintained by repeated activation in peri...

    journal_title:BMC biology

    pub_type: 杂志文章


    authors: Zeng J,Howard JC

    更新日期:2010-11-30 00:00:00

  • Will human influences on evolutionary dynamics in the wild pervade the Anthropocene?

    abstract::The five most pervasive anthropogenic threats to biodiversity are over-exploitation, habitat changes, climate change, invasive species, and pollution. Since all of these threats can affect intraspecific biodiversity-including genetic variation within populations-humans have the potential to induce contemporary microev...

    journal_title:BMC biology

    pub_type: 杂志文章,评审


    authors: Pelletier F,Coltman DW

    更新日期:2018-01-15 00:00:00

  • A tissue-specific protein purification approach in Caenorhabditis elegans identifies novel interaction partners of DLG-1/Discs large.

    abstract:BACKGROUND:Affinity purification followed by mass spectrometry (AP/MS) is a widely used approach to identify protein interactions and complexes. In multicellular organisms, the accurate identification of protein complexes by AP/MS is complicated by the potential heterogeneity of complexes in different tissues. Here, we...

    journal_title:BMC biology

    pub_type: 杂志文章


    authors: Waaijers S,Muñoz J,Berends C,Ramalho JJ,Goerdayal SS,Low TY,Zoumaro-Djayoon AD,Hoffmann M,Koorman T,Tas RP,Harterink M,Seelk S,Kerver J,Hoogenraad CC,Bossinger O,Tursun B,van den Heuvel S,Heck AJ,Boxem M

    更新日期:2016-08-09 00:00:00

  • Open questions: how does Wolbachia do what it does?

    abstract::A common symbiont of insects, the bacterium Wolbachia has been implicated in phenomena as diverse as sex determination, pathogen defence and speciation and is being used in public health programs to prevent mosquitoes transmitting disease. Despite decades of research, we know remarkably little about how it exerts its ...

    journal_title:BMC biology

    pub_type: 社论


    authors: Jiggins FM

    更新日期:2016-10-19 00:00:00

  • Modelling the suppression of a malaria vector using a CRISPR-Cas9 gene drive to reduce female fertility.

    abstract:BACKGROUND:Gene drives based on CRISPR-Cas9 technology are increasingly being considered as tools for reducing the capacity of mosquito populations to transmit malaria, and one of the most promising options is driving endonuclease genes that reduce the fertility of female mosquitoes. In particular, there is much intere...

    journal_title:BMC biology

    pub_type: 杂志文章


    authors: North AR,Burt A,Godfray HCJ

    更新日期:2020-08-11 00:00:00

  • Stem cell biology and drug discovery.

    abstract::There are many reasons to be interested in stem cells, one of the most prominent being their potential use in finding better drugs to treat human disease. This article focuses on how this may be implemented. Recent advances in the production of reprogrammed adult cells and their regulated differentiation to disease-re...

    journal_title:BMC biology

    pub_type: 杂志文章,评审


    authors: Rubin LL,Haston KM

    更新日期:2011-06-07 00:00:00

  • Unlocking the origins and biology of domestic animals using ancient DNA and paleogenomics.

    abstract::Animal domestication has fascinated biologists since Charles Darwin first drew the parallel between evolution via natural selection and human-mediated breeding of livestock and companion animals. In this review we show how studies of ancient DNA from domestic animals and their wild progenitors and congeners have shed ...

    journal_title:BMC biology

    pub_type: 杂志文章,评审


    authors: McHugo GP,Dover MJ,MacHugh DE

    更新日期:2019-12-02 00:00:00

  • Microtubule plus-ends reveal essential links between intracellular polarization and localized modulation of endocytosis during division-plane establishment in plant cells.

    abstract:BACKGROUND:A key event in plant morphogenesis is the establishment of a division plane. A plant-specific microtubular preprophase band (PPB) accurately predicts the line of cell division, whereas the phragmoplast, another plant-specific array, executes cell division by maintaining this predicted line. Although establis...

    journal_title:BMC biology

    pub_type: 杂志文章


    authors: Dhonukshe P,Mathur J,Hülskamp M,Gadella TW Jr

    更新日期:2005-04-14 00:00:00

  • 2R and remodeling of vertebrate signal transduction engine.

    abstract:BACKGROUND:Whole genome duplication (WGD) is a special case of gene duplication, observed rarely in animals, whereby all genes duplicate simultaneously through polyploidisation. Two rounds of WGD (2R-WGD) occurred at the base of vertebrates, giving rise to an enormous wave of genetic novelty, but a systematic analysis ...

    journal_title:BMC biology

    pub_type: 杂志文章


    authors: Huminiecki L,Heldin CH

    更新日期:2010-12-13 00:00:00

  • Brief inactivation of c-Myc is not sufficient for sustained regression of c-Myc-induced tumours of pancreatic islets and skin epidermis.

    abstract:BACKGROUND:Tumour regression observed in many conditional mouse models following oncogene inactivation provides the impetus to develop, and a platform to preclinically evaluate, novel therapeutics to inactivate specific oncogenes. Inactivating single oncogenes, such as c-Myc, can reverse even advanced tumours. Intrigui...

    journal_title:BMC biology

    pub_type: 杂志文章


    authors: Pelengaris S,Abouna S,Cheung L,Ifandi V,Zervou S,Khan M

    更新日期:2004-12-21 00:00:00

  • Docosahexaenoic and eicosapentaenoic acids increase prion formation in neuronal cells.

    abstract:BACKGROUND:The transmissible spongiform encephalopathies, otherwise known as prion diseases, occur following the conversion of the cellular prion protein (PrPC) to an alternatively folded, disease-associated isoform (PrPSc). Recent studies suggest that this conversion occurs via a cholesterol-sensitive process, as chol...

    journal_title:BMC biology

    pub_type: 杂志文章


    authors: Bate C,Tayebi M,Diomede L,Salmona M,Williams A

    更新日期:2008-09-12 00:00:00

  • An automated aquatic rack system for rearing marine invertebrates.

    abstract:BACKGROUND:One hundred years ago, marine organisms were the dominant systems for the study of developmental biology. The challenges in rearing these organisms outside of a marine setting ultimately contributed to a shift towards work on a smaller number of so-called model systems. Those animals are typically non-marine...

    journal_title:BMC biology

    pub_type: 杂志文章


    authors: Henry JQ,Lesoway MP,Perry KJ

    更新日期:2020-05-04 00:00:00

  • Precise A•T to G•C base editing in the zebrafish genome.

    abstract:BACKGROUND:Base editors are a class of genome editing tools with the ability to efficiently induce point mutations in genomic DNA, without inducing double-strand breaks or relying on homology-direct repair as in other such technologies. Recently, adenine base editors (ABEs) have been developed to mediate the conversion...

    journal_title:BMC biology

    pub_type: 杂志文章


    authors: Qin W,Lu X,Liu Y,Bai H,Li S,Lin S

    更新日期:2018-11-20 00:00:00

  • Concerted evolution of male and female display traits in the European corn borer, Ostrinia nubilalis.

    abstract:BACKGROUND:Sexual reproduction entails the encounter of the sexes and the multiplicity of rituals is parallel to the diversity of mating systems. Evolutionary mechanisms such as sexual selection and sexual conflict have led to the elaboration of traits to gain attention and favours from potential partners. A paradox ex...

    journal_title:BMC biology

    pub_type: 杂志文章


    authors: Lassance JM,Löfstedt C

    更新日期:2009-03-03 00:00:00

  • Evolving eukaryotes: an interview with Joel Dacks.

    abstract::Joel Dacks is an Associate Professor and Canada Research Chair in Evolutionary Cell Biology at the University of Alberta, a Scientific Associate at the Natural History Museum (London), and the current President of the International Society for Evolutionary Protistology. His research group studies the evolution and div...

    journal_title:BMC biology

    pub_type: 传,历史文章,面试


    authors: Dacks JB

    更新日期:2018-11-01 00:00:00

  • Inland post-glacial dispersal in East Asia revealed by mitochondrial haplogroup M9a'b.

    abstract:BACKGROUND:Archaeological studies have revealed a series of cultural changes around the Last Glacial Maximum in East Asia; whether these changes left any signatures in the gene pool of East Asians remains poorly indicated. To achieve deeper insights into the demographic history of modern humans in East Asia around the ...

    journal_title:BMC biology

    pub_type: 杂志文章


    authors: Peng MS,Palanichamy MG,Yao YG,Mitra B,Cheng YT,Zhao M,Liu J,Wang HW,Pan H,Wang WZ,Zhang AM,Zhang W,Wang D,Zou Y,Yang Y,Chaudhuri TK,Kong QP,Zhang YP

    更新日期:2011-01-10 00:00:00

  • Be the change you seek in science.

    abstract::Few would argue that science is better done in silos, with no transparency or sharing of methods and resources. Yet scientists and scientific stakeholders (e.g., academic institutions, funding agencies, journals) alike continue to find themselves at a relative impasse in the implementation of open science practices, s...

    journal_title:BMC biology

    pub_type: 杂志文章


    authors: Milham MP,Klein A

    更新日期:2019-03-27 00:00:00

  • Generation of an integrated Hieracium genomic and transcriptomic resource enables exploration of small RNA pathways during apomixis initiation.

    abstract:BACKGROUND:Application of apomixis, or asexual seed formation, in crop breeding would allow rapid fixation of complex traits, economizing improved crop delivery. Identification of apomixis genes is confounded by the polyploid nature, high genome complexity and lack of genomic sequence integration with reproductive tiss...

    journal_title:BMC biology

    pub_type: 杂志文章


    authors: Rabiger DS,Taylor JM,Spriggs A,Hand ML,Henderson ST,Johnson SD,Oelkers K,Hrmova M,Saito K,Suzuki G,Mukai Y,Carroll BJ,Koltunow AM

    更新日期:2016-10-06 00:00:00

  • Erv1 of Arabidopsis thaliana can directly oxidize mitochondrial intermembrane space proteins in the absence of redox-active Mia40.

    abstract:BACKGROUND:Many proteins of the mitochondrial intermembrane space (IMS) contain structural disulfide bonds formed by the mitochondrial disulfide relay. In fungi and animals, the sulfhydryl oxidase Erv1 'generates' disulfide bonds that are passed on to the oxidoreductase Mia40, which oxidizes substrate proteins. A diffe...

    journal_title:BMC biology

    pub_type: 杂志文章


    authors: Peleh V,Zannini F,Backes S,Rouhier N,Herrmann JM

    更新日期:2017-11-08 00:00:00

  • Non-coding-regulatory regions of human brain genes delineated by bacterial artificial chromosome knock-in mice.

    abstract:BACKGROUND:The next big challenge in human genetics is understanding the 98% of the genome that comprises non-coding DNA. Hidden in this DNA are sequences critical for gene regulation, and new experimental strategies are needed to understand the functional role of gene-regulation sequences in health and disease. In thi...

    journal_title:BMC biology

    pub_type: 杂志文章


    authors: Schmouth JF,Castellarin M,Laprise S,Banks KG,Bonaguro RJ,McInerny SC,Borretta L,Amirabbasi M,Korecki AJ,Portales-Casamar E,Wilson G,Dreolini L,Jones SJ,Wasserman WW,Goldowitz D,Holt RA,Simpson EM

    更新日期:2013-10-14 00:00:00

  • Comparative analysis of Wnt expression identifies a highly conserved developmental transition in flatworms.

    abstract:BACKGROUND:Early developmental patterns of flatworms are extremely diverse and difficult to compare between distant groups. In parasitic flatworms, such as tapeworms, this is confounded by highly derived life cycles involving indirect development, and even the true orientation of the tapeworm antero-posterior (AP) axis...

    journal_title:BMC biology

    pub_type: 杂志文章


    authors: Koziol U,Jarero F,Olson PD,Brehm K

    更新日期:2016-03-04 00:00:00

  • Vaccines, emerging viruses, and how to avoid disaster.

    abstract::Rino Rappuoli is a graduate of Siena University, where he also earned his PhD before moving to the Sclavo Research Center, the Italian vaccine institute, also in Siena. He then spent two years in the USA, mostly at Harvard with John Murphy and Alwin Pappenheimer working on a new diphtheria vaccine based on a non-toxic...

    journal_title:BMC biology

    pub_type: 面试


    authors: Rappuoli R

    更新日期:2014-11-29 00:00:00

  • A metabolic signature of long life in Caenorhabditis elegans.

    abstract:BACKGROUND:Many Caenorhabditis elegans mutations increase longevity and much evidence suggests that they do so at least partly via changes in metabolism. However, up until now there has been no systematic investigation of how the metabolic networks of long-lived mutants differ from those of normal worms. Metabolomic te...

    journal_title:BMC biology

    pub_type: 杂志文章


    authors: Fuchs S,Bundy JG,Davies SK,Viney JM,Swire JS,Leroi AM

    更新日期:2010-02-10 00:00:00

  • Synaptopathy, circuitopathy and the computational biology of Huntington's disease.

    abstract::Huntington's disease (HD) is one of the most common tandem repeat disorders and presents as a unique trilogy of cognitive, psychiatric and motor symptoms. One of the major mysteries of HD is why it selectively affects specific neuronal populations. A new article in BMC Biology provides a piece in the puzzle of pathoge...

    journal_title:BMC biology

    pub_type: 评论,杂志文章


    authors: Hannan AJ

    更新日期:2018-06-27 00:00:00

  • An elevated plus-maze in mixed reality for studying human anxiety-related behavior.

    abstract:BACKGROUND:A dearth of laboratory tests to study actual human approach-avoidance behavior has complicated translational research on anxiety. The elevated plus-maze (EPM) is the gold standard to assess approach-avoidance behavior in rodents. METHODS:Here, we translated the EPM to humans using mixed reality through a co...

    journal_title:BMC biology

    pub_type: 杂志文章,随机对照试验


    authors: Biedermann SV,Biedermann DG,Wenzlaff F,Kurjak T,Nouri S,Auer MK,Wiedemann K,Briken P,Haaker J,Lonsdorf TB,Fuss J

    更新日期:2017-12-21 00:00:00

  • Assigning strains to bacterial species via the internet.

    abstract:BACKGROUND:Methods for assigning strains to bacterial species are cumbersome and no longer fit for purpose. The concatenated sequences of multiple house-keeping genes have been shown to be able to define and circumscribe bacterial species as sequence clusters. The advantage of this approach (multilocus sequence analysi...

    journal_title:BMC biology

    pub_type: 杂志文章


    authors: Bishop CJ,Aanensen DM,Jordan GE,Kilian M,Hanage WP,Spratt BG

    更新日期:2009-01-26 00:00:00

  • Contributions of chaperone and glycosyltransferase activities of O-fucosyltransferase 1 to Notch signaling.

    abstract:BACKGROUND:O-fucosyltransferase1 (OFUT1) is a conserved ER protein essential for Notch signaling. OFUT1 glycosylates EGF domains, which can then be further modified by the N-acetylglucosaminyltransferase Fringe. OFUT1 also possesses a chaperone activity that promotes the folding and secretion of Notch. Here, we investi...

    journal_title:BMC biology

    pub_type: 杂志文章


    authors: Okajima T,Reddy B,Matsuda T,Irvine KD

    更新日期:2008-01-14 00:00:00

  • Ribosomal RNA fragmentation into short RNAs (rRFs) is modulated in a sex- and population of origin-specific manner.

    abstract:BACKGROUND:The advent of next generation sequencing (NGS) has allowed the discovery of short and long non-coding RNAs (ncRNAs) in an unbiased manner using reverse genetics approaches, enabling the discovery of multiple categories of ncRNAs and characterization of the way their expression is regulated. We previously sho...

    journal_title:BMC biology

    pub_type: 杂志文章


    authors: Cherlin T,Magee R,Jing Y,Pliatsika V,Loher P,Rigoutsos I

    更新日期:2020-04-13 00:00:00

  • Features of the ancestral bilaterian inferred from Platynereis dumerilii ParaHox genes.

    abstract:BACKGROUND:The ParaHox gene cluster is the evolutionary sister to the Hox cluster. Whilst the role of the Hox cluster in patterning the anterior-posterior axis of bilaterian animals is well established, and the organisation of vertebrate Hox clusters is intimately linked to gene regulation, much less is known about the...

    journal_title:BMC biology

    pub_type: 杂志文章


    authors: Hui JH,Raible F,Korchagina N,Dray N,Samain S,Magdelenat G,Jubin C,Segurens B,Balavoine G,Arendt D,Ferrier DE

    更新日期:2009-07-23 00:00:00

  • The hidden diversity of ribosomal peptide natural products.

    abstract::A recent report in BMC Biology on the discovery and analysis of biosynthetic genes for ribosomal peptide natural products confirms that these pathways are much more common and diverse than previously suspected, contributing substantially to the chemical arsenal employed by bacteria. See research article

    journal_title:BMC biology

    pub_type: 评论,杂志文章


    authors: Schmidt EW

    更新日期:2010-06-17 00:00:00