Characterization of genome-wide SNPs for the water flea Daphnia pulicaria generated by genotyping-by-sequencing (GBS)

Muñoz, Joaquín; Chaturvedi, Anurag; Meester, Luc De; Weider, Lawrence J.

doi:10.1038/srep28569

Cited by 15 publications

(9 citation statements)

References 49 publications

(75 reference statements)

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“…Genetic differentiation among populations of passively dispersed aquatic invertebrates is strong in most cases, despite the dispersal probability expedited by water birds and other vectors carrying their diapausing eggs (Mills et al 2007; Munoz et al 2016; Ventura et al 2014). Population genetic differentiation has been observed even at small spatial scales (i.e., less than 1 km) in Daphnia (Hamrova et al 2011; Yin et al 2010).…”

Section: Discussionmentioning

confidence: 99%

Contrasting patterns of divergence at the regulatory and sequence level in EuropeanDaphnia galeatanatural populations

Ravindran

Herrmann

Cordellier

2018

Preprint

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15Understanding the genetic basis of local adaptation has long been a focus of 16 evolutionary biology. Recently there has been increased interest in deciphering the 17 evolutionary role of Daphnia's plasticity and the molecular mechanisms of local 18 adaptation. Using transcriptome data, we assessed the differences in gene 19 expression profiles and sequences in four European Daphnia galeata populations. In 20 total, ~33% of 32,903 transcripts were differentially expressed between populations. 21Among 10,280 differentially expressed transcripts, 5,209 transcripts deviated from 22 neutral expectations and their population-specific expression pattern is likely the 23 result of local adaptation processes. Furthermore, a SNP analysis allowed inferring 24 population structure and distribution of genetic variation. The population divergence 25 at the sequence-level was comparatively higher than the gene expression level by 26 several orders of magnitude and consistent with strong founder effects and lack of 27 gene flow between populations. Using sequence information, the candidate 28 transcripts were annotated using a comparative genomics approach. Thus, we 29 identified candidate transcriptomic regions for local adaptation in a key species of 30 aquatic ecosystems in the absence of any laboratory induced stressor. 31

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Section: Discussionmentioning

confidence: 99%

Contrasting patterns of divergence at the regulatory and sequence level in EuropeanDaphnia galeatanatural populations

Ravindran

Herrmann

Cordellier

2018

Preprint

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“…It forms an important part of the food chain and displays parthenogenetic reproduction under ideal environmental conditions 1 , 2 . Daphnid crustaceans are model organisms in certain research fields, such as ecotoxicology, ecotoxigenomics and evolutionary ecology 3 – 6 . The entire genome of D. pulex is sequenced and represents the first crustacean genome available for data mining 7 , making it very interesting for comparative bioinformatic analyses, especially with a focus on peptide hormones 8 , 9 .…”

Section: Introductionmentioning

confidence: 99%

Characterisation and pharmacological analysis of a crustacean G protein-coupled receptor: the red pigment-concentrating hormone receptor of Daphnia pulex

Marco

Verlinden

Broeck

et al. 2017

Sci Rep

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This is the first pharmacological characterisation of a neuropeptide G protein-coupled receptor (GPCR) in a crustacean. We cloned the ORF of the red pigment-concentrating hormone from a German strain of Daphnia pulex (Dappu-RPCH), as well as that of the cognate receptor (Dappu-RPCHR). Dappu-RPCHR has the hallmarks of the rhodopsin superfamily of GPCRs, and is more similar to insect adipokinetic hormone (AKH) receptor sequences than to receptor sequences for AKH/corazonin-like peptide or corazonin. We provide experimental evidence that Dappu-RPCH specifically activates the receptor (EC50 value of 65 pM) in a mammalian cell-based bioluminescence assay. We further characterised the properties of the ligands for the Dappu-RPCHR by investigating the activities of a variety of naturally-occurring peptides (insect AKH and crustacean RPCH peptides). The insect AKHs had lower EC50 values than the crustacean RPCHs. In addition, we tested a series of Dappu-RPCH analogues, where one residue at a time is systematically replaced by an alanine to learn about the relative importance of the termini and side chains for activation. Mainly amino acids in positions 1 to 4 and 8 of Dappu-RPCH appear responsible for effective activation of Dappu-RPCHR. The substitution of Phe4 in Dappu-RPCH had the most damaging effect on its agonistic activity.

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“…SNPs became the absolute marker of choice for molecular genetic analysis as the mining of polymorphisms is the cheapest source for Genetic differentiation among populations of passively dispersed aquatic invertebrates is strong in most cases, despite the dispersal probability expedited by water birds and other vectors carrying their diapausing eggs (Mills, Lunt, & Gomez, 2007;Munoz, Chaturvedi, De Meester, & Weider, 2016;Ventura et al, 2014). Population genetic differentiation has been observed even at small spatial scales (i.e., less than 1 km) in Daphnia (Hamrova, Mergeay, & Petrusek, 2011;Yin et al, 2010).…”

Section: Population Divergence At the Sequence Levelmentioning

confidence: 99%

Contrasting patterns of divergence at the regulatory and sequence level in European Daphnia galeata natural populations

Ravindran

Herrmann

Cordellier

2019

Ecology and Evolution

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Understanding the genetic basis of local adaptation has long been a focus of evolutionary biology. Recently, there has been increased interest in deciphering the evolutionary role of Daphnia 's plasticity and the molecular mechanisms of local adaptation. Using transcriptome data, we assessed the differences in gene expression profiles and sequences in four European Daphnia galeata populations. In total, ~33% of 32,903 transcripts were differentially expressed between populations. Among 10,280 differentially expressed transcripts, 5,209 transcripts deviated from neutral expectations and their population‐specific expression pattern is likely the result of local adaptation processes. Furthermore, a SNP analysis allowed inferring population structure and distribution of genetic variation. The population divergence at the sequence level was comparatively higher than the gene expression level by several orders of magnitude consistent with strong founder effects and lack of gene flow between populations. Using sequence homology, the candidate transcripts were annotated using a comparative genomics approach. Additionally, we also performed a weighted gene co‐expression analysis to identify population‐specific regulatory patterns of transcripts in D. galeata . Thus, we identified candidate transcriptomic regions for local adaptation in this key species of aquatic ecosystems in the absence of any laboratory‐induced stressor.

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Characterization of genome-wide SNPs for the water flea Daphnia pulicaria generated by genotyping-by-sequencing (GBS)

Cited by 15 publications

References 49 publications

Contrasting patterns of divergence at the regulatory and sequence level in EuropeanDaphnia galeatanatural populations

Contrasting patterns of divergence at the regulatory and sequence level in EuropeanDaphnia galeatanatural populations

Characterisation and pharmacological analysis of a crustacean G protein-coupled receptor: the red pigment-concentrating hormone receptor of Daphnia pulex

Contrasting patterns of divergence at the regulatory and sequence level in European Daphnia galeata natural populations

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