Meiosis genes in Daphnia pulex and the role of parthenogenesis in genome evolution

Background  

Thousands of parthenogenetic animal species have been described and cytogenetic manifestations of this reproductive mode are well known. However, little is understood about the molecular determinants of parthenogenesis. The Daphnia pulex genome must contain the molecular machinery for different reproductive modes: sexual (both male and female meiosis) and parthenogenetic (which is either cyclical or obligate). This feature makes D. pulex an ideal model to investigate the genetic basis of parthenogenesis and its consequences for gene and genome evolution. Here we describe the inventory of meiotic genes and their expression patterns during meiotic and parthenogenetic reproduction to help address whether parthenogenesis uses existing meiotic and mitotic machinery, or whether novel processes may be involved.     

The chemoreceptor genes of the waterflea Daphnia pulex : many Grs but no Ors

Background  

Chemoreception is vitally important for all animals, yet little is known about the genetics of chemoreception in aquatic organisms. The keystone species Daphnia pulex, a well known crustacean, is the first aquatic invertebrate to have its genome sequenced. This has allowed us the initial investigation of chemoreceptor genes in an aquatic invertebrate, and to begin the study of chemoreceptor evolution across the arthropod phylum.     

Unusual duplication of the insulin-like receptor in the crustacean <Emphasis Type="Italic">Daphnia pulex</Emphasis>

Background  

The insulin signaling pathway (ISP) has a key role in major physiological events like carbohydrate metabolism and growth regulation. The ISP has been well described in vertebrates and in a few invertebrate model organisms but remains largely unexplored in non-model invertebrates. This study is the first detailed genomic study of this pathway in a crustacean species, Daphnia pulex.     

The role of hybridization in the origin and spread of asexuality in Daphnia

The molecular mechanisms leading to asexuality remain little understood despite their substantial bearing on why sexual reproduction is dominant in nature. Here, we examine the role of hybridization in the origin and spread of obligate asexuality in Daphnia pulex, arguably the best‐documented case of contagious asexuality. Obligately parthenogenetic (OP) clones of D. pulex have traditionally been separated into ‘hybrid’ (Ldh SF) and ‘nonhybrid’ (Ldh SS) forms because the lactase dehydrogenase (Ldh) locus distinguishes the cyclically parthenogenetic (CP) lake dwelling Daphnia pulicaria (Ldh FF) from its ephemeral pond dwelling sister species D. pulex (Ldh SS). The results of our population genetic analyses based on microsatellite loci suggest that both Ldh SS and SF OP individuals can originate from the crossing of CP female F₁ (D. pulex × D. pulicaria) and backcross with males from OP lineages carrying genes that suppress meiosis specifically in female offspring. In previous studies, a suite of diagnostic markers was found to be associated with OP in Ldh SS D. pulex lineages. Our association mapping supports a similar genetic mechanism for the spread of obligate parthenogenesis in Ldh SF OP individuals. Interestingly, our study shows that CP D. pulicaria carry many of the diagnostic microsatellite alleles associated with obligate parthenogenesis. We argue that the assemblage of mutations that suppress meiosis and underlie obligate parthenogenesis in D. pulex originated due to a unique historical hybridization and introgression event between D. pulex and D. pulicaria.     

Predicting the ecological impacts of a new freshwater invader: functional responses and prey selectivity of the ‘killer shrimp’, Dikerogammarus villosus,compared to the native Gammarus pulex

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Gene up-regulation in response to predator kairomones in the water flea, <Emphasis Type="Italic">Daphnia pulex</Emphasis>

Background

Numerous cases of predator-induced polyphenisms, in which alternate phenotypes are produced in response to extrinsic stimuli, have been reported in aquatic taxa to date. The genus Daphnia (Branchiopoda, Cladocera) provides a model experimental system for the study of the developmental mechanisms and evolutionary processes associated with predator-induced polyphenisms. In D. pulex, juveniles form neckteeth in response to predatory kairomones released by Chaoborus larvae (Insecta, Diptera).

Results

Previous studies suggest that the timing of the sensitivity to kairomones in D. pulex can generally be divided into the embryonic and postembryonic developmental periods. We therefore examined which of the genes in the embryonic and first-instar juvenile stages exhibit different expression levels in the presence or absence of predator kairomones. Employing a candidate gene approach and identifying differentially-expressed genes revealed that the morphogenetic factors, Hox3, extradenticle and escargot, were up-regulated by kairomones in the postembryonic stage and may potentially be responsible for defense morph formation. In addition, the juvenile hormone pathway genes, JHAMT and Met, and the insulin signaling pathway genes, InR and IRS-1, were up-regulated in the first-instar stage. It is well known that these hormonal pathways are involved in physiological regulation following morphogenesis in many insect species. During the embryonic stage when morphotypes were determined, one of the novel genes identified by differential display was up-regulated, suggesting that this gene may be related to morphotype determination. Biological functions of the up-regulated genes are discussed in the context of defense morph formation.

Conclusions

It is suggested that, following the reception of kairomone signals, the identified genes are involved in a series of defensive phenotypic alterations and the production of a defensive phenotype.

     

Acclimatory responses of the Daphnia pulex proteome to environmental changes. II. Chronic exposure to different temperatures (10 and 20°C) mainly affects protein metabolism

Background  

Temperature affects essentially every aspect of the biology of poikilothermic animals including the energy and mass budgets, activity, growth, and reproduction. While thermal effects in ecologically important groups such as daphnids have been intensively studied at the ecosystem level and at least partly at the organismic level, much less is known about the molecular mechanisms underlying the acclimation to different temperatures. By using 2D gel electrophoresis and mass spectrometry, the present study identified the major elements of the temperature-induced subset of the proteome from differently acclimated Daphnia pulex.     

Fine-scale genetic mapping of a hybrid sterility factor between <Emphasis Type="Italic">Drosophila simulans</Emphasis> and <Emphasis Type="Italic">D. mauritiana</Emphasis>: the varied and elusive functions of "speciation genes"

Background  

Hybrid male sterility (HMS) is a usual outcome of hybridization between closely related animal species. It arises because interactions between alleles that are functional within one species may be disrupted in hybrids. The identification of genes leading to hybrid sterility is of great interest for understanding the evolutionary process of speciation. In the current work we used marked P-element insertions as dominant markers to efficiently locate one genetic factor causing a severe reduction in fertility in hybrid males of Drosophila simulans and D. mauritiana.     

Selection of internal reference genes for SYBR green qRT-PCR studies of rhesus monkey (<Emphasis Type="Italic">Macaca mulatta</Emphasis>) tissues

Background  

The rhesus monkey (Macaca mulatta) is a valuable and widely used model animal for biomedical research. However, quantitative analyses of rhesus gene expression profiles under diverse experimental conditions are limited by a shortage of suitable internal controls for the normalization of mRNA levels. In this study, we used a systematic approach for the selection of potential reference genes in the rhesus monkey and compared their suitability to that of the corresponding genes in humans.     

Cholesterol‐α‐glucosyltransferase gene is present in most Helicobacter species including gastric non‐Helicobacter pylori helicobacters obtained from Japanese patients

Background

Non‐Helicobacter pylori helicobacters (NHPHs) besides H. pylori infect human stomachs and cause chronic gastritis and mucosa‐associated lymphoid tissue lymphoma. Cholesteryl‐α‐glucosides have been identified as unique glycolipids present in H. pylori and some Helicobacter species. Cholesterol‐α‐glucosyltransferase (αCgT), a key enzyme for the biosynthesis of cholesteryl‐α‐glucosides, plays crucial roles in the pathogenicity of H. pylori. Therefore, it is important to examine αCgTs of NHPHs.

Materials and Methods

Six gastric NHPHs were isolated from Japanese patients and maintained in mouse stomachs. The αCgT genes were amplified by PCR and inverse PCR. We retrieved the αCgT genes of other Helicobacter species by BLAST searches in GenBank.

Results

αCgT genes were present in most Helicobacter species and in all Japanese isolates examined. However, we could find no candidate gene for αCgT in the whole genome of Helicobacter cinaedi and several enterohepatic species. Phylogenic analysis demonstrated that the αCgT genes of all Japanese isolates show high similarities to that of a zoonotic group of gastric NHPHs including Helicobacter suis, Helicobacter heilmannii, and Helicobacter ailurogastricus. Of 6 Japanese isolates, the αCgT genes of 4 isolates were identical to that of H. suis, and that of another 2 isolates were similar to that of H. heilmannii and H. ailurogastricus.

Conclusions

All gastric NHPHs examined showed presence of αCgT genes, indicating that αCgT may be beneficial for these helicobacters to infect human and possibly animal stomachs. Our study indicated that NHPHs could be classified into 2 groups, NHPHs with αCgT genes and NHPHs without αCgT genes.     

Costs of predator‐induced morphological defences in Daphnia

1. Inducible defences are advantageous because they protect the prey while limiting associated fitness costs. The presence of these costs is an essential component of this conditional strategy, since their absence would favour constitutive (fixed) defences. In some cases, however, these costs have been difficult to measure because of complex interactions between the defences themselves, resultant life history changes and the organism’s environment. 2. The pond‐dwelling water flea, Daphnia pulex, forms defensive neck spines in response to kairomones released by predatory larvae of the phantom midge, Chaoborus. This predator–prey interaction and the formation of these inducible defences have been well studied, but costs associated with the development of neck spines remain unclear. In this study, I address this problem by analysing the effect of Chaoborus kairomones on the life history responses (and fitness costs associated with these responses) of two clones of D. pulex that are from the same pond population, but differ greatly in their degree of neck spine development. 3. Both D. pulex clones exhibited the same predator‐induced shifts in life history: larger size at birth, reduced juvenile growth rate (producing a smaller size at maturity), delayed reproduction and a reduction in the number of neonates produced after the first clutch. Relative fitness decreased significantly and to the same degree (c. 10% reduction in r) in each clone. This observed fitness cost was not directly related to the neck spines per se since the cost was the same in both clones, despite their considerable differences in neck spine development. Rather, it appears to be indirectly related to this antipredator morphology via a combination of delayed reproduction and a set of life history trade‐offs (decreased growth rate, decreased reproduction after the first clutch) for increased neonate body size, which is necessary for neck spines to be effective defences. This suite of induced responses is probably a result of local adaptation of these two D. pulex clones to their common pond environment. 4. Costs of inducible defences do not always entail direct allocation costs associated with forming and maintaining a defence, but may also involve indirect life history responses that are specific to particular environmental situations. This local adaptation would explain the highly variable life history responses observed among D. pulex clones from different pond environments.     

The influence of predator regime on reproductive traits in <Emphasis Type="Italic">Gammarus</Emphasis> <Emphasis Type="Italic">pulex</Emphasis> populations

Selection on traits conferring reduced predation may be opposed by selection on other traits associated with reproduction. Here, we examined the hypothesis that traits associated with reproduction in Gammarus pulex are driven by predation. We studied G. pulex originating from ponds with two different kinds of predator regimes: (1) ponds with fish—often large, non-gap-limited predators and (2) ponds without fish where invertebrates are the dominant predators—often small, gap-limited predators with a much more restricted prey size range. We examined the body size of males and females in G. pulex amplexus pairs originating from fish and fishless ponds. We also examined, in the laboratory, their mating success, the number of offspring per female and offspring mortality under different rearing conditions, with or without fish cue. Mating success, defined as the percentage of amplexus pairs that produced live offspring, was higher for G. pulex from fishless ponds independent of rearing condition. Individuals from fish ponds were larger and they produced a higher number of offspring which tended to be related to female body size. Offspring mortality was higher in populations from fish ponds compared to populations from fishless ponds. Despite the higher offspring mortality, females from fish ponds had a higher number of offspring alive after 13 weeks, which is the approximate time it takes for G. pulex to reach maturity. Our data imply that no trade-off between reducing body size to reduce mortality caused by fish and maximising reproductive success exist in G. pulex from fish ponds. The strategy with many offspring may be the correct strategy in fishponds where predation pressure generally is higher than in fishless ponds.     

Functionality of the GAL4/UAS system in <Emphasis Type="Italic">Tribolium</Emphasis> requires the use of endogenous core promoters

Background  

The red flour beetle Tribolium castaneum has developed into an insect model system second only to Drosophila. Moreover, as a coleopteran it represents the most species-rich metazoan taxon which also includes many pest species. The genetic toolbox for Tribolium research has expanded in the past years but spatio-temporally controlled misexpression of genes has not been possible so far.     

Exploring valid reference genes for gene expression studies in <Emphasis Type="Italic">Brachypodium distachyon</Emphasis>by real-time PCR

Background  

The wild grass species Brachypodium distachyon (Brachypodium hereafter) is emerging as a new model system for grass crop genomics research and biofuel grass biology. A draft nuclear genome sequence is expected to be publicly available in the near future; an explosion of gene expression studies will undoubtedly follow. Therefore, stable reference genes are necessary to normalize the gene expression data.     

Cytoplasmic- and extracellular-proteome analysis of <Emphasis Type="Italic">Diplodia seriata</Emphasis>: a phytopathogenic fungus involved in grapevine decline

Background  

The phytopathogenic fungus Diplodia seriata, whose genome remains unsequenced, produces severe infections in fruit trees (fruit blight) and grapevines. In this crop is recognized as one of the most prominent pathogens involved in grapevine trunk disease (or grapevine decline). This pathology can result in the death of adult plants and therefore it produces severe economical losses all around the world. To date no genes or proteins have been characterized in D. seriata that are involved in the pathogenicity process. In an effort to help identify potential gene products associated with pathogenicity and to gain a better understanding of the biology of D. seriata, we initiated a proteome-level study of the fungal mycelia and secretome.     

Trophic ecology of an aquatic mite (<Emphasis Type="Italic">Piona carnea</Emphasis>) preying on <Emphasis Type="Italic">Daphnia pulex</Emphasis>: effects of predator density,nutrient supply and a second predator (<Emphasis Type="Italic">Chaoborus americanus</Emphasis>)

As compared to other aquatic invertebrates, relatively little is known about the ecology of predaceous, pelagic water mites. Studies to date do, however, show that water mites can be important components of aquatic food webs. Here, we used manipulative field experiments to better understand the trophic ecology of a predaceous water mite (Piona carnea). Three experiments were conducted that examined (i) the effect of P. carnea density on the per-capita interaction strength (PCIS) of P. carnea preying on zooplankton; (ii) how the effects of P. carnea predation change with prey productivity; and (iii) how P. carnea interacts with another pelagic predator (Chaoborus americanus) to affect a shared prey species (Daphnia pulex). Results from the first experiment showed that P. carnea can strongly impact D. pulex populations, and that the PCIS of P. carnea decreases with an increase in P. carnea density. The second experiment showed that the effects of P. carnea on D. pulex populations depend on bottom-up factors that influence D. pulex population biomass and the reproductive potential of a D. pulex population relative to its size. The third experiment uncovered a non-additive interaction between P. carnea and C. americanus that resulted in a risk reducing situation for D. pulex in the presence of both predators. Together these experiments show that P. carnea imposes a strong negative impact on D. pulex, that the magnitude of this negative impact is dependent on the P. carnea density and the productivity of the system, and that the trophic ecology of P. carnea is modified by coexisting predator species.     

Construction and model-based analysis of a promoter library for <Emphasis Type="Italic">E. coli</Emphasis>: an indispensable tool for metabolic engineering

Background  

Nowadays, the focus in metabolic engineering research is shifting from massive overexpression and inactivation of genes towards the model-based fine tuning of gene expression. In this context, the construction of a library of synthetic promoters of Escherichia coli as a useful tool for fine tuning gene expression is discussed here.     

Conservation of <Emphasis Type="Italic">ParaHox</Emphasis> genes' function in patterning of the digestive tract of the marine gastropod <Emphasis Type="Italic">Gibbula varia</Emphasis>

Background  

Presence of all three ParaHox genes has been described in deuterostomes and lophotrochozoans, but to date one of these three genes, Xlox has not been reported from any ecdysozoan taxa and both Xlox and Gsx are absent in nematodes. There is evidence that the ParaHox genes were ancestrally a single chromosomal cluster. Colinear expression of the ParaHox genes in anterior, middle, and posterior tissues of several species studied so far suggest that these genes may be responsible for axial patterning of the digestive tract. So far, there are no data on expression of these genes in molluscs.