Genetic, morphometric, and molecular analyses of interspecies differences in head shape and hybrid developmental defects in the wasp genus Nasonia

2019 ◽  
Author(s):  
Lorna B Cohen ◽  
Rachel Edwards ◽  
Dyese Moody ◽  
Deanna Arsala ◽  
Jack H Werren ◽  
...  
Keyword(s):  
Parasitoid Wasp ◽  
Gene Interaction ◽  
Distinct Species ◽  
Diploid Male ◽  
Gene Interactions ◽  
Morphological Development ◽  
Head Shape ◽  
Developmental Defects ◽  
Primary Driver ◽  
Species Specific

AbstractMales in the parasitoid wasp genus Nasonia (N. vitripennis, N. giraulti, N. longicornis) have distinct, species specific, head shapes. Fertile hybrids among the species are readily produced in the lab allowing genetic analysis of the evolved differences. In addition, the obligate haploidy of males makes these wasps a uniquely powerful model for analyzing the role of complex gene interactions in development and evolution. Previous analyses have shown that complex gene interactions underpin different aspects of the shape differences, and developmental incompatibilities that are specific to the head in F2 haploid hybrid males are also governed by networks of gene interaction. Here we use the genetic tools available in Nasonia to extend our understanding of the gene interactions that affect development and morphogenesis in male heads. Using artificial diploid male hybrids, we show that alleles affecting head shape are codominant, leading to uniform, averaged hybrid F1 diploid male heads, while the alleles mediating developmental defects are recessive, and are not visible in the diploid hybrids. We also determine that divergence in time, rather than in morphological disparity is the primary driver of hybrid developmental defects. In addition, we show that doublesex is necessary for the male head shape differences, but is not the only important factor. Finally we demonstrate that we can dissect complex interspecies gene interaction networks using introgression in this system. These advances represent significant progress in the complex web of gene interactions that govern morphological development, and chart the connections between genomic and phenotypic variation.

scholarly journals Genetic, morphometric, and molecular analyses of interspecies differences in head shape and hybrid developmental defects in the wasp genus Nasonia

2021 ◽  
Author(s):  
Lorna B Cohen ◽  
Rachel Jewell ◽  
Dyese Moody ◽  
Deanna Arsala ◽  
John H Werren ◽  
...  
Keyword(s):  
Gene Networks ◽  
Parasitoid Wasp ◽  
Distinct Species ◽  
Gene Interactions ◽  
Genetic Dissection ◽  
Head Shape ◽  
Developmental Defects ◽  
Genetic Changes ◽  
Head Morphology ◽  
Species Specific

Abstract Males in the parasitoid wasp genus Nasonia have distinct, species-specific, head shapes. The availability of fertile hybrids among the species, along with obligate haploidy of males, facilitates analysis of complex gene interactions in development and evolution. Previous analyses showed that both the divergence in head shape between N. vitripennis and N. giraulti, and the head-specific developmental defects of F2 haploid hybrid males, are governed by multiple changes in networks of interacting genes. Here we extend our understanding of the gene interactions that affect morphogenesis in male heads. Use of artificial diploid male hybrids shows that alleles mediating developmental defects are recessive, while there are diverse dominance relationships among other head shape traits. At the molecular level, the sex determination locus doublesex plays a major role in male head shape differences, but it is not the only important factor. Introgression of a giraulti region on chromsome 2 reveals a recessive locus that causes completely penetrant head clefting in both males and females in a vitripennis background. Finally, a third species (N. longicornis) was used to investigate the timing of genetic changes related to head morphology, revealing that most changes causing defects arose after the divergence of N. vitripennis from the other species, but prior to the divergence of N. giraulti and N. longicornis from each other. Our results demonstrate that developmental gene networks can be dissected using interspecies crosses in Nasonia, and set the stage for future fine-scale genetic dissection of both head shape and hybrid developmental defects.

scholarly journals Sequence Comparison of Vaginolysin from Different Gardnerella Species

Pathogens ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 86
Author(s):  
Erin M. Garcia ◽  
Myrna G. Serrano ◽  
Laahirie Edupuganti ◽  
David J. Edwards ◽  
Gregory A. Buck ◽  
...  
Keyword(s):  
Amino Acid ◽  
Human Microbiome ◽  
Human Microbiome Project ◽  
Distinct Species ◽  
Vaginal Swab ◽  
Metagenomic Data ◽  
Gardnerella Vaginalis ◽  
Vaginal Epithelial Cells ◽  
Species Specific

Gardnerella vaginalis has recently been split into 13 distinct species. In this study, we tested the hypotheses that species-specific variations in the vaginolysin (VLY) amino acid sequence could influence the interaction between the toxin and vaginal epithelial cells and that VLY variation may be one factor that distinguishes less virulent or commensal strains from more virulent strains. This was assessed by bioinformatic analyses of publicly available Gardnerella spp. sequences and quantification of cytotoxicity and cytokine production from purified, recombinantly produced versions of VLY. After identifying conserved differences that could distinguish distinct VLY types, we analyzed metagenomic data from a cohort of female subjects from the Vaginal Human Microbiome Project to investigate whether these different VLY types exhibited any significant associations with symptoms or Gardnerella spp.-relative abundance in vaginal swab samples. While Type 1 VLY was most prevalent among the subjects and may be associated with increased reports of symptoms, subjects with Type 2 VLY dominant profiles exhibited increased relative Gardnerella spp. abundance. Our findings suggest that amino acid differences alter the interaction of VLY with vaginal keratinocytes, which may potentiate differences in bacterial vaginosis (BV) immunopathology in vivo.

Benthic species as mud patrol - modelled effects of bioturbators and biofilms on large-scale estuarine mud and morphology

2021 ◽  
Author(s):  
Muriel Brückner ◽  
Christian Schwarz ◽  
Giovanni Coco ◽  
Anne Baar ◽  
Márcio Boechat Albernaz ◽  
...  
Keyword(s):  
Morphological Change ◽  
Species Interactions ◽  
Large Scale ◽  
Habitat Degradation ◽  
Species Abundance ◽  
Estuarine Sediments ◽  
Morphological Development ◽  
Benthic Species ◽  
Species Dominance ◽  
Species Specific

<p>Benthic species that live within estuarine sediments stabilize or destabilize local mud deposits through their eco-engineering activities, affecting the erosion of intertidal sediments. Possibly, the altered magnitudes in eroded sediment affect the large-scale redistribution of fines and hence morphological change. To quantify this biological control on the morphological development of estuaries, we numerically model i) biofilms, ii) two contrasting bioturbating species present in NW-Europe, and iii) their combinations by means of our novel eco-morphodynamic model. The model predicts local mud erodibility based on species pattern, which dynamically evolves from the hydrodynamics, soil mud content, competition and grazing, and is fed back into the hydromorphodynamic computations.</p><p>We find that biofilms reduce mud erosion on intertidal floodplains and stabilize estuarine morphology, whereas the two bioturbators significantly enhance inter- and supratidal mud erosion and bed elevation change, leading to a large-scale reduction in deposited mud and a widening of the estuary. In turn, the species-dependent changes in mud content redefines their habitat and leads to a redistribution of species abundances. Here, the eco-engineering affects habitat conditions and species abundance while species interactions determine species dominance. Our results show that species-specific biostabilization and bioturbation determine large-scale morphological change through mud redistribution, and at the same time affect species distribution. This suggests that benthic species have subtly changed estuarine morphology through space and time and that aggravating habitat degradation might lead to large effects on the morphology of future estuaries.</p>

Microbiomes of pathogenic Vibrio species reveal environmental and planktonic associations

2019 ◽  
Author(s):  
Rachel E. Diner ◽  
Ariel J. Rabines ◽  
Hong Zheng ◽  
Joshua A. Steele ◽  
John F. Griffith ◽  
...  
Keyword(s):  
Distinct Species ◽  
Human Infection ◽  
Model Systems ◽  
Taxonomic Resolution ◽  
Environmental Preferences ◽  
Pathogenic Vibrio ◽  
Photosynthetic Organism ◽  
One Year ◽  
Species Specific ◽  
Planktonic Community

Abstract Background Many species of coastal Vibrio spp. bacteria can infect humans, representing an emerging health threat linked to increasing seawater temperatures. Vibrio interactions with the planktonic community impact coastal ecology and human infection potential. In particular, interactions with eukaryotic and photosynthetic organism may provide attachment substrate and critical nutrients (e.g. chitin, phytoplankton exudates) that facilitate the persistence, diversification, and spread of pathogenic Vibrio spp. Vibrio interactions with these organisms in an environmental context are, however, poorly understood.Results We quantified pathogenic Vibrio species, including V. cholerae, V. parahaemolyticus, and V. vulnificus, and two virulence-associated genes for one year at five coastal sites in Southern California and used metabarcoding to profile associated prokaryotic and eukaryotic communities, including vibrio-specific communities. These Vibrio spp. reached high abundances, particularly during Summer months, and inhabited distinct species-specific environmental niches driven by temperature and salinity. Associated bacterial and eukaryotic taxa identified at fine-scale taxonomic resolution revealed genus and species-level relationships. For example, common Thalassiosira genera diatoms capable of exuding chitin were positively associated with V. cholerae and V. vulnificus in a species-specific manner, while the most abundant eukaryotic genus, the diatom Chaetoceros, was positively associated with V. parahaemolyticus. Associations were often linked to shared environmental preferences, and several copepod genera were linked to low-salinity environmental conditions and abundant V. cholerae and V. vulnificus.Conclusions This study clarifies ecological relationships between pathogenic Vibrio spp. and the planktonic community, elucidating new functionally relevant associations, establishing a workflow for examining environmental pathogen microbiomes, and highlighting prospective model systems for future mechanistic studies.

scholarly journals 31P-NMR Metabolomics Revealed Species-Specific Use of Phosphorous in Trees of a French Guiana Rainforest

Molecules ◽  
2020 ◽  
Vol 25 (17) ◽  
pp. 3960
Author(s):  
Albert Gargallo-Garriga ◽  
Jordi Sardans ◽  
Joan Llusià ◽  
Guille Peguero ◽  
Dolores Asensio ◽  
...  
Keyword(s):  
Tree Species ◽  
French Guiana ◽  
31P Nmr ◽  
Principal Component ◽  
Distinct Species ◽  
Community Diversity ◽  
N:P Ratios ◽  
High Concentrations ◽  
Species Specific ◽  
Total P

Productivity of tropical lowland moist forests is often limited by availability and functional allocation of phosphorus (P) that drives competition among tree species and becomes a key factor in determining forestall community diversity. We used non-target 31P-NMR metabolic profiling to study the foliar P-metabolism of trees of a French Guiana rainforest. The objective was to test the hypotheses that P-use is species-specific, and that species diversity relates to species P-use and concentrations of P-containing compounds, including inorganic phosphates, orthophosphate monoesters and diesters, phosphonates and organic polyphosphates. We found that tree species explained the 59% of variance in 31P-NMR metabolite profiling of leaves. A principal component analysis showed that tree species were separated along PC 1 and PC 2 of detected P-containing compounds, which represented a continuum going from high concentrations of metabolites related to non-active P and P-storage, low total P concentrations and high N:P ratios, to high concentrations of P-containing metabolites related to energy and anabolic metabolism, high total P concentrations and low N:P ratios. These results highlight the species-specific use of P and the existence of species-specific P-use niches that are driven by the distinct species-specific position in a continuum in the P-allocation from P-storage compounds to P-containing molecules related to energy and anabolic metabolism.

scholarly journals CGINet: graph convolutional network-based model for identifying chemical-gene interaction in an integrated multi-relational graph

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Wei Wang ◽  
Xi Yang ◽  
Chengkun Wu ◽  
Canqun Yang
Keyword(s):  
Biological Network ◽  
Gene Interaction ◽  
Gene Interactions ◽  
Target Node ◽  
Convolutional Network ◽  
Initial Node ◽  
Interactive Relation ◽  
Drug Leads ◽  
Node Embeddings ◽  
Novel Therapeutic

Abstract Background Elucidation of interactive relation between chemicals and genes is of key relevance not only for discovering new drug leads in drug development but also for repositioning existing drugs to novel therapeutic targets. Recently, biological network-based approaches have been proven to be effective in predicting chemical-gene interactions. Results We present CGINet, a graph convolutional network-based method for identifying chemical-gene interactions in an integrated multi-relational graph containing three types of nodes: chemicals, genes, and pathways. We investigate two different perspectives on learning node embeddings. One is to view the graph as a whole, and the other is to adopt a subgraph view that initial node embeddings are learned from the binary association subgraphs and then transferred to the multi-interaction subgraph for more focused learning of higher-level target node representations. Besides, we reconstruct the topological structures of target nodes with the latent links captured by the designed substructures. CGINet adopts an end-to-end way that the encoder and the decoder are trained jointly with known chemical-gene interactions. We aim to predict unknown but potential associations between chemicals and genes as well as their interaction types. Conclusions We study three model implementations CGINet-1/2/3 with various components and compare them with baseline approaches. As the experimental results suggest, our models exhibit competitive performances on identifying chemical-gene interactions. Besides, the subgraph perspective and the latent link both play positive roles in learning much more informative node embeddings and can lead to improved prediction.

scholarly journals Genome-Wide microRNA Profiling Using Oligonucleotide Microarray Reveals Regulatory Networks of microRNAs in Nicotiana benthamiana During Beet Necrotic Yellow Vein Virus Infection

Viruses ◽  
2020 ◽  
Vol 12 (3) ◽  
pp. 310 ◽  
Author(s):  
Junying Liu ◽  
Huiyan Fan ◽  
Ying Wang ◽  
Chenggui Han ◽  
Xianbing Wang ◽  
...  
Keyword(s):  
Nicotiana Benthamiana ◽  
Regulatory Networks ◽  
Target Genes ◽  
Tobacco Rattle Virus ◽  
Yellow Vein ◽  
Differentially Expressed ◽  
Virus Induced Gene Silencing ◽  
Developmental Defects ◽  
Differentially Expressed Mirnas ◽  
Species Specific

Beet necrotic yellow vein virus (BNYVV) infections induce stunting and leaf curling, as well as root and floral developmental defects and leaf senescence in Nicotiana benthamiana. A microarray analysis with probes capable of detecting 1596 candidate microRNAs (miRNAs) was conducted to investigate differentially expressed miRNAs and their targets upon BNYVV infection of N. benthamiana plants. Eight species-specific miRNAs of N. benthamiana were identified. Comprehensive characterization of the N. benthamiana microRNA profile in response to the BNYVV infection revealed that 129 miRNAs were altered, including four species-specific miRNAs. The targets of the differentially expressed miRNAs were predicted accordingly. The expressions of miR164, 160, and 393 were up-regulated by BNYVV infection, and those of their target genes, NAC21/22, ARF17/18, and TIR, were down-regulated. GRF1, which is a target of miR396, was also down-regulated. Further genetic analysis of GRF1, by Tobacco rattle virus-induced gene silencing, assay confirmed the involvement of GRF1 in the symptom development during BNYVV infection. BNYVV infection also induced the up-regulation of miR168 and miR398. The miR398 was predicted to target umecyanin, and silencing of umecyanin could enhance plant resistance against viruses, suggesting the activation of primary defense response to BNYVV infection in N. benthamiana. These results provide a global profile of miRNA changes induced by BNYVV infection and enhance our understanding of the mechanisms underlying BNYVV pathogenesis.

The Anopheles maculipennis complex (Diptera: Culicidae) in Iran: molecular characterization and recognition of a new species

2003 ◽  
Vol 93 (6) ◽  
pp. 527-535 ◽  
Author(s):  
M.M. Sedaghat ◽  
Y.-M. Linton ◽  
M.A. Oshaghi ◽  
H. Vatandoost ◽  
R.E. Harbach
Keyword(s):  
New Species ◽  
Distinct Species ◽  
Nuclear Rdna ◽  
Pcr Assay ◽  
Dna Evidence ◽  
Anopheles Maculipennis Complex ◽  
Anopheles Maculipennis ◽  
Species Specific ◽  
A New Species ◽  
Maculipennis Complex

AbstractMosquitoes of the Anopheles maculipennis complex were collected in nine provinces of Iran (Esfahan, Fars, Gilan, Golestan, Kohkiluyeh va Boyerahmad, Mazandaran, Tehran, Azarbaijan-e Gharbi and Zanjan) between June 1983 and September 2002. The nuclear rDNA ITS2 sequences of 86 specimens were compared with those of seven species of the complex available in GenBank. Three genetically distinct species of the complex were distinguished: A. maculipennis Meigen, A. sacharovi Favre and a previously unrecognized species. The last species is most similar to, but clearly distinct from, A. martinius Shingarev and A. sacharovi. The taxonomy of A. martinius and A. sacharovi is critically reviewed, and justification is provided for formally recognizing the third species as Anopheles persiensissp.n. The new species is the first culicid to be characterized and named principally on the basis of DNA evidence. Anopheles persiensis was collected only in the northern Caspian Sea littoral provinces of Gilan and Mazandaran, and it seems likely that this species could be responsible for malaria transmission in this region that was previously attributed to A. maculipennis. A species-specific RFLP–PCR assay based on ITS2 sequences was developed to facilitate further studies of the three species in Iran.

scholarly journals An Exploration of Gene-Gene Interactions and Their Effects on Hypertension

2017 ◽  
Vol 2017 ◽  
pp. 1-9 ◽  
Author(s):  
Ying Meng ◽  
Susan Groth ◽  
Jill R. Quinn ◽  
John Bisognano ◽  
Tong Tong Wu
Keyword(s):  
Interaction Analysis ◽  
Association Studies ◽  
Independent Set ◽  
Gene Interaction ◽  
Single Locus ◽  
Gene Interactions ◽  
Genome Wide Association Studies ◽  
Original Cohort ◽  
Genome Wide ◽  
Heart Study

Hypertension tends to perpetuate in families and the heritability of hypertension is estimated to be around 20–60%. So far, the main proportion of this heritability has not been found by single-locus genome-wide association studies. Therefore, the current study explored gene-gene interactions that have the potential to partially fill in the missing heritability. A two-stage discovery-confirmatory analysis was carried out in the Framingham Heart Study cohorts. The first stage was an exhaustive pairwise search performed in 2320 early-onset hypertensive cases with matched normotensive controls from the offspring cohort. Then, identified gene-gene interactions were assessed in an independent set of 694 subjects from the original cohort. Four unique gene-gene interactions were found to be related to hypertension. Three detected genes were recognized by previous studies, and the other 5 loci/genes (MAN1A1, LMO3, NPAP1/SNRPN, DNAL4, and RNA5SP455/KRT8P5) were novel findings, which had no strong main effect on hypertension and could not be easily identified by single-locus genome-wide studies. Also, by including the identified gene-gene interactions, more variance was explained in hypertension. Overall, our study provides evidence that the genome-wide gene-gene interaction analysis has the possibility to identify new susceptibility genes, which can provide more insights into the genetic background of blood pressure regulation.

Head morphological variation in Podarcis muralis and Podarcis sicula: a landmark-based approach

2007 ◽  
Vol 28 (4) ◽  
pp. 566-573 ◽  
Author(s):  
David Costantini ◽  
Emiliano Bruner
Keyword(s):  
Euclidean Distance ◽  
Distance Matrix ◽  
Matrix Analysis ◽  
Head Shape ◽  
Euclidean Distance Matrix ◽  
Podarcis Muralis ◽  
Podarcis Sicula ◽  
Head Morphology ◽  
Species Specific ◽  
Range Of Variation

Abstract The geometry of the cephalic scales in lizards is easily represented by using landmark based approaches. The cephalic scales may prove useful structures in the investigation of the evolution and morphogenesis of lizards because of their biomechanical relationships with the underlying bones and muscular anatomy. In the present paper the head morphology in Podarcis muralis and Podarcis sicula is compared by using geometric morphometrics and Euclidean distance matrix analysis. The head shape in these two species is largely influenced by a shared allometric pattern, with P. sicula displaying a reduced range of variation. This pattern is probably influenced by the cranial morphogenesis at the fronto-parietal suture, and by the parieto-occipital musculature involved in diet and social behaviours. Minor species-specific differences are evidenced, and should be further investigated.

Sign in / Sign up

Export Citation Format

Share Document