scholarly journals Comparison of developmental genome expression in rodent molars reveals extensive developmental system drift

2020 ◽  
Author(s):  
Marie Sémon ◽  
Laurent Guéguen ◽  
Coraline Petit ◽  
Carine Rey ◽  
Anne Lambert ◽  
...  
Keyword(s):  
Gene Networks ◽  
Morphological Changes ◽  
Rapid Evolution ◽  
Theoretical Work ◽  
Causal Link ◽  
Developmental System ◽  
Developmental States ◽  
Developmental System Drift ◽  
Species Specific ◽  
Upper Molar

AbstractIn evolution, it is widely believed that phenotypic changes root in developmental changes and phenotype conservation, in developmental conservation. Seeming phenotype conservation may however hide evolutionary changes in the underlying developmental mechanisms by which a trait is produced. This cryptic evolution is also called Developmental System Drift, and the extent of this phenomenon unclear. We used a well-characterized evo-devo model system, rodent molars, to test the correlation between phenotypic and developmental evolution. Between mouse and hamster, the morphology of the lower molars has much less diverged than the morphology of the upper molars. Is development accordingly more conserved? We compared molar crown formation with a standard approach, and with a tight transcriptome time-series to get a quantitative molecular profiling of developmental states. Our data identify common trends in the development of all molars. Upper and lower molars have their specificities since the early steps of morphogenesis, at the levels of the pattern of cusp formation, cellular composition and biased gene expression. The extent of difference in lower vs. upper molar development within one species does correlate with the extent of difference in final morphology. However, the specificity of lower vs. upper molar development is drowned among the rapid evolution of development, which is highly species-specific in term of expression levels and temporal profiles. Divergence in developmental systems is almost as high for lower as it is for upper molar, despite much lesser morphological changes in lower molar crown. Hence, our results point an extensive drift in this developmental system. Because serial organs are largely sharing gene networks, it supports previous theoretical work that suggest a causal link between pleiotropy and DSD.

scholarly journals Single-cell RNA sequencing of Plasmodium vivax sporozoites reveals stage- and species-specific transcriptomic signatures

2021 ◽  
Author(s):  
Anthony A Ruberto ◽  
Caitlin Bourke ◽  
Amélie Vantaux ◽  
Steven P Maher ◽  
Aaron Jex ◽  
...  
Keyword(s):  
Single Cell ◽  
Salivary Glands ◽  
Plasmodium Vivax ◽  
Translational Regulation ◽  
Developmental Trajectory ◽  
Specific Gene ◽  
Developmental States ◽  
Usage Patterns ◽  
Gene Usage ◽  
Species Specific

Plasmodium vivax sporozoites reside in the salivary glands of a mosquito before infecting a human host. Previous transcriptome-wide studies in populations of these forms were limited in their ability to elucidate cell-to-cell variation, thereby masking cellular states potentially important in understanding transmission outcomes. In this study, we performed transcription profiling on 9,947 P. vivax sporozoites to assess the extent to which they differ at single-cell resolution. We show that sporozoites residing in the mosquito's salivary glands exist in distinct developmental states, as defined by their transcriptomic signatures. Additionally, relative to P. falciparum, P. vivax displays overlapping and unique gene usage patterns, highlighting conserved and species-specific gene programs. Notably, distinguishing P. vivax from P. falciparum were a subset of P. vivax sporozoites expressing genes associated with translational regulation and repression. Finally, our comparison of single-cell transcriptomic data from P. vivax sporozoite and erythrocytic forms reveals gene usage patterns unique to sporozoites. In defining the transcriptomic signatures of individual P. vivax sporozoites, our work provides new insights into the factors driving their developmental trajectory and lays the groundwork for a more comprehensive P. vivax cell atlas.

scholarly journals Cause and Effectors: Whole-Genome Comparisons Reveal Shared but Rapidly Evolving Effector Sets among Host-Specific Plant-Castrating Fungi

mBio ◽  
2019 ◽  
Vol 10 (6) ◽  
Author(s):  
William C. Beckerson ◽  
Ricardo C. Rodríguez de la Vega ◽  
Fanny E. Hartmann ◽  
Marine Duhamel ◽  
Tatiana Giraud ◽  
...  
Keyword(s):  
Positive Selection ◽  
Plant Pathogens ◽  
Pfam Domain ◽  
Rapid Evolution ◽  
Host Specialization ◽  
Secreted Proteins ◽  
Smut Fungi ◽  
Core Proteins ◽  
Genes Encoding ◽  
Species Specific

ABSTRACT Plant pathogens utilize a portfolio of secreted effectors to successfully infect and manipulate their hosts. It is, however, still unclear whether changes in secretomes leading to host specialization involve mostly effector gene gains/losses or changes in their sequences. To test these hypotheses, we compared the secretomes of three host-specific castrating anther smut fungi (Microbotryum), two being sister species. To address within-species evolution, which might involve coevolution and local adaptation, we compared the secretomes of strains from differentiated populations. We experimentally validated a subset of signal peptides. Secretomes ranged from 321 to 445 predicted secreted proteins (SPs), including a few species-specific proteins (42 to 75), and limited copy number variation, i.e., little gene family expansion or reduction. Between 52% and 68% of the SPs did not match any Pfam domain, a percentage that reached 80% for the small secreted proteins, indicating rapid evolution. In comparison to background genes, we indeed found SPs to be more differentiated among species and strains, more often under positive selection, and highly expressed in planta; repeat-induced point mutations (RIPs) had no role in effector diversification, as SPs were not closer to transposable elements than background genes and were not more RIP affected. Our study thus identified both conserved core proteins, likely required for the pathogenic life cycle of all Microbotryum species, and proteins that were species specific or evolving under positive selection; these proteins may be involved in host specialization and/or coevolution. Most changes among closely related host-specific pathogens, however, involved rapid changes in sequences rather than gene gains/losses. IMPORTANCE Plant pathogens use molecular weapons to successfully infect their hosts, secreting a large portfolio of various proteins and enzymes. Different plant species are often parasitized by host-specific pathogens; however, it is still unclear whether the molecular basis of such host specialization involves species-specific weapons or different variants of the same weapons. We therefore compared the genes encoding secreted proteins in three plant-castrating pathogens parasitizing different host plants, producing their spores in plant anthers by replacing pollen. We validated our predictions for secretion signals for some genes and checked that our predicted secreted proteins were often highly expressed during plant infection. While we found few species-specific secreted proteins, numerous genes encoding secreted proteins showed signs of rapid evolution and of natural selection. Our study thus found that most changes among closely related host-specific pathogens involved rapid adaptive changes in shared molecular weapons rather than innovations for new weapons.

How the sperm triggers development of the egg: what have we learned and what can we expect in the next millennium?

Zygote ◽  
1999 ◽  
Vol 8 (S1) ◽  
pp. S7-S8
Author(s):  
David Epel
Keyword(s):  
Sea Urchin ◽  
Cell Biology ◽  
Control Cell ◽  
Rapid Evolution ◽  
Cell Activity ◽  
Turn Of The Century ◽  
Direct Demonstration ◽  
Creative Research ◽  
Contemporary Work ◽  
Species Specific

The problem of how the sperm activates the egg has captivated the attention of cell and developmental biologists since the turn of the century. An early focus concerned species-specific fertilisation and the pioneering work of Lilly and Tyler (Tyler & Tyler, 1966) used immunological analogies to provide explanations of species-specific fertilisation. Contemporary work has focused on the identity of unique receptors on the sperm and the egg as exemplified in the work of Lennarz (Ohlendieck & Lennarz, 1996), Vacquier (Vacquier, et al., 1995) and Wasserman (1999). Lately, this approach has provided unexpected insights on how speciation might occur. Speciation requires reproductive isolation and creative research from the Vacquier laboratory has demonstrated how reproductive barriers might occur through rapid evolution of sperm/egg recognition systems (Lee et al., 1995).Studies on the cell biology of activation received a major impetus in the 1930s with Mazia's observation of a calcium increase in eggs of the sea urchin following fertilisation (Mazia, 1937). His discovery, however, was a premature one in that there was no satisfactory model at that time for explaining how a calcium increase could affect cell activity. It took almost 40 years to develop a paradigm, and this came from studies on muscle and nerve which revealed how calcium increases could somehow control cell activity. Work in the 1970s rapidly established a similar role for calcium in activation of the egg at fertilisation. The first break-through was the direct demonstration by Steinhardt & Epel (1974) that calcium was involved in egg activation, through manipulation of calcium levels in sea urchin oocytes by use of calcium ionophores.

scholarly journals Variable Rates of Simple Satellite Gains across the Drosophila Phylogeny

2018 ◽  
Vol 35 (4) ◽  
pp. 925-941 ◽  
Author(s):  
Kevin H -C Wei ◽  
Sarah E Lower ◽  
Ian V Caldas ◽  
Trevor J S Sless ◽  
Daniel A Barbash ◽  
...  
Keyword(s):  
Evolutionary Dynamics ◽  
Rapid Evolution ◽  
Single Mutation ◽  
Closely Related Species ◽  
Interspecific Differences ◽  
Limited Sampling ◽  
Drosophila Phylogeny ◽  
Males And Females ◽  
Species Specific ◽  
Turn Over

Abstract Simple satellites are tandemly repeating short DNA motifs that can span megabases in eukaryotic genomes. Because they can cause genomic instability through nonallelic homologous exchange, they are primarily found in the repressive heterochromatin near centromeres and telomeres where recombination is minimal, and on the Y chromosome, where they accumulate as the chromosome degenerates. Interestingly, the types and abundances of simple satellites often vary dramatically between closely related species, suggesting that they turn over rapidly. However, limited sampling has prevented detailed understanding of their evolutionary dynamics. Here, we characterize simple satellites from whole-genome sequences generated from males and females of nine Drosophila species, spanning 40 Ma of evolution. We show that PCR-free library preparation and postsequencing GC-correction better capture satellite quantities than conventional methods. We find that over half of the 207 simple satellites identified are species-specific, consistent with previous descriptions of their rapid evolution. Based on a maximum parsimony framework, we determined that most interspecific differences are due to lineage-specific gains. Simple satellites gained within a species are typically a single mutation away from abundant existing satellites, suggesting that they likely emerge from existing satellites, especially in the genomes of satellite-rich species. Interestingly, unlike most of the other lineages which experience various degrees of gains, the lineage leading up to the satellite-poor D. pseudoobscura and D. persimilis appears to be recalcitrant to gains, providing a counterpoint to the notion that simple satellites are universally rapidly evolving.

scholarly journals Symbiotic Outcome Modified by the Diversification from 7 to over 700 Nodule-Specific Cysteine-Rich Peptides

Genes ◽  
2020 ◽  
Vol 11 (4) ◽  
pp. 348 ◽  
Author(s):  
Proyash Roy ◽  
Mingkee Achom ◽  
Helen Wilkinson ◽  
Beatriz Lagunas ◽  
Miriam L. Gifford
Keyword(s):  
Morphological Changes ◽  
Expression Patterns ◽  
Terminal State ◽  
Rapid Expansion ◽  
Bacterial Cells ◽  
Positive Regulators ◽  
Bacterial Cell Cycle ◽  
Species Specific ◽  
Secreted Peptides

Legume-rhizobium symbiosis represents one of the most successfully co-evolved mutualisms. Within nodules, the bacterial cells undergo distinct metabolic and morphological changes and differentiate into nitrogen-fixing bacteroids. Legumes in the inverted repeat lacking clade (IRLC) employ an array of defensin-like small secreted peptides (SSPs), known as nodule-specific cysteine-rich (NCR) peptides, to regulate bacteroid differentiation and activity. While most NCRs exhibit bactericidal effects in vitro, studies confirm that inside nodules they target the bacterial cell cycle and other cellular pathways to control and extend rhizobial differentiation into an irreversible (or terminal) state where the host gains control over bacteroids. While NCRs are well established as positive regulators of effective symbiosis, more recent findings also suggest that NCRs affect partner compatibility. The extent of bacterial differentiation has been linked to species-specific size and complexity of the NCR gene family that varies even among closely related species, suggesting a more recent origin of NCRs followed by rapid expansion in certain species. NCRs have diversified functionally, as well as in their expression patterns and responsiveness, likely driving further functional specialisation. In this review, we evaluate the functions of NCR peptides and their role as a driving force underlying the outcome of rhizobial symbiosis, where the plant is able to determine the outcome of rhizobial interaction in a temporal and spatial manner.

Comparative spermatology of 11 species of Polyplacophora (Mollusca) from the suborders Lepidopleurina, Chitonina and Acanthochitonina

1988 ◽  
Vol 235 (1279) ◽  
pp. 161-177 ◽  
Keyword(s):  
Electron Microscopy ◽  
Morphological Changes ◽  
Chromatin Condensation ◽  
Nuclear Material ◽  
Taxonomic Character ◽  
Anterior Portion ◽  
Preliminary Examination ◽  
Transmission Electron ◽  
Species Specific ◽  
Egg Coat

Transmission electron microscopy of the spermatozoa and spermatogenesis of 11 species (in three suborders Chitonina, Acanthochitonina, Lepidopleurina) of chiton has shown that each species has a sperm with a unique morphology indicating that spermatozoa can be used as a taxonomic character. Although structure is species-specific, similarities between species within suborders and subfamilies can be recognized. The spermatozoa of species from the suborders Chitonina and Acanthochitonina have a head comprising nuclear material only, the anterior portion of which is in the form of a long thin (approximately 80 nm diameter) filament. In many species the centrioles and mitochondria of the mid-piece are lateral in position, the mitochondria often being sited anteriorly alongside the nucleus. By contrast, Leptochiton asellus , a member of the more ancient suborder Lepidopleurina, has a sperm with a head comprising a nucleus and an acrosome. The mid-piece is also more conven­tional in structure with a ring of five or six spherical mitochondria (sited behind the nucleus) that surround the centrioles. The presence of the acrosome in L. asellus suggests that in the more recent chitons the acro­some has been secondarily lost. It is proposed that loss of the acrosome is correlated to a modification in egg-coat thickness. A preliminary examination of the structure of the eggs of three species has shown that those of L. asellus are surrounded by a very thick chorion (14-30 μm) whereas in Acanthochitona crinitus and Dinoplax gigas there are regions of the chorion that are less than 2 μm thick. The morphological changes that occur during spermatogenesis are very similar in the Chitonina and Acanthochitonina. During spermiogenesis the nucleus elongates to develop a long anterior filament. Chro­matin condensation within the nucleus involves the formation of fibrils that become orientated along its long axis. Closely associated with the elongating nucleus is a manchette. In L . asellus a spherical proacrosomal vesicle appears in the spermatocytes. This vesicle becomes compressed as it matures and simultaneously it migrates to the presumptive anterior end of the spermatid where it invaginates and elongates. Although the pattern of chromatin condensation in the nucleus is similar to that described above, a manchette has not been observed.

Developmental variations among Panagrolaimid nematodes indicate developmental system drift within a small taxonomic unit

2014 ◽  
Vol 224 (3) ◽  
pp. 183-188 ◽  
Author(s):  
Philipp H. Schiffer ◽  
Ndifon A. Nsah ◽  
Henny Grotehusmann ◽  
Michael Kroiher ◽  
Curtis Loer ◽  
...  
Keyword(s):  
Developmental System ◽  
Developmental System Drift ◽  
Developmental Variations

scholarly journals Lack of signal for the impact of venom gene diversity on speciation rates in cone snails

2018 ◽  
Author(s):  
Mark A Phuong ◽  
Michael E Alfaro ◽  
Gusti N Mahardika ◽  
Ristiyanti M Marwoto ◽  
Romanus Edy Prabowo ◽  
...  
Keyword(s):  
Gene Diversity ◽  
Rapid Evolution ◽  
Limiting Factor ◽  
Exon Capture ◽  
Speciation Rates ◽  
Intrinsic Capacity ◽  
Cone Snails ◽  
Species Specific ◽  
Capture Techniques ◽  
The Impact

AbstractUnderstanding why some groups of organisms are more diverse than others is a central goal in macroevolution. Evolvability, or lineages’ intrinsic capacity for evolutionary change, is thought to influence disparities in species diversity across taxa. Over macroevolutionary time scales, clades that exhibit high evolvability are expected to have higher speciation rates. Cone snails (family: Conidae, >900 spp.) provide a unique opportunity to test this prediction because their venom genes can be used to characterize differences in evolvability between clades. Cone snails are carnivorous, use prey-specific venom (conotoxins) to capture prey, and the genes that encode venom are known and diversify through gene duplication. Theory predicts that higher gene diversity confers a greater potential to generate novel phenotypes for specialization and adaptation. Therefore, if conotoxin gene diversity gives rise to varying levels of evolvability, conotoxin gene diversity should be coupled with macroevolutionary speciation rates. We applied exon capture techniques to recover phylogenetic markers and conotoxin loci across 314 species, the largest venom discovery effort in a single study. We paired a reconstructed timetree using 12 fossil calibrations with species-specific estimates of conotoxin gene diversity and used trait-dependent diversification methods to test the impact of evolvability on diversification patterns. Surprisingly, did not detect any signal for the relationship between conotoxin gene diversity and speciation rates, suggesting that venom evolution may not be the rate-limiting factor controlling diversification dynamics in Conidae. Comparative analyses showed some signal for the impact of diet and larval dispersal strategy on diversification patterns, though whether or not we detected a signal depended on the dataset and the method. If our results remain true with increased sampling in future studies, they suggest that the rapid evolution of Conidae venom may cause other factors to become more critical to diversification, such as ecological opportunity or traits that promote isolation among lineages.

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