scholarly journals Smelling in the dark: phylogenomic insights on the chemosensory system of a subterranean beetle

2020 ◽  
Author(s):  
Pau Balart-García ◽  
Alexandra Cieslak ◽  
Paula Escuer ◽  
Julio Rozas ◽  
Ignacio Ribera ◽  
...  
Keyword(s):  
Gene Duplication ◽  
De Novo ◽  
Chemical Signals ◽  
Gene Repertoire ◽  
Ionotropic Receptor ◽  
Specific Chemical ◽  
Chemosensory System ◽  
Chemosensory Gene ◽  
Sugar Receptors ◽  
Genomic Basis

ABSTRACTThe chemosensory system has experienced relevant changes in subterranean animals, facilitating the orientation into darkness via the perception of specific chemical signals critical to survive in this particular environment. However, the genomic basis of chemoreception in cave-dwelling fauna is largely unexplored. We generated de novo transcriptomes for antennae and body samples of the troglobitic beetle Speonomus longicornis (whose characters suggest an extreme adaptation to the deep subterranean) in order to interrogate the evolutionary origin and diversification of the chemosensory gene repertoire across coleopterans through a phylogenomic approach. Our results suggested a diminished diversity of odorant and gustatory gene repertoires compared to polyphagous epigean beetles. Moreover, S. longicornis showed a large diversity of odorant-binding proteins, suggesting an important role of these proteins in capturing airborne chemical cues. We identified a gene duplication in the ionotropic co-receptor I R25a, a highly conserved single-copy gene in protostomes involved in thermal and humidity sensing. In addition, no homologous genes to sugar receptors or the ionotropic receptor IR41a were detected. Our findings suggest that the chemosensory gene repertoire of this cave beetle may have been reshaped by the low complexity of chemical signals of this particular environment, and that gene duplication and loss may have played an important role in the evolution of genes involved in chemoreception. Altogether, our results shed light on the genomic basis of chemoreception in a cave-dwelling invertebrate and pave the road towards understanding the genomic underpinnings of adaptation to the subterranean lifestyle at a deeper level.

A Novel Method for the Analysis of Volatile Organic Compounds (VOCs) from Red Flour Beetle Tribolium castaneum (H.) using Headspace-SPME Technology

2020 ◽  
Vol 16 (4) ◽  
pp. 404-412 ◽  
Author(s):  
Ihab Alnajim ◽  
Manjree Agarwal ◽  
Tao Liu ◽  
YongLin Ren
Keyword(s):  
Volatile Organic Compounds ◽  
Organic Compounds ◽  
Tribolium Castaneum ◽  
Solid Phase ◽  
Chemical Signals ◽  
Red Flour Beetle ◽  
Specific Chemical ◽  
Flour Beetle ◽  
Volatile Organic ◽  
Spme Fibre

Background: The red flour beetle, Tribolium castaneum (Herbst) (Coleoptera: Tenebrionidae) is one of the world’s most serious stored grain insect pests. A method of early and rapid identification of red flour beetle in stored products is urgently required to improve control options. Specific chemical signals identified as Volatile Organic Compounds (VOCs) that are released by the beetle can serve as biomarkers. Methods: The Headspace Solid Phase Microextraction (HS-SPME) technique and the analytical conditions with GC and GCMS were optimised and validated for the determination of VOCs released from T. castaneum. Results: The 50/30 μm DVB/CAR/PDMS SPME fibre was selected for extraction of VOCs from T. castaneum. The efficiency of extraction of VOCs was significantly affected by the extraction time, temperature, insect density and type of SPME fibre. Twenty-three VOCs were extracted from insects in 4 mL flask at 35 ± 1°C for four hours of extraction and separated and identified with gas chromatography-mass spectroscopy. The major VOCs or chemical signals from T. castaneum were 1-pentadecene, p-Benzoquinone, 2-methyl- and p-Benzoquinone, 2-ethyl. Conclusion: This study showed that HS-SPME GC technology is a robust and cost-effective method for extraction and identification of the unique VOCs produced by T. castaneum. Therefore, this technology could lead to a new approach in the timely detection of T. castaneum and its subsequent treatment.

De novo gene duplication versus reactivation of cryptic genes inEscherichia coli K-12

1970 ◽  
Vol 108 (2) ◽  
pp. 154-157 ◽  
Author(s):  
Raymond Cunin ◽  
Dirk Elseviers ◽  
Nicolas Glansdorff
Keyword(s):  
Gene Duplication ◽  
De Novo ◽  
Inescherichia Coli ◽  
Cryptic Genes ◽  
De Novo Gene ◽  
K 12

scholarly journals Analysis of the Genomic Basis of Functional Diversity in Dinoflagellates using a Transcriptome-Based Sequence Similarity Network

2017 ◽  
Author(s):  
Arnaud Meng ◽  
Erwan Corre ◽  
Ian Probert ◽  
Andres Gutierrez-Rodriguez ◽  
Raffaele Siano ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
De Novo ◽  
Sequence Similarity ◽  
Connected Components ◽  
Similarity Network ◽  
Network Analyses ◽  
Comprehensive Picture ◽  
Core Proteome ◽  
Functional Features ◽  
Genomic Basis

ABSTRACTDinoflagellates are one of the most abundant and functionally diverse groups of eukaryotes. Despite an overall scarcity of genomic information for dinoflagellates, constantly emerging high-throughput sequencing resources can be used to characterize and compare these organisms. We assembled de novo and processed 46 dinoflagellate transcriptomes and used a sequence similarity network (SSN) to compare the underlying genomic basis of functional features within the group. This approach constitutes the most comprehensive picture to date of the genomic potential of dinoflagellates. A core proteome composed of 252 connected components (CCs) of putative conserved protein domains (pCDs) was identified. Of these, 206 were novel and 16 lacked any functional annotation in public databases. Integration of functional information in our network analyses allowed investigation of pCDs specifically associated to functional traits. With respect to toxicity, sequences homologous to those of proteins involved in toxin biosynthesis pathways (e.g. sxtA1-4 and sxtG) were not specific to known toxin-producing species. Although not fully specific to symbiosis, the most represented functions associated with proteins involved in the symbiotic trait were related to membrane processes and ion transport. Overall, our SSN approach led to identification of 45,207 and 90,794 specific and constitutive pCDs of respectively the toxic and symbiotic species represented in our analyses. Of these, 56% and 57% respectively (i.e. 25,393 and 52,193 pCDs) completely lacked annotation in public databases. This stresses the extent of our lack of knowledge, while emphasizing the potential of SSNs to identify candidate pCDs for further functional genomic characterization.

scholarly journals Prediction and Characterization of RXLR Effectors in Pythium Species

2019 ◽  
Author(s):  
Gan Ai ◽  
Kun Yang ◽  
Yuee Tian ◽  
Wenwu Ye ◽  
Hai Zhu ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Plant Pathogens ◽  
Genome Rearrangement ◽  
Common Ancestor ◽  
De Novo ◽  
Protein Structures ◽  
Plant Diseases ◽  
Biocontrol Agents ◽  
Ecological Niches ◽  
Rxlr Effectors

AbstractBeing widely existed in oomycetes, the RXLR effector features conserved RXLR-dEER motifs in its N terminal. Every known Phytophthora or Hyaloperonospora pathogen harbors hundreds of RXLRs. In Pythium species, however, none of the RXLR effectors has been characterized yet. Here, we developed a stringent method for de novo identification of RXLRs and characterized 359 putative RXLR effectors from nine tested Pythium species. Phylogenetic analysis revealed a single superfamily formed by all oomycetous RXLRs, suggesting they descent from a common ancestor. RXLR effectors from Pythium and Phytophthora species exhibited similar sequence features, protein structures and genome locations. In particular, the mosquito biological agent P. guiyangense contains a significantly larger RXLR repertoire than the other eight Pythium species examined, which may result from gene duplication and genome rearrangement events as indicated by synteny analysis. Expression pattern analysis of RXLR-encoding genes in the plant pathogen P. ultimum detected transcripts from the vast majority of predicted RXLRs with some of them being induced at infection stages. One such RXLRs showed necrosis-inducing activity. Furthermore, all predicted RXLRs were cloned from two biocontrol agents P. oligandrum and P. periplocum. Three of them were found to encode effectors inducing defense response in Nicotiana benthamiana. Taken together, our findings represent the first complete synopsis of Pythium RXLR effectors, which provides critical clues on their evolutionary patterns as well as the mechanisms of their interactions with diverse hosts.Author summaryPathogens from the Pythium genus are widespread across multiple ecological niches. Most of them are soilborne plant pathogens whereas others cause infectious diseases in mammals. Some Pythium species can be used as biocontrol agents for plant diseases or mosquito management. Despite that phylogenetically close oomycete pathogens secrete RXLR effectors to enable infection, no RXLR protein was previously characterized in any Pythium species. Here we developed a stringent method to predict Pythium RXLR effectors and compared them with known RXLRs from other species. All oomycetous RXLRs form a huge superfamily, which indicates they may share a common ancestor. Our sequence analysis results suggest that the expansion of RXLR repertoire results from gene duplication and genome recombination events. We further demonstrated that most predicted Pythium RXLRs can be transcribed and some of them encode effectors exhibiting pathogenic or defense-inducing activities. This work expands our understanding of RXLR evolution in oomycetes in general, and provides novel insights into the molecular interactions between Pythium pathogens and their diverse hosts.

scholarly journals Diversity in olfactory receptor repertoires is associated with dietary specialization in a genus of frugivorous bat

2021 ◽  
Author(s):  
Laurel R Yohe ◽  
Leith B Leiser-Miller ◽  
Zofia A Kaliszewska ◽  
Paul Donat ◽  
Sharlene E Santana ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Receptor Gene ◽  
Olfactory Receptors ◽  
Sympatric Species ◽  
Gene Repertoire ◽  
Plant Resources ◽  
Environmental Chemical ◽  
Dietary Specialization ◽  
Genes Encoding ◽  
Repertoire Diversity

Abstract Mammalian olfactory receptors (ORs) are a diverse family of genes encoding proteins that directly interact with environmental chemical cues. ORs evolve via gene duplication in a birth-death fashion, neofunctionalizing and pseudogenizing over time. Olfaction is a primary sense used for food detection in plant-visiting bats, but the relationship between dietary specialization and OR repertoire diversity is unclear. Within neotropical Leaf-nosed bats (Phyllostomidae), many lineages are plant specialists, and some have a distinct OR repertoire compared to insectivorous species. Yet, whether specialization on particular plant genera is associated with the evolution of specialized OR repertoires with narrower diversity has never been tested. Using targeted sequence capture, we sequenced the OR repertoires of three sympatric species of short-tailed fruit bats (Carollia), which vary in their degree of specialization on the fruits of Piper plants. We characterized orthologous versus duplicated receptors among Carollia species, and explored the diversity and redundancy of the receptor gene repertoire. At the species level, the most dedicated Piper specialist, Carollia castanea, had lower OR diversity compared to the two generalists (C. sowelli, C. perspicillata), but we discovered a few unique sets of ORs within C. castanea with high redundancy of similar gene duplicates. These unique receptors potentially enable C. castanea to detect Piper fruit odorants better than its two congeners. Carollia perspicillata, the species with the most generalist diet, had a higher diversity of intact receptors, suggesting the ability to detect a wider range of odorant molecules. Variation among ORs may be a factor in the coexistence of these sympatric species, facilitating the exploitation of different plant resources. Our study sheds light on how gene duplication and changes in OR diversity may play a role in dietary adaptations and underlies patterns of ecological interactions between bats and plants.

scholarly journals Pandoravirus celtis illustrates the microevolution processes at work in the giant Pandoraviridae genomes

2018 ◽  
Author(s):  
Matthieu Legendre ◽  
Jean-Marie Alempic ◽  
Nadège Philippe ◽  
Audrey Lartigue ◽  
Sandra Jeudy ◽  
...  
Keyword(s):  
De Novo ◽  
Gene Repertoire ◽  
Protein Coding ◽  
Genomic Changes ◽  
Coding Regions ◽  
Protein Coding Genes ◽  
Intergenic Regions ◽  
Mere Existence ◽  
Increasing Functions ◽  
Similar Gene

AbstractWith genomes of up to 2.7 Mb propagated in µm-long oblong particles and initially predicted to encode more than 2000 proteins, members of the Pandoraviridae family display the most extreme features of the known viral world. The mere existence of such giant viruses raises fundamental questions about their origin and the processes governing their evolution. A previous analysis of six newly available isolates, independently confirmed by a study including 3 others, established that the Pandoraviridae pan-genome is open, meaning that each new strain exhibits protein-coding genes not previously identified in other family members. With an average increment of about 60 proteins, the gene repertoire shows no sign of reaching a limit and remains largely coding for proteins without recognizable homologs in other viruses or cells (ORFans). To explain these results, we proposed that most new protein-coding genes were created de novo, from pre-existing non-coding regions of the G+C rich pandoravirus genomes. The comparison of the gene content of a new isolate, P. celtis, closely related (96% identical genome) to the previously described P. quercus is now used to test this hypothesis by studying genomic changes in a microevolution range. Our results confirm that the differences between these two similar gene contents mostly consist of protein-coding genes without known homologs (ORFans), with statistical signatures close to that of intergenic regions. These newborn proteins are under slight negative selection, perhaps to maintain stable folds and prevent protein aggregation pending the eventual emergence of fitness-increasing functions. Our study also unraveled several insertion events mediated by a transposase of the hAT family, 3 copies of which are found in P. celtis and are presumably active. Members of the Pandoraviridae are presently the first viruses known to encode this type of transposase.

scholarly journals Sex pheromone signal and stability covary with fitness

2021 ◽  
Vol 8 (6) ◽  
pp. 210180
Author(s):  
Thomas Blankers ◽  
Rik Lievers ◽  
Camila Plata ◽  
Michiel van Wijk ◽  
Dennis van Veldhuizen ◽  
...  
Keyword(s):  
Sex Pheromone ◽  
Individual Variation ◽  
De Novo ◽  
Species Recognition ◽  
Chemical Signals ◽  
Condition Dependence ◽  
Supporting Evidence ◽  
Heritable Variation ◽  
Mate Finding ◽  
Signal Stability

If sexual signals are costly, covariance between signal expression and fitness is expected. Signal–fitness covariance is important, because it can contribute to the maintenance of genetic variation in signals that are under natural or sexual selection. Chemical signals, such as female sex pheromones in moths, have traditionally been assumed to be species-recognition signals, but their relationship with fitness is unclear. Here, we test whether chemical, conspecific mate finding signals covary with fitness in the moth Heliothis subflexa . Additionally, as moth signals are synthesized de novo every night, the maintenance of the signal can be costly. Therefore, we also hypothesized that fitness covaries with signal stability (i.e. lack of temporal intra-individual variation). We measured among- and within-individual variation in pheromone characteristics as well as fecundity, fertility and lifespan in two independent groups that differed in the time in between two pheromone samples. In both groups, we found fitness to be correlated with pheromone amount, composition and stability, supporting both our hypotheses. This study is, to our knowledge, the first to report a correlation between fitness and sex pheromone composition in moths, supporting evidence of condition-dependence and highlighting how signal–fitness covariance may contribute to heritable variation in chemical signals both among and within individuals.

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