scholarly journals Identification and expression pattern of chemosensory genes in the transcriptome of Propsilocerus akamusi

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9584
Author(s):  
Chuncai Yan ◽  
Xiaoya Sun ◽  
Wei Cao ◽  
Ruoqun Li ◽  
Cong Zhao ◽  
...  
Keyword(s):  
Differential Expression Analysis ◽  
Odorant Receptors ◽  
Indicator Organisms ◽  
Illumina Hiseq ◽  
Chemosensory Genes ◽  
Chironomid Species ◽  
Gene Level ◽  
Illumina Hiseq Platform ◽  
Odorant Binding ◽  
Simple Sequence

Chironomidae is the most ecologically diverse insects in aquatic and semi-aquatic habitats. Propsilocerus akamusi (Tokunaga) is a dominant and ubiquitous chironomid species in Eastern Asia and its morphologically unique larvae are also considered as indicator organisms to detect water contamination, potential toxicity and waterborne pathogens. Since few studies to date have focused on the olfactory system of P. akamusi, our study aims to elucidate the potential functions of chemosensory genes in P. akamusi. In our study, we found that although signals released from male groups might attract female swarmers, it was a completely male-dominated mating process. Sequencing the transcriptome of P. akamusi on an Illumina HiSeq platform generated 4.42, 4.46 and 4.53 Gb of clean reads for heads, legs, and antennae, respectively. 27,609 unigenes, 20,379 coding sequences (CDSs), and 8,073 simple sequence repeats were finally obtained. The gene-level differential expression analysis demonstrated variants among three different tissues, including 2,019 genes specifically expressed in heads, 1,540 genes in legs, and 2,071 genes in antennae. Additionally, we identified an assortment of putative olfactory genes consisting of 34 odorant binding proteins, 17 odorant receptors, 32 gustatory receptors, 22 ionotropic receptors, six chemosensory proteins as well as 3 sensory neuron membrane proteins; their relative abundances in the above three tissues were also determined by RT-qPCR. Our finding could allow a more plausible understanding of certain olfaction-mediated behaviors in groups of this macroinvertebrate.

scholarly journals Identification and Expression Profiling of Peripheral Olfactory Genes in the Parasitoid Wasp Aphidius ervi (Hymenoptera: Braconidae) Reared on Different Aphid Hosts

Insects ◽  
2019 ◽  
Vol 10 (11) ◽  
pp. 397
Author(s):  
Gabriel I. Ballesteros ◽  
Daniela A. Sepúlveda ◽  
Christian C. Figueroa
Keyword(s):  
Binding Proteins ◽  
Host Preference ◽  
Odorant Receptors ◽  
Aphidius Ervi ◽  
Host Acceptance ◽  
Odorant Binding Proteins ◽  
Expression Levels ◽  
Host Fidelity ◽  
Chemosensory Genes ◽  
Odorant Binding

Generalist parasitoids of aphids, such as the wasp Aphidius ervi, display significant differences in terms of host preference and host acceptance, depending on the host on which they developed (natal host), which is preferred over a non-natal host, a trait known as host fidelity. This trait allows females to quickly find hosts in heterogeneous environments, a process mediated by chemosensory/olfactory mechanisms, as parasitoids rely on olfaction and chemical cues during host selection. Thus, it is expected that proteins participating in chemosensory recognition, such as odorant-binding proteins (OBPs) and odorant receptors (ORs) would play a key role in host preference. In this study, we addressed the effect of parasitoid reciprocal host switching between two aphid hosts (Sitobion avenae and Acyrthosiphon pisum) on the expression patterns of chemosensory genes in the wasp A. ervi. First, by using a transcriptomic approach based on RNAseq of A. ervi females reared on S. avenae and A. pisum, we were able to annotate a total of 91 transcripts related to chemoperception. We also performed an in-silico expression analysis and found three OBPs and five ORs displaying different expression levels. Then, by using qRT-PCR amplification, we found significant differences in the expression levels of these eight genes when the parasitoids were reciprocally transplanted from S. avenae onto A. pisum and vice versa. This suggests that the expression levels of genes coding for odorant receptors and odorant-binding proteins would be regulated by the specific plant–aphid host complex where the parasitoids develop (maternal previous experience) and that chemosensory genes coding for olfactory mechanisms would play a crucial role on host preference and host acceptance, ultimately leading to the establishment of host fidelity in A. ervi parasitoids.

scholarly journals Identification of candidate chemosensory genes of Ophraella communa LeSage (Coleoptera: Chrysomelidae) based on antennal transcriptome analysis

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Chao Ma ◽  
Chenchen Zhao ◽  
Shaowei Cui ◽  
Yan Zhang ◽  
Guangmei Chen ◽  
...  
Keyword(s):  
Host Plants ◽  
Odorant Receptors ◽  
Oviposition Site Selection ◽  
Odorant Binding Proteins ◽  
Chemosensory Genes ◽  
Olfactory Systems ◽  
Ophraella Communa ◽  
Polymerase Chain ◽  
Odorant Binding ◽  
Generation Sequencing

Abstract Antennal olfaction plays a key role in insect survival, which mediates important behaviors like host search, mate choice, and oviposition site selection. As an oligophagous insect, olfaction is extremely important for Ophraella communa to locate host plants. However, information on the olfactory genes has been lacking in O. communa. Using next generation sequencing, we assembled the antennal transcriptome of O. communa and first reported the major chemosensory genes necessary for olfaction in this species. In this study, a total 105 candidate chemosensory genes were identified in O. communa antennae, including 25 odorant-binding proteins (OBPs), 11 chemosensory proteins (CSPs), four sensory neuron membrane proteins (SNMPs), 30 odorant receptors (ORs), 18 ionotropic receptors (IRs), and 17 gustatory receptors (GRs). We also identified full-length sequences of the highly conserved ORco and IR8a/25a family in O. communa. In addition, the expression profile of 15 ORs and four OBPs were validated by quantitative real-time polymerase chain reaction (qPCR). We found that OcomOR2/4/19 and OcomOBP19/20 had a biased expression in male antennae, and OcomOR8 had a biased expression in the female antennae. This large number of chemosensory genes handled by homology analysis and qPCR results will provide the first insights into molecular basis for the olfactory systems of O. communa as well as advance our understanding of olfactory mechanisms in Coleoptera.

scholarly journals Antennal Transcriptome Analysis and Identification of Candidate Chemosensory Genes of the Harlequin Ladybird Beetle, Harmonia axyridis (Pallas) (Coleoptera: Coccinellidae)

Insects ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 209
Author(s):  
Gabriele Rondoni ◽  
Alessandro Roman ◽  
Camille Meslin ◽  
Nicolas Montagné ◽  
Eric Conti ◽  
...  
Keyword(s):  
Binding Proteins ◽  
Harmonia Axyridis ◽  
Differential Expression Analysis ◽  
Mate Location ◽  
Gene Repertoire ◽  
Odorant Binding Proteins ◽  
Chemosensory Genes ◽  
Males And Females ◽  
Odorant Binding ◽  
Harmonia Axyridis Pallas

In predatory ladybirds (Coleoptera: Coccinellidae), antennae are important for chemosensory reception used during food and mate location, and for finding a suitable oviposition habitat. Based on NextSeq 550 Illumina sequencing, we assembled the antennal transcriptome of mated Harmonia axyridis (Pallas) (Coleoptera: Coccinellidae) males and females and described the first chemosensory gene repertoire expressed in this species. We annotated candidate chemosensory sequences encoding 26 odorant receptors (including the coreceptor, Orco), 17 gustatory receptors, 27 ionotropic receptors, 31 odorant-binding proteins, 12 chemosensory proteins, and 4 sensory neuron membrane proteins. Maximum-likelihood phylogenetic analyses allowed to assign candidate H. axyridis chemosensory genes to previously described groups in each of these families. Differential expression analysis between males and females revealed low variability between sexes, possibly reflecting the known absence of relevant sexual dimorphism in the structure of the antennae and in the distribution and abundance of the sensilla. However, we revealed significant differences in expression of three chemosensory genes, namely two male-biased odorant-binding proteins and one male-biased odorant receptor, suggesting their possible involvement in pheromone detection. Our data pave the way for improving the understanding of the molecular basis of chemosensory reception in Coccinellidae.

scholarly journals Transcriptome Analysis and Characterization of Chemosensory Genes in the Forest Pest, Dioryctria abietella (Lepidoptera: Pyralidae)

2021 ◽  
Vol 9 ◽  
Author(s):  
Zheng-Quan Wang ◽  
Chun Wu ◽  
Gen-Ceng Li ◽  
Shu-Mei Nuo ◽  
Ning-Na Yin ◽  
...  
Keyword(s):  
Sex Pheromones ◽  
Gene Families ◽  
Odorant Receptors ◽  
Neuron Membrane ◽  
Odorant Binding Proteins ◽  
Chemosensory Gene ◽  
Chemosensory Genes ◽  
Lepidoptera Pyralidae ◽  
Odorant Binding

In Lepidoptera, RNA sequencing has become a useful tool in identifying chemosensory genes from antennal transcriptomes, but little attention is paid to non-antennal tissues. Though the antennae are primarily responsible for olfaction, studies have found that a certain number of chemosensory genes are exclusively or highly expressed in the non-antennal tissues, such as proboscises, legs and abdomens. In this study, we report a global transcriptome of 16 tissues from Dioryctria abietella, including chemosensory and non-chemosensory tissues. Through Illumina sequencing, totally 952,658,466 clean reads were generated, summing to 142.90 gigabases of data. Based on the transcriptome, 235 chemosensory-related genes were identified, comprising 42 odorant binding proteins (OBPs), 23 chemosensory proteins (CSPs), 75 odorant receptors (ORs), 62 gustatory receptors (GRs), 30 ionotropic receptors (IRs), and 3 sensory neuron membrane proteins (SNMPs). Compared to a previous study in this species, 140 novel genes were found. A transcriptome-wide analysis combined with PCR results revealed that except for GRs, the majority of other five chemosensory gene families in Lepidoptera were expressed in the antennae, including 160 chemosensory genes in D. abietella. Using phylogenetic and expression profiling analyses, members of the six chemosensory gene repertoires were characterized, in which 11 DabiORs were candidates for detecting female sex pheromones in D. abietella, and DabiOR23 may be involved in the sensing of plant-derived phenylacetaldehyde. Intriguingly, more than half of the genes were detected in the proboscises, and one fourth of the genes were found to have the expression in the legs. Our study not only greatly extends and improves the description of chemosensory genes in D. abietella, but also identifies potential molecular targets involved in olfaction, gustation and non-chemosensory functions for control of this pest.

scholarly journals Functional characterisation of the transcriptome from leaf tissue of the fluoroacetate-producing plant, Dichapetalum cymosum, in response to mechanical wounding

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Selisha A. Sooklal ◽  
Phelelani T. Mpangase ◽  
Mihai-Silviu Tomescu ◽  
Shaun Aron ◽  
Scott Hazelhurst ◽  
...  
Keyword(s):  
Differential Expression Analysis ◽  
Leaf Tissue ◽  
Wound Response ◽  
Future Research ◽  
Mechanical Wounding ◽  
Illumina Hiseq ◽  
Functional Characterisation ◽  
Wound Responses ◽  
Illumina Hiseq Platform ◽  
And Function

AbstractDichapetalum cymosum produces the toxic fluorinated metabolite, fluoroacetate, presumably as a defence mechanism. Given the rarity of fluorinated metabolites in nature, the biosynthetic origin and function of fluoroacetate have been of particular interest. However, the mechanism for fluorination in D. cymosum was never elucidated. More importantly, there is a severe lack in knowledge on a genetic level for fluorometabolite-producing plants, impeding research on the subject. Here, we report on the first transcriptome for D. cymosum and investigate the wound response for insights into fluorometabolite production. Mechanical wounding studies were performed and libraries of the unwounded (control) and wounded (30 and 60 min post wounding) plant were sequenced using the Illumina HiSeq platform. A combined reference assembly generated 77,845 transcripts. Using the SwissProt, TrEMBL, GO, eggNOG, KEGG, Pfam, EC and PlantTFDB databases, a 69% annotation rate was achieved. Differential expression analysis revealed the regulation of 364 genes in response to wounding. The wound responses in D. cymosum included key mechanisms relating to signalling cascades, phytohormone regulation, transcription factors and defence-related secondary metabolites. However, the role of fluoroacetate in inducible wound responses remains unclear. Bacterial fluorinases were searched against the D. cymosum transcriptome but transcripts with homology were not detected suggesting the presence of a potentially different fluorinating enzyme in plants. Nevertheless, the transcriptome produced in this study significantly increases genetic resources available for D. cymosum and will assist with future research into fluorometabolite-producing plants.

scholarly journals Genome survey and microsatellite motif identification of Pogonophryne albipinna

2021 ◽  
Author(s):  
Euna Jo ◽  
Yll Hwan Cho ◽  
Seung Jae Lee ◽  
Eunkyung Choi ◽  
Jinmu Kim ◽  
...  
Keyword(s):  
Microsatellite Motif ◽  
Illumina Hiseq ◽  
Genome Survey ◽  
Deep Waters ◽  
Genome Wide ◽  
Illumina Hiseq Platform ◽  
Species Groups ◽  
The Antarctic ◽  
Simple Sequence ◽  
Living Group

The genus Pogonophryne is a speciose group that includes 28 species inhabiting the coastal or deep waters of the Antarctic Southern Ocean. The genus has been divided into five species groups, among which the P. albipinna group is the most deep-living group and is characterized by a lack of spots on the top of the head. Here, we carried out genome survey sequencing of P. albipinna using the Illumina HiSeq platform to estimate the genomic characteristics and identify genome-wide microsatellite motifs. The genome size was predicted to be ~883.8 Mb by K-mer analysis (K=25), and the heterozygosity and repeat ratio were 0.289% and 39.03%, respectively. The genome sequences were assembled into 571,624 contigs, covering a total length of ~819.3 Mb with an N50 of 2,867 bp. A total of 2,217,422 simple sequence repeat motifs were identified from the assembly data, and the number of repeats decreased as the length and number of repeats increased. These data will provide a useful foundation for the development of new molecular markers for the P. albipinna group as well as for further whole genome sequencing of P. albipinna.

Abstract P625: Non-coding Rna Regulation Of Gene Expression In Angiotensin Ii-induced Vascular Damage

Hypertension ◽  
2015 ◽  
Vol 66 (suppl_1) ◽  
Author(s):  
Kugeng Huo ◽  
Tlili Barhoumi ◽  
Júlio C Fraulob-Aquino ◽  
Chantal Richer ◽  
Mathieu Lajoie ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differential Expression Analysis ◽  
Regulation Of Gene Expression ◽  
Vascular Damage ◽  
Mesenteric Arteries ◽  
Functional Enrichment ◽  
Molecular Networks ◽  
Mirna Cluster ◽  
Ang Ii ◽  
Illumina Hiseq

Introduction: Non-coding RNAs (ncRNAs), including long ncRNAs (lncRNAs) and microRNAs (miRs), account for ~98% of the transcribed RNAs. They have been shown to play a role in cardiovascular disease. Vascular damage is an early manifestation and a cause of end-organ damage in hypertension. However, it is unknown whether ncRNAs are involved in the development of vascular injury in hypertension. We hypothesize that ncRNA regulation participates in mechanisms of vascular remodeling and plays an important role in the pathophysiology of hypertension. Methods and Results: Ten-week old male C57BL/6 mice were infused or not with angiotensin (Ang) II for 14 days. Systolic blood pressure (BP) determined by telemetry was increased by Ang II infusion compared to control (146±8 vs 113±5 mmHg, P<0.001). Total RNA was extracted from mesenteric arteries for total and small RNA deep sequencing using Illumina HiSeq-2500. Sequences were aligned to the mm10 genome with STAR, annotated and counted using HTSeq-count or miRDeep2. Differential expression analysis was done in R. Differentially expressed (DE) mRNAs (550 up & 266 down), lncRNAs (7 up & 42 down), miRs (23 up & 12 down) were identified in the Ang II-treated group (1.5 fold change, q<0.05). Targetscan was used to predict interactions between DE miRs and the inversely correlated DE mRNAs or DE lncRNAs. MEME Suite was used to predict DE transcription factor binding sites in the promoter region of genes encoding DE mRNAs, lncRNAs and miRs. Cytoscape was used to construct molecular networks integrating the above interactions and the gene expression profile and to perform functional enrichment analysis, which revealed enrichment of extracellular matrix and developmental processes in DE miR-targeting DE mRNAs (q<1E-20). Ten DE miRNAs whose expression levels correlated (P<0.05) with BP were identified, 9 of which are located in a single miRNA cluster that is conserved in humans. Conclusions: We have identified a conserved miRNA cluster that may play a pivotal role in the regulation of vascular damage in hypertension. A sub-network of genes that participates in the interaction between the miRNA cluster and other BP-correlated RNAs was selected for future investigation to identify therapeutic targets.

scholarly journals Transcriptome and proteome of the corm, leaf and flower of Hypoxis hemerocallidea (African potato)

PLoS ONE ◽  
2021 ◽  
Vol 16 (7) ◽  
pp. e0253741
Author(s):  
Mihai-Silviu Tomescu ◽  
Selisha Ann Sooklal ◽  
Thuto Ntsowe ◽  
Previn Naicker ◽  
Barbara Darnhofer ◽  
...  
Keyword(s):  
De Novo ◽  
Differential Expression Analysis ◽  
Terpene Synthase ◽  
Future Research ◽  
Terpene Synthases ◽  
Illumina Hiseq ◽  
Prostate Hyperplasia ◽  
Inflammatory Conditions ◽  
Urinary Infections ◽  
Hypoxis Hemerocallidea

The corm of Hypoxis hemerocallidea, commonly known as the African potato, is used in traditional medicine to treat several medical conditions such as urinary infections, benign prostate hyperplasia, inflammatory conditions and testicular tumours. The metabolites contributing to the medicinal properties of H. hemerocallidea have been identified in several studies and, more recently, the active terpenoids of the plant were profiled. However, the biosynthetic pathways and the enzymes involved in the production of the terpene metabolites in H. hemerocallidea have not been characterised at a transcriptomic or proteomic level. In this study, total RNA extracted from the corm, leaf and flower tissues of H. hemerocallidea was sequenced on the Illumina HiSeq 2500 platform. A total of 143,549 transcripts were assembled de novo using Trinity and 107,131 transcripts were functionally annotated using the nr, GO, COG, KEGG and SWISS-PROT databases. Additionally, the proteome of the three tissues were sequenced using LC-MS/MS, revealing aspects of secondary metabolism and serving as data validation for the transcriptome. Functional annotation led to the identification of numerous terpene synthases such as nerolidol synthase, germacrene D synthase, and cycloartenol synthase amongst others. Annotations also revealed a transcript encoding the terpene synthase phytoalexin momilactone A synthase. Differential expression analysis using edgeR identified 946 transcripts differentially expressed between the three tissues and revealed that the leaf upregulates linalool synthase compared to the corm and the flower tissues. The transcriptome as well as the proteome of Hypoxis hemerocallidea presented here provide a foundation for future research.

Identification and analysis of chemosensory genes encoding odorant-binding proteins, chemosensory proteins and sensory neuron membrane proteins in the antennae of Lissorhoptrus oryzophilus

2021 ◽  
pp. 1-11
Author(s):  
Yu Pan ◽  
Xinxin Zhang ◽  
Zhun Wang ◽  
Lizhong Qi ◽  
Xinsheng Zhang ◽  
...  
Keyword(s):  
Membrane Proteins ◽  
Sensory Neuron ◽  
Binding Proteins ◽  
Mate Location ◽  
Lissorhoptrus Oryzophilus ◽  
Neuron Membrane ◽  
Odorant Binding Proteins ◽  
Chemosensory Proteins ◽  
Chemosensory Genes ◽  
Odorant Binding

Abstract The rice water weevil, Lissorhoptrus oryzophilus Kuschel (Coleoptera: Curculionidae), is a destructive pest that causes damage to rice crops worldwide. The olfactory system is critical for host or mate location by weevils, but only limited information about the molecular mechanism of olfaction-related behaviour has been reported in this insect. In this study, we conducted SMRT-seq transcriptome analysis and obtained 54,378 transcripts, 38,706 of which were annotated. Based on these annotations, we identified 40 candidate chemosensory genes, including 31 odorant-binding proteins (OBPs), six chemosensory proteins (CSPs) and three sensory neuron membrane proteins (SNMPs). Phylogenetic analysis showed that LoryOBPs, LoryCSPs and LorySNMPs were distributed in various clades. The results of tissue expression patterns indicated that LoryOBPs were highly abundant in the antennae, whereas LoryCSPs were highly abundant not only in the antennae but also in the abdomen, head and wings. Our findings substantially expand the gene database of L. oryzophilus and may serve as a basis for identifying novel targets to disrupt key olfactory genes, potentially providing an eco-friendly strategy to control this pest in the future.

The mitochondrial genome and phylogenetic analysis of the tick Haemaphysalis qinghaiensis Teng, 1980 (Acari:Ixodidae)

2022 ◽  
Author(s):  
Tianhong Wang ◽  
Zihao Wang ◽  
Ruwei Bai ◽  
Zhijun Yu ◽  
Jingze Liu
Keyword(s):  
Phylogenetic Analysis ◽  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Rrna Genes ◽  
Trna Genes ◽  
Illumina Hiseq ◽  
Protein Coding ◽  
Haemaphysalis Qinghaiensis ◽  
Mitogenome Sequence ◽  
Illumina Hiseq Platform

Haemaphysalis qinghaiensis is an endemic species and mainly inhabiting in the northwestern plateau of China, which can transmit many zoonotic pathogens and cause great harm to animals. In this study, the complete mitochondrial genome (mitogenome) of H. qinghaiensis was assembled through the Illumina HiSeq platform. The mitogenome was 14,533 bp in length, consisting of 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes and 3 noncoding regions (NCRs). The bias towards a high A+T content with 77.65% in mitogenome of H. qinghaiensis. The rearrangement of mitochondrial genes in H. qinghaiensis was consistent with other hard ticks. The phylogenetic analysis based on the concatenation of 13 PCGs from 65 tick mitogenomes showed that the H. qinghaiensis was clustered into a well-supported clade within the Haemaphysalis genus. This is the first complete mitogenome sequence of H. qinghaiensis, which provides a useful reference for understanding of the taxonomic and genetics of ticks.

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