scholarly journals De novo transcriptome sequencing of the northern fowl mite, Ornithonyssus sylviarum, shed light into parasitiform poultry mites evolution and its chemoreceptor repertoires

2021 ◽  
Author(s):  
Biswajit Bhowmick ◽  
Huaqing Chen ◽  
Jesus Lozano-Fernandez ◽  
Joel Vizueta ◽  
Rickard Ignell ◽  
...  
Keyword(s):  
De Novo ◽  
Functional Characterization ◽  
Dermanyssus Gallinae ◽  
Gene Repertoire ◽  
Transcriptome Data ◽  
Poultry Red Mite ◽  
Additional Species ◽  
Ornithonyssus Sylviarum ◽  
Northern Fowl Mite ◽  
Parasitic Lifestyle

The poultry red mite (PRM), Dermanyssus gallinae (De Geer), and the northern fowl mite (NFM), Ornithonyssus sylviarum (Canestrini and Fanzago), are the most serious pests of poultry, both of which have an expanding global prevalence. Research on NFM has been constrained by a lack of genomic and transcriptomic data. Here, we report and analyze the first transcriptome data for this species. A total of 28,999 unigenes were assembled, of which 19,750 (68.10%) were annotated using seven functional databases. The biological function of these unigenes was predicted using the GO, KOG, and KEGG databases. To gain insight into the chemosensory receptor-based system of parasitiform mites, we furthermore assessed the gene repertoire of gustatory receptors (GRs) and ionotropic receptors (IRs), both of which encode putative ligand-gated ion channel proteins. While these receptors are well characterized in insect model species, our understanding of chemosensory detection in mites and ticks is in its infancy. To address this paucity of data, we identified 9 IR/iGluRs and 2 GRs genes by analyzing transcriptome data in the NFM, while 9 GRs and 41 IR/iGluRs genes were annotated in the PRM genome. Taken together, the transcriptomic and genomic annotation of these two species provide a valuable reference for studies of parasitiform mites, and also helps to understand how chemosensory gene family expansion/contraction events may have been reshaped by an obligate parasitic lifestyle compared with their free-living closest relatives. Future studies should include additional species to validate this observation, and functional characterization of the identified proteins as a step forward in identifying tools for controlling these poultry pests.

scholarly journals Collecting and Monitoring for Northern Fowl Mite (Acari: Macronyssidae) and Poultry Red Mite (Acari: Dermanyssidae) in Poultry Systems

2020 ◽  
Vol 20 (6) ◽  
Author(s):  
Amy C Murillo ◽  
Bradley A Mullens
Keyword(s):  
Decision Making ◽  
Sampling Methods ◽  
Dermanyssus Gallinae ◽  
Poultry Red Mite ◽  
Future Directions ◽  
Ornithonyssus Sylviarum ◽  
Northern Fowl Mite ◽  
Basic Biology

Abstract The two most economically important poultry ectoparasites are the northern fowl mite, Ornithonyssus sylviarum (Canestrini and Fanzago), and the poultry red mite, Dermanyssus gallinae (De Geer). Both mites are obligate blood feeders but differ in where they reside. Sampling methods thus focus on-host, especially the vent feathers, for northern fowl mite and off-host, especially cracks and crevices near the nighttime roosting areas, for poultry red mite. Much remains unknown, however, about the basic biology and ecology of both mites. Here we discuss mite detection, quantification, and decision making and provide thoughts on future directions for research.

scholarly journals Whole transcriptome analysis of the poultry red mite Dermanyssus gallinae (De Geer, 1778)

Parasitology ◽  
2013 ◽  
Vol 141 (3) ◽  
pp. 336-346 ◽  
Author(s):  
SABINE SCHICHT ◽  
WEIHONG QI ◽  
LUCY POVEDA ◽  
CHRISTINA STRUBE
Keyword(s):  
Drug Targets ◽  
De Novo ◽  
Ixodes Scapularis ◽  
Economic Losses ◽  
Dermanyssus Gallinae ◽  
28S Rrna ◽  
Poultry Red Mite ◽  
Kegg Pathways ◽  
Metaseiulus Occidentalis ◽  
Nucleotide Data

SUMMARYAlthough the poultry red mite Dermanyssus gallinae (De Geer, 1778) is the major parasitic pest in poultry farming causing substantial economic losses every year, nucleotide data are rare in the public databases. Therefore, de novo sequencing covering the transcriptome of D. gallinae was carried out resulting in a dataset of 232 097 singletons and 42 130 contiguous sequences (contigs) which were subsequently clustered into 24 140 isogroups consisting of 35 788 isotigs. After removal of sequences possibly originating from bacteria or the chicken host, 267 464 sequences (231 657 singletons, 56 contigs and 35 751 isotigs) remained, of which 10·3% showed homology to proteins derived from other organisms. The most significant Blast top-hit species was the mite Metaseiulus occidentalis followed by the tick Ixodes scapularis. To gain functional knowledge of D. gallinae transcripts, sequences were mapped to Gene Ontology terms, Kyoto Encyclopedia of Gene and Genomes (KEGG) pathways and parsed to InterProScan. The transcriptome dataset provides new insights in general mite genetics and lays a foundation for future studies on stage-specific transcriptomics as well as genomic, proteomic, and metabolomic explorations and might provide new perspectives to control this parasitic mite by identifying possible drug targets or vaccine candidates. It is also worth noting that in different tested species of the class Arachnida no 28S rRNA was detectable in the rRNA profile, indicating that 28S rRNA might consists of two separate, hydrogen-bonded fragments, whose (heat-induced) disruption may led to co-migration with 18S rRNA.

scholarly journals Draft Genome Assembly of the Poultry Red Mite, Dermanyssus gallinae

2018 ◽  
Vol 7 (18) ◽  
Author(s):  
Stewart T. G. Burgess ◽  
Kathryn Bartley ◽  
Francesca Nunn ◽  
Harry W. Wright ◽  
Margaret Hughes ◽  
...  
Keyword(s):  
Genome Assembly ◽  
De Novo ◽  
Gene Prediction ◽  
Draft Genome ◽  
Egg Laying ◽  
Dermanyssus Gallinae ◽  
Poultry Red Mite ◽  
Draft Genome Assembly ◽  
Long Read

The poultry red mite, Dermanyssus gallinae, is a major worldwide concern in the egg-laying industry. Here, we report the first draft genome assembly and gene prediction of Dermanyssus gallinae, based on combined PacBio and MinION long-read de novo sequencing.

scholarly journals TRAPID 2.0: a web application for taxonomic and functional analysis of de novo transcriptomes

2020 ◽  
Author(s):  
François Bucchini ◽  
Andrea Del Cortona ◽  
Łukasz Kreft ◽  
Alexander Botzki ◽  
Michiel Van Bel ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Web Application ◽  
High Throughput Sequencing ◽  
De Novo ◽  
Gene Repertoire ◽  
Transcriptome Data ◽  
Evolutionary Context ◽  
Efficient Processing ◽  
Specific Tissue ◽  
Initial Processing

ABSTRACTAdvances in high-throughput sequencing have resulted in a massive increase of RNA-Seq transcriptome data. However, the promise of rapid gene expression profiling in a specific tissue, condition, unicellular organism, or microbial community comes with new computational challenges. Owing to the limited availability of well-resolved reference genomes, de novo assembled (meta)transcriptomes have emerged as popular tools for investigating the gene repertoire of previously uncharacterized organisms. Yet, despite their potential, these datasets often contain fragmented or contaminant sequences, and their analysis remains difficult. To alleviate some of these challenges, we developed TRAPID 2.0, a web application for the fast and efficient processing of assembled transcriptome data. The initial processing phase performs a global characterization of the input data, providing each transcript with several layers of annotation, comprising structural, functional, and taxonomic information. The exploratory phase enables downstream analyses from the web application. Available analyses include the assessment of gene space completeness, the functional analysis and comparison of transcript subsets, and the study of transcripts in an evolutionary context. A comparison with similar tools highlights TRAPID’s unique features. Finally, analyses performed within TRAPID 2.0 are complemented by interactive data visualizations, facilitating the extraction of new biological insights, as demonstrated with diatom community metatranscriptomes.

scholarly journals Aster spathulifolius Maxim. a leaf transcriptome provides an overall functional characterization, discovery of SSR marker and phylogeny analysis

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0244132
Author(s):  
Sivagami Jean Claude ◽  
SeonJoo Park
Keyword(s):  
Functional Annotation ◽  
De Novo ◽  
Functional Characterization ◽  
Signal Transduction Pathway ◽  
Single Copy ◽  
Phenylpropanoid Pathway ◽  
Transcriptome Data ◽  
Flavonoid Pathway ◽  
Molecular Functions ◽  
Asteraceae Family

Aster spathulifolius Maxim. is belongs to the Asteraceae family, which is distributed only in Korea and Japan. The species is traditionally a medicinal plant and is economically valuable in the ornamental field. On the other hand, the Aster genus, among the Asteraceae family, lacks genomic resources and its molecular functions. Therefore, in our study the high-throughput RNA-sequencing transcriptome data of A. spathulifolius were obtained to identify the molecular functions and its characterization. The de novo assembly produced 98660 uniqueness with an N50 value of 1126bp. Total unigenes were procure to analyze the functional annotation against databases like non-redundant protein, Pfam, Uniprot, KEGG and Gene ontology. The overall percentage of functional annotation to the nr database (43.71%), uniprotein database (49.97%), Pfam (39.94%), KEGG (42.3%) and to GO (30.34%) were observed. Besides, 377 unigenes were found to be involved in the terpenoids pathway and 666 unigenes were actively engaged in other secondary metabolites synthesis, given that 261 unigenes were within phenylpropanoid pathway and 81 unigenes to flavonoid pathway. A further prediction of stress resistance (9,513) unigenes and transcriptional factor (3,027) unigenes in 53 types were vastly regulated in abiotic stress respectively in salt, heat, MAPK and hormone signal transduction pathway. This study discovered 29,692 SSR markers that assist the genotyping approaches and the genetic diversity perspectives. In addition, eight Asteraceae species as in-group together with one out-group were used to construct the phylogenetic relationship by employing their plastid genome and single-copy orthologs genes. Among 50 plastid protein-coding regions, A. spathulifolius is been closely related to A. annua and by 118 single copy orthologs genes, O. taihangensis is more neighboring species to A. spathulifolius. Apart from this, A. spathulifolius and O. taihangensis, genera have recently diverged from other species. Overall, this research gains new insights into transcriptome data by revealing and exposing the secondary metabolite compounds for drug development, the stress-related genes for producing resilient crops and an ortholog gene of A. spathulifolius for the robustness of phylogeny reconstruction among Asteraceae genera.

scholarly journals Case of Human Infestation with Dermanyssus gallinae (Poultry Red Mite) from Swallows (Hirundinidae)

Pathogens ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 299
Author(s):  
Georgios Sioutas ◽  
Styliani Minoudi ◽  
Katerina Tiligada ◽  
Caterina Chliva ◽  
Alexandros Triantafyllidis ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Clinical Symptoms ◽  
Skin Lesions ◽  
Coi Gene ◽  
Dermanyssus Gallinae ◽  
Poultry Red Mite ◽  
Human Form ◽  
Bayesian Phylogenetic Analysis

Dermanyssus gallinae (the poultry red mite, PRM) is an important ectoparasite in the laying hen industry. PRM can also infest humans, causing gamasoidosis, which is manifested as skin lesions characterized by rash and itching. Recently, there has been an increase in the reported number of human infestation cases with D. gallinae, mostly associated with the proliferation of pigeons in cities where they build their nests. The human form of the disease has not been linked to swallows (Hirundinidae) before. In this report, we describe an incident of human gamasoidosis linked to a nest of swallows built on the window ledge of an apartment in the island of Kefalonia, Greece. Mites were identified as D. gallinae using morphological keys and amplifying the Cytochrome C oxidase subunit I (COI) gene by PCR. Bayesian phylogenetic analysis and median-joining network supported the identification of three PRM haplogroups and the haplotype isolated from swallows was identical to three PRM sequences isolated from hens in Portugal. The patient was treated with topical corticosteroids, while the house was sprayed with deltamethrin. After one week, the mites disappeared and clinical symptoms subsided. The current study is the first report of human gamasoidosis from PRM found in swallows’ nest.

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