Genome-wide identification, characterization and classification of ionotropic glutamate receptor genes (iGluRs) in the malaria vector Anopheles sinensis (Diptera: Culicidae)

Abstract

BackgroundIonotropic glutamate receptors (iGluRs) are conserved ligand-gated ion channel receptors, and ionotropic receptors (IRs) were revealed as a new family of iGluRs. Their subdivision was unsettled, and their characteristics are little known. Anopheles sinensis is a major malaria vector in eastern Asia, and its genome was recently well sequenced and annotated.MethodsWe identified iGluR genes in the An. sinensis genome, analyzed their characteristics including gene structure, genome distribution, domains and specific sites by bioinformatic methods, and deduced phylogenetic relationships of all iGluRs in An. sinensis, Anopheles gambiae and Drosophila melanogaster. Based on the characteristics and phylogenetics, we generated the classification of iGluRs, and comparatively analyzed the intron number and selective pressure of three iGluRs subdivisions, iGluR group, Antenna IR and Divergent IR subfamily.ResultsA total of 56 iGluR genes were identified and named in the whole-genome of An. sinensis. These genes were located on 18 scaffolds, and 31 of them (29 being IRs) are distributed into 10 clusters that are suggested to form mainly from recent gene duplication. These iGluRs can be divided into four groups: NMDA, non-NMDA, Antenna IR and Divergent IR based on feature comparison and phylogenetic analysis. IR8a and IR25a were suggested to be monophyletic, named as Putative in the study, and moved from the Antenna subfamily in the IR family to the non-NMDA group as a sister of traditional non-NMDA. The generated iGluRs of genes (including NMDA and regenerated non-NMDA) are relatively conserved, and have a more complicated gene structure, smaller ω values and some specific functional sites. The iGluR genes in An. sinensis, An. gambiae and D. melanogaster have amino-terminal domain (ATD), ligand binding domain (LBD) and Lig_Chan domains, except for IR8a that only has the LBD and Lig_Chan domains. However, the new concept IR family of genes (including regenerated Antenna IR, and Divergent IR), especially for Divergent IR are more variable, have a simpler gene structure (intron loss phenomenon) and larger ω values, and lack specific functional sites. These IR genes have no other domains except for Antenna IRs that only have the Lig_Chan domain.ConclusionsThis study provides a comprehensive information framework for iGluR genes in An. sinensis, and generated the classification of iGluRs by feature and bioinformatics analyses. The work lays the foundation for further functional study of these genes.Electronic supplementary materialThe online version of this article (10.1186/s13071-017-2610-x) contains supplementary material, which is available to authorized users.

UDP-glycosyltransferase genes and their association and mutations associated with pyrethroid resistance in Anopheles sinensis (Diptera: Culicidae)

“…Recently, genome sequencing in An. sinensis facilitated identification and characterization of some families of genes involved in pyrethroid resistance, such as P450s [44, 45], GSTs [44], CCEs [44, 46], cuticular proteins [47], ionotropic glutamate receptors [48] and odorant-binding proteins [49]. Besides, enzyme overproduction and enzyme modification caused by coding sequence alteration (another way to enhance the metabolic capability) have also been reported in some insect species [50], but not in UGT genes of An.…”

ATP-Binding Cassette (ABC) Transporter Genes Involved in Pyrethroid Resistance in the Malaria Vector Anopheles sinensis: Genome-Wide Identification, Characteristics, Phylogenetics, and Expression Profile

“…We have deeply sequenced and assembled the genome of A. sinensis [15,21,23], and we are conducting comprehensive research on the molecular mechanism of pyrethroid resistance using the species as model. Some families of genes have been identified at whole-genome level and their association with pyrethroid resistance have been investigated or summarized, such as CCEs [14], P450s [15], CSPs [23], CPs [24], OBPs [25], and iGluRs [26]. However, little information has been known about the ABC transporter genes and their association with pyrethroid resistance in A. sinensis .…”

Comparative analyses of simple sequence repeats (SSRs) in 23 mosquito species genomes: Identification, characterization and distribution (Diptera: Culicidae)

“…With the increasing of mosquito omics data, the diversity, characterization and functional analyses of a given group of genes are progressively increasing (He et al ., ; Liu et al ., ; Mei et al ., ; Wang et al ., ; Wu et al ., ; Yan et al ., ). However, the in silico SSR identification and analysis are relatively insufficient, and therefore the SSR features and the association with different species of mosquito genomes are still not well understood.…”

“…albopictus (Chen et al, 2015) have been sequenced and annotated, and more recently 16 Anopheles genomes have been reported (Neafsey et al, 2015). A number of transcriptomes and mitochondrial genomes have also been sequenced and comparatively analyzed (e.g., Chen et al, 2014;Hua et al, 2016;Hao et al, 2017;Fang et al, 2018) With the increasing of mosquito omics data, the diversity, characterization and functional analyses of a given group of genes are progressively increasing (He et al, 2016;Liu et al, 2018;Mei et al, 2018;Wang et al, 2018;Wu et al, 2018;Yan et al, 2018). However, the in silico SSR identification and analysis are relatively insufficient, and therefore the SSR features and the association with different species of mosquito genomes are still not well understood.…”