The complete mt genomes of Lutzia halifaxia, Lt. fuscanus and Culex pallidothorax (Diptera: Culicidae) and comparative analysis of 16 Culex and Lutzia mt genome sequences

Abstract

Background Despite the medical importance of the genus Culex , the mitochondrial genome (mt genome) characteristics of Culex spp. are not well understood. The phylogeny of the genus and particularly the generic status of the genus Lutzia and the subgenus Culiciomyia remain unclear. Methods The present study sequenced and analyzed the complete mt genomes of Lutzia halifaxia , Lutzia fuscanus and Cx. ( Culiciomyia ) pallidothorax and assessed the general characteristics and phylogenetics of all known 16 mt genome sequences for species in the genera Culex and Lutzia. Results The complete mt genomes of Lt. halifaxia , Lt. fuscanus and Cx. pallidothorax are 15,744, 15,803 and 15,578 bp long, respectively, including 13 PCGs, 22 tRNAs, two tRNAs and a control region (CR). Length variations in the Culex and Lutzia mt genomes involved mainly the CR, and gene arrangements are the same as in other mosquitoes. We identified four types of repeat units in the CR sequences, and the poly-T stretch exists in all of these mt genomes. The repeat units of CR are conserved to different extent and provide information on their evolution. Phylogenetic analyses demonstrated that the Coronator and Sitiens groups are each monophyletic, whereas the monophyletic status of the Pipiens Group was not supported; Cx. pallidothorax is more closely related to the Sitiens and Pipiens groups; and both phylogenetics analysis and repeat unit features in CR show that Lutzia is a characteristic monophyletic entity, which should be an independent genus. Conclusions To our knowledge, this is the first comprehensive review of the mt genome sequences and taxonomic discussion based on the mt genomes of Culex spp. and Lutzia spp. The research provides general information on the mt genome of these two genera, and the phylogenetic and taxonomic status of Lutzia and Culiciomyia . Electronic supplementary material The online version of this article (10.1186/s13071-019-3625-2) contains supplementary material, which is available to authorized users.

Culicidae evolutionary history focusing on the Culicinae subfamily based on mitochondrial phylogenomics

“…In addition, mitogenomes have uniparental heritage, high copy number by cells and single-copy genes which facilitates DNA recovery and phylogenetic analysis 18 – 20 . Recently, some studies have sequenced a larger number of mitochondrial genomes from different mosquito species, but they are mostly focused on species from the Anopheles genus 21 – 23 . Mosquito mitogenomes are structurally conserved following the metazoa gene number and order, with few exceptions, showing 37 genes comprising 13 protein coding genes, 22 tRNAs and 2 rRNA genes 24 – 26 .…”

Time and mode of Culicidae evolutionary history

“…The first mosquito mitogenome from Anopheles gambiae was sequenced using the Sanger method on PCR amplified fragments 25 and further mitochondrial genomes were slowly sequenced along with whole genome projects. Currently, most studies have been using high throughput sequencing or PCR amplification followed by high throughput sequencing to characterize several mitogenomes at once 20,21,24 in a wide range of insect species showing promising results to reconstruct mitogenomes 30, 57 Here, we performed low-coverage sequencing to assemble and characterize the mitogenomes from many mosquito species generating around 4.95 million reads per species. We were able to assemble sixteen draft mitogenomes from Culicidae species, not characterized so far, belonging to 8 different genera.…”

“…The Anophelinae subfamily phylogenetic relationship was recently investigated using the mitochondrial genomes from many species and the authors proposed a number of taxonomic status changes such as the elevation of some groups from the subgenus to genus level 19 . Some other studies also characterized the mitogenomes of some species to solve the phylogenetic positioning of culicids, however, most of them focused on a specific group ( Anopheles , Culex and Sabethes ) or few genera of the Culicidae family 10,11,[19][20][21]66 .…”

“…In addition, mitogenomes have a uniparental heritage, high copy number per cells and single-copy genes which facilitates DNA recovery and phylogenetic analysis [16][17][18] . Recently, some studies have sequenced a larger number of mitochondrial genomes from different mosquito species, but they are mostly focused on Anopheles species [19][20][21] . Mosquito mitogenomes are structurally conserved following the metazoa gene number and order, with few exceptions, showing 37 genes comprising 13 protein coding genes, 22 tRNAs and 2 rRNA genes [22][23][24] .…”

“…Other approaches available allow the recovery of mitogenomes by PCR amplification from environment samples and pooled DNA and mitogenome recovery from low-coverage sequencing [29][30][31] . Moreover, a number of bioinformatics tools were developed to specifically assembly and annotate mitogenomes [32][33][34][35][36] Most of the available mitogenomes belong to Anopheles species with much fewer genomes from Culex, Aedes and other genera such as Haemagogus, Bironella, Sabethes, and Lutzia [19][20][21]24,37 , but there is no available molecular data for the large majority of the species. Aiming to contribute with this basic and fundamental knowledge we performed low-coverage sequencing and data mining on already published Culicidae SRA data in order to characterize the mitogenomes from different species and genera and better understand the evolutionary history of mosquitoes focusing in Culicinae subfamily.…”