Dataset Information

A Draft Genome Assembly of Culex pipiens pallens (Diptera: Culicidae) Using PacBio Sequencing.

ABSTRACT: The Northern house mosquito, Culex pipiens pallens, serves as important temperate vectors of several diseases, particularly the epidemic encephalitis and lymphatic filariasis. Reference genome of the Cx. pipiens pallens is helpful to understand its genomic basis underlying the complexity of mosquito biology. Using 142?Gb (?250×) of the PacBio long reads, we assembled a draft genome of 567.56?Mb. The assembly includes 1,714 contigs with a N50 length of 0.84?Mb and a Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness of 95.6% (n?=?1,367). We masked 60.63% (344.11?Mb) of the genome as repetitive elements and identified 2,032 noncoding RNAs. A total of 18,122 protein-coding genes captured a 94.1% of BUSCO gene set. Gene family evolution and function enrichment analyses revealed that significantly expanded gene families mainly involved in immunity, gustatory and olfactory chemosensation, and DNA replication/repair.

SUBMITTER: Peng C

PROVIDER: S-EPMC7936019 | biostudies-literature | 2021 Mar

REPOSITORIES: biostudies-literature

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A Draft Genome Assembly of Culex pipiens pallens (Diptera: Culicidae) Using PacBio Sequencing.

Peng Cheng C Qian Zhang Z Xinyu Zhang Z Qianqian Le L Maoqing Gong G Zhong Zhang Z Ruiling Zhang Z

Genome biology and evolution 20210301 3

The Northern house mosquito, Culex pipiens pallens, serves as important temperate vectors of several diseases, particularly the epidemic encephalitis and lymphatic filariasis. Reference genome of the Cx. pipiens pallens is helpful to understand its genomic basis underlying the complexity of mosquito biology. Using 142 Gb (∼250×) of the PacBio long reads, we assembled a draft genome of 567.56 Mb. The assembly includes 1,714 contigs with a N50 length of 0.84 Mb and a Benchmarking Universal Single- ...[more]

PMID: 33501937

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Project description:BackgroundCulex tritaeniorhynchus and Culex pipiens pallens are the major vectors of the Japanese encephalitis virus and Wuchereria bancrofti, the causative agent of filariasis. The knowledge of mitochondrial genomes has been widely useful for the studies on molecular evolution, phylogenetics and population genetics.MethodsIn this study, we sequenced and annotated the mitochondrial (mt) genomes of Cx. tritaeniorhynchus and Cx. p. pallens, and performed a comparative analysis including four known mt genomes of species of the subgenus Culex (Culex). The phylogenetic relationships of Cx. tritaeniorhynchus, Cx. p. pallens and four known Culex mt genome sequences were reconstructed by maximum likelihood based on concatenated protein-coding gene sequences.ResultsCulex tritaeniorhynchus and Cx. p. pallens mt genomes are 14,844 bp and 15,617 bp long, both consists of 13 PCGs, 22 tRNAs, 2 rRNAs and 1 CR (not sequenced for Cx. tritaeniorhynchus). The initiation and termination codons of PCGs are ATN and TAA, respectively, except for COI starting with TCG, and COI and COII terminated with T. tRNAs have the typical clover-leaf secondary structures except for trnS ((AGN)) that is lacking the DHU stem. 16S rRNA and 12S rRNA secondary structures were drawn for the first time for mosquito mt genomes. The control region of Cx. p. pallens mt genome is 747 bp long and with four tandem repeat structures. Phylogenetic analyses demonstrated that the mt genome of Cx. tritaeniorhynchus was significantly separated from the remaining five mt genomes of Culex spp. Culex p. pipiens, Cx. p. pallens and Cx. p. quinquefasciatus formed a monophyletic clade with Cx. p. quinquefasciatus linked in the middle of the clade, and Cx. p. pallens should have the same taxonomic level as Culex p. pipiens and Cx. p. quinquefasciatus.ConclusionsThe mt genomes of Cx. tritaeniorhynchus and Cx. p. pallens share the same gene composition and order with those of two other Culex species. Culex p. pallens of the Pipiens complex should have the same taxonomic level as Culex p. pipiens and Cx. p. quinquefasciatus investigated. We enriched the Culex mt genome data and provided a reference basis for further Culex mt genome sequencing and analyses.

Project description:BACKGROUND: Culex spp. mosquitoes are considered to be the most important vectors of West Nile virus (WNV) detected in at least 34 species of mosquitoes in the United States. In North America, Culex pipiens pipiens, Culex pipiens quinquefasciatus, and Culex tarsalis are all competent vectors of WNV, which is considered to be enzootic in the United States and has also been detected in equines and birds in many states of Mexico and in humans in Nuevo Leon. There is potential for WNV to be introduced into Mexico City by various means including infected mosquitoes on airplanes, migrating birds, ground transportation and infected humans. Little is known of the geographic distribution of Culex pipiens complex mosquitoes and hybrids in Mexico City. Culex pipiens pipiens preferentially feed on avian hosts; Culex pipiens quinquefasciatus have historically been considered to prefer mammalian hosts; and hybrids of these two species could theoretically serve as bridge vectors to transmit WNV from avian hosts to humans and other mammalian hosts. In order to address the potential of WNV being introduced into Mexico City, we have determined the identity and spatial distribution of Culex pipiens complex mosquitoes and their hybrids. RESULTS: Mosquito larvae collected from 103 sites throughout Mexico City during 2004-2005 were identified as Culex, Culiseta or Ochlerotatus by morphological analysis. Within the genus Culex, specimens were further identified as Culex tarsalis or as belonging to the Culex pipiens complex. Members of the Culex pipiens complex were separated by measuring the ratio of the dorsal and ventral arms (DV/D ratio) of the male genitalia and also by using diagnostic primers designed for the Ace.2 gene. Culex pipiens quinquefasciatus was the most abundant form collected. CONCLUSIONS: Important WNV vectors species, Cx. p. pipiens, Cx. p. quinquefasciatus and Cx. tarsalis, are all present in Mexico City. Hybrids of Cx. p. pipiens and Cx. p. quinquefasciatus were also collected and identified. The presence and abundance of these WNV competent vectors is a cause for concern. Understanding the distribution of these vectors can help improve viral surveillance activities and mosquito control efforts in Mexico City.

Dataset Information

A Draft Genome Assembly of Culex pipiens pallens (Diptera: Culicidae) Using PacBio Sequencing.

Publications

A Draft Genome Assembly of Culex pipiens pallens (Diptera: Culicidae) Using PacBio Sequencing.

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