Mitochondrial genomes of Anopheles arabiensis, An. gambiae and An. coluzzii show no clear species division

Hanemaaijer, Mark J.; Houston, Parker D.; Collier, Travis C.; Norris, L. C.; Fofana, Abdrahamane; Lanzaro, Gregory C.; Cornel, Anthony J.; Y, Lee

doi:10.12688/f1000research.13807.1

Cited by 13 publications

(12 citation statements)

References 32 publications

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“…Some species groups and complexes clustered into well-supported clades using COI, which is consistent with widespread use of COI as a good discriminator at the approximate level of species groups ( 26 , 30 , 31 ). However, some sequences were clustered in exclusive clades without any recognized species included in them (clades H-L in Figure 3 ).…”

Section: Resultssupporting

confidence: 80%

“…However, reliance on mitochondrial loci for species relatedness could be problematic for mosquitoes because researchers have demonstrated the lack of species-specific markers in the An. gambiae complex ( 31 ) or different gene genealogies between mitochondrial and nuclear markers in other mosquito species such as Ae. aegypti ( 32 ).…”

Section: Introductionmentioning

confidence: 99%

“…For this reason, the internal transcribed spacer 2 (ITS2) ribosomal region could be used an alternative target in the nuclear genome for species identification. In the Anopheles gambiae complex, ITS2 experiences a higher rate of divergence than COI and has better discriminating power for phylogenetic relationships at the level of species complexes ( 31 , 33 ). The use of these complementary targets also allows for a fuller picture of phylogenetic relationships, with COI representing mitochondrial/maternal inheritance and ITS2 reflecting nuclear inheritance ( 24 ).…”

Section: Introductionmentioning

confidence: 99%

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Multiple Novel Clades of Anopheline Mosquitoes Caught Outdoors in Northern Zambia

Jones¹,

Ciubotariu²,

Muleba³

et al. 2021

Front. Trop. Dis

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Residual vector populations that do not come in contact with the most frequently utilized indoor-directed interventions present major challenges to global malaria eradication. Many of these residual populations are mosquito species about which little is known. As part of a study to assess the threat of outdoor exposure to malaria mosquitoes within the Southern and Central Africa International Centers of Excellence for Malaria Research, foraging female anophelines were collected outside households in Nchelenge District, northern Zambia. These anophelines proved to be more diverse than had previously been reported in the area. In order to further characterize the anopheline species, sequencing and phylogenetic approaches were utilized. Anopheline mosquitoes were collected from outdoor light traps, morphologically identified, and sent to Johns Hopkins Bloomberg School of Public Health for sequencing. Sanger sequencing from 115 field-derived samples yielded mitochondrial COI sequences, which were aligned with a homologous 488 bp gene segment from known anophelines (n = 140) retrieved from NCBI. Nuclear ITS2 sequences (n = 57) for at least one individual from each unique COI clade were generated and compared against NCBI’s nucleotide BLAST database to provide additional evidence for taxonomical identity and structure. Molecular and morphological data were combined for assignment of species or higher taxonomy. Twelve phylogenetic groups were characterized from the COI and ITS2 sequence data, including the primary vector species Anopheles funestus s.s. and An. gambiae s.s. An unexpectedly large proportion of the field collections were identified as An. coustani and An. sp. 6. Six phylogenetic groups remain unidentified to species-level. Outdoor collections of anopheline mosquitoes in areas frequented by people in Nchelenge, northern Zambia, proved to be extremely diverse. Morphological misidentification and underrepresentation of some anopheline species in sequence databases confound efforts to confirm identity of potential malaria vector species. The large number of unidentified anophelines could compromise the malaria vector surveillance and malaria control efforts not only in northern Zambia but other places where surveillance and control are focused on indoor-foraging and resting anophelines. Therefore, it is critical to continue development of methodologies that allow better identification of these populations and revisiting and cleaning current genomic databases.

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Section: Resultssupporting

confidence: 80%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Multiple Novel Clades of Anopheline Mosquitoes Caught Outdoors in Northern Zambia

Jones¹,

Ciubotariu²,

Muleba³

et al. 2021

Front. Trop. Dis

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“…Dataset 1. Aligned FASTA file of mitogenome samples 10.5256/f1000research.13807.d192892 ( Hanemaaijer et al ., 2018)…”

Section: Data Availabilitymentioning

confidence: 99%

Mitochondrial genomes of Anopheles arabiensis, An. gambiae and An. coluzzii show no clear species division

et al. 2019

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Here we report the complete mitochondrial sequences of 70 individual field collected mosquito specimens from throughout Sub-Saharan Africa. We generated this dataset to identify species specific markers for the following Anopheles species and chromosomal forms: An. arabiensis, An. coluzzii (The Forest and Mopti chromosomal forms) and An. gambiae (The Bamako and Savannah chromosomal forms). The raw Illumina sequencing reads were mapped to the NC_002084 reference mitogenome sequence. A total of 783 single nucleotide polymorphisms (SNPs) were detected on the mitochondrial genome, of which 460 are singletons (58.7%). None of these SNPs are suitable as molecular markers to distinguish among An. arabiensis, An. coluzzii and An. gambiae or any of the chromosomal forms. The lack of species or chromosomal form specific markers is also reflected in the constructed phylogenetic tree, which shows no clear division among the operational taxonomic units considered here.

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“…As for the consensus mitochondrial genomes, we compared them to NCBI available genomes, some of which were published mitochondrial phylogenies of species in the An. gambiae complex (Beard et al 1993;Peng et al 2016;Hanemaaijer et al 2018) and An. funestus complex (Hua et al 2016;Peng et al 2016;Jones et al 2018;Liu et al 2019;Small et al 2020), and created maximum likelihood trees using MAFFT and FastTree incorporating both present-day samples and historic specimens (Supplementary Figure S8, S9).…”

Section: Discussionmentioning

confidence: 99%

A minimally morphologically destructive approach for DNA retrieval and whole genome shotgun sequencing of pinned historic Dipteran vector species

Korlević

McAlister

Mayho

et al. 2021

Preprint

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Museum collections contain enormous quantities of insect specimens collected over the past century, covering a period of increased and varied insecticide usage. These historic collections are therefore incredibly valuable as genomic snapshots of organisms before, during, and after exposure to novel selective pressures. However, these samples come with their own challenges compared to present-day collections, as they are fragile and retrievable DNA is low yield and fragmented. In this paper we tested several DNA extraction procedures across pinned historic Diptera specimens from four disease vector genera: Anopheles, Aedes, Culex and Glossina. We identify an approach that minimizes morphological damage while maximizing DNA retrieval for Illumina library preparation and sequencing that can accommodate the fragmented and low yield nature of historic DNA. We identify several key points in retrieving sufficient DNA while keeping morphological damage to a minimum: an initial rehydration step, a short incubation without agitation in a low salt Proteinase K buffer, and critical point drying of samples post-extraction to prevent tissue collapse caused by air drying. The suggested method presented here provides a solid foundation for exploring the genomes and morphology of historic Diptera collections.

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Mitochondrial genomes of Anopheles arabiensis, An. gambiae and An. coluzzii show no clear species division

Abstract: Here we report the complete mitochondrial sequences of 70 individual field collected mosquito specimens from throughout Sub-Saharan Africa. We generated this dataset to identify species specific markers for the following species and chromosomal forms:

Cited by 13 publications

References 32 publications

Multiple Novel Clades of Anopheline Mosquitoes Caught Outdoors in Northern Zambia

Multiple Novel Clades of Anopheline Mosquitoes Caught Outdoors in Northern Zambia

Mitochondrial genomes of Anopheles arabiensis, An. gambiae and An. coluzzii show no clear species division

A minimally morphologically destructive approach for DNA retrieval and whole genome shotgun sequencing of pinned historic Dipteran vector species

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