Anopheles atroparvus Assembly and Gene Annotation

About Anopheles atroparvus

Range

Anopheles atroparvus belongs to the A. maculipennis species complex. Anopheles atroparvus is distributed in northern and western Europe, Spain, Portugal and northern Italy and was one of the main malaria vectors in Europe.

Habitats

An. atroparvus is described as a species with a preference for brackish larval habitats, however, it has been found in a number of predominantly fresh water habitats as well. For example larvae have been found in canals, ditches, river margins, pools in river beds and rice fields. Larvae have been identified in marshes and ditches/ ground flood pools, pools in river beds, river margins and streams, rock pools, cement tanks, rice fields, wells and ground pools and in small collections of water in used tyres. It prefers relatively cool water, and therefore its range is not considered to overlap with An. labranchiae. Sites may usually be sun exposed and often contain filamentous green algae and other floating submerged vegetation.

Resting and feeding preferences

An. atroparvus is generally considered zoophilic, however, it has also been described as anthropophilic, which perhaps indicates the opportunistic nature of this species. Collection of An. atroparvus has been reported during night catches on horse bait, from indoor resting sites and during day- or night-time catches on humans. There is no clear evidence that identifies this species as preferentially biting indoors or outdoors. The opportunistic nature of its feeding habits and zoophilic preference, however, would suggest it is probably exophagic but that biting location could also depend upon the setting and accessibility of the host. An. atroparvus rests and hibernates in animal sheds and stables.

Vectorial capacity

An. atroparvus is largely unable to transmit tropical strains of Plasmodium falciparum but competent in supporting a European strain.

This text was modified from Sinka ME et al. (2010) The dominant Anopheles vectors of human malaria in Africa, Europe and the Middle East: occurrence data, distribution maps and bionomic précis Parasites & Vectors 3:117.

EBRO strain

Originally isolated from Spain, isofemale selection was performed prior to genome sequencing. For more details click here.

Source: VectorBase

AatrE3 assembly

This assembly is a recaffolding of the AatrE1 assembly using in situ hybridization of genomic scaffolds and synteny information from the paper
"Partial-arm translocations in evolution of malaria mosquitoes revealed by high- coverage physical mapping of the Anopheles atroparvus genome
", Artemov et al, BMC Genomics. The assembly differs from the Aatre2 version by the inclusion of spacer sequences between scaffolds, and the presence of a 1MB gap of chromosome 2L. No sequences have changed, and the order of assembly components remains the same as Aaetr2. In all 201MB (89.6% of the genome) and 56 scaffolds were anchored to chromosomes, leaving 1,315 scaffolds (10.4% of the genome assembly) unmapped.

The original Aaetr1 assembly was generated using 101 bp paired-end Illumina HiSeq2000 reads generated from three libraries: a 180 bp insert 'fragment' library, a 1.5 kb 'jump' library, and a 38 kb 'fosill' library. Sequencing template for the fragment and jump libraries was derived from genomic DNA extracted from a single individual, which was preserved by freezing at -80C. Native genomic DNA was used for the fragment library and whole genome amplified DNA was used for the jump library. Template for the fosill library was generated from a pooled extraction of many individuals. Reads were assembled at the Broad Institute using the ALLPATHS LG algorithm, with the Haploidify option enabled to address high allelic heterozygosity in the template.

AatrE3.2 gene set

Community annotation patch build for July 2019.

References

1. Partial-arm translocations in evolution of malaria mosquitoes revealed by high-coverage physical mapping of the Anopheles atroparvus genome.
   Artemov GN, Bondarenko SM, Naumenko AN, Stegniy VN, Sharakhova MV, Sharakhov IV.. 2018. BMC Genomics. 19(1):278.
2. The dominant Anopheles vectors of human malaria in Africa, Europe and the Middle East: occurrence data, distribution maps and bionomic prcis.
   Sinka ME, Bangs MJ, Manguin S, Coetzee M, Mbogo CM, Hemingway J, Patil AP, Temperley WH, Gething PW, Kabaria CW et al. 2010. Parasit Vectors. 3:117.

Picture credit: VectorBase.org