Anopheles atroparvus (EBRE) - GCA_914969975.1 Assembly and Gene Annotation
About Anopheles atroparvus
Anopheles atroparvus belongs to the A. maculipennis species complex. Current suitability studies indicate that habitat and climate in 21st century Europe are extensively appropriate for A. atroparvus, being distributed in northern and western Europe, Spain (including the Canary Islands), Portugal and northern Italy and was one of the main malaria vectors in Europe. However the speceis has known ranges covering: Belgium, Bosnia and Herzegovina, Bulgaria, Croatia, Czech Republic, Denmark, Estonia, France, Hungary, Latvia, Lithuania, Macedonia, Moldova, Montenegro, Poland, Romania, Russia, Serbia & Slovakia, Slovenia, Sweden and Ukraine. Anopheles atroparvus was the most abundant species of the A. maculipennis complex found in south-east England . Flight range of A. atroparvus is suggested to be at least three kilometres . A. atroparvus hibernate as adult females, often seeking shelter indoor in stables or man-made dwellings during the autumn where they can remain active .
Although research interest in A. atroparvus has been low in the past several decades, recent concern for an increase in vector-borne disease has encouraged new research into this species. The current dominant Anopheles vector species in Europe and the Mediterranean includes A. atroparvus, among other species of Anopheles. Anopheles atroparvus, the dominant vector in large parts of Europe, might play an important role with respect to changes of the potential transmission stability. Anopheles atroparvus is generally considered as primarily zoophilic, however, it has also been described as anthropophilic, with host choice dependednt on availability thus reflecting the opportunistic nature of this species. Implicated in the transmission of autochhtonous malaria in Europe via the human malaria parasite Plasmodium vivax; and known to be involved in winter transmission of malaria at the start of the twentieth century in Britain, coastal areas in the Netherlands and Germany and elsewhere in Europe. In Portugal, Anopheles atroparvus is the only mosquito species implicated in malaria transmission.
The genome assembly presented here is linked to the assembly accession [GCA_914969975.1]. This genome assembly was produced as part of the Infravec2 project to study A. atroparvus. This material sample is from A. atroparvus strain 'EBRE', made available as biological resource for distribution via the Infravec product catalog (https://infravec2.eu/). The assembly produced from a single PacBio SMRT cell (CLR) HIFI library (ERX6138161). Assembly was generated de-novo on a set of taxonomically pre-filtered genomic reads (Kraken2 ), assembled with HIFIasm v0.15  and finally examined with Blobtools  to identify and remove potential non Anopheles contaminant scaffolds.
Redudant/partial mitochondrial scaffolds were removed, retaining the single longest which was rescaffolded and fully annotated with MitoFinder . The finalised assembly is composed of 225 scaffolds, 227.7Mb (8.9% scaffolds > 1Mb; 2.7% scaffolds > 10Mb) with a scaffold N50 of 44.9Mb and an L50 of 3. Draft quality and performance assessed with comparison to a previous Infravec reference assembly for A. atroparvus (AatrE3); which itself was generated via rescaffolding of a short read Illumina assembly (AatrE1). High concordance of chromosomal sequecne overlap was observed between AatrE3 and this reference assembly.
RNA-Seq data utilized for genome annotation were obtained from publically available RNA-seq SRR826830 (PRJNA196857 - "RNA sequencing of 15 genomes of Anopheles") generated from Illumina PE sequencing of cDNA (HiSeq 2000). Genomic annotation was generated with the Ensembl gene annotation pipeline . Transcript models are supported by RNA-seq experimental evidence. Gene model layering was supported with protein-to-genome alignment of previously generated protein models from A. atroparvus assembly version GCA_000473505.1 along with experimentally verified proteins obtained from closely related Hexapoda species - (Uniprot, April 2021). The Ensembl Gene Annotation pipeline implemented transcript consensus filtration to remove unsupported alternate transcript isoforms.
Small ncRNAs were obtained using a combination of BLAST and Infernal/RNAfold. Pseudogenes were calculated by examining genes with a large percentage of non-biological introns (introns of <10bp), where the gene was covered in repeats, or where the gene was single exon and evidence of a functional multi-exon paralog was found elsewhere in the genome.
lncRNAs were generated via RNA-seq data where no evidence of protein homology or protein domains could be found in the transcript.
For in-depth overview of the Gene Annotation pipeline see detailed information here.
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|Assembly||atroparvus_hifiasm_n225_277Mb, INSDC Assembly GCA_914969975.1,|
|Golden Path Length||277,763,289|
|Data source||Ensembl Metazoa|
|Non coding genes||1,214|
|Small non coding genes||1,191|
|Long non coding genes||20|
|Misc non coding genes||3|