A near-chromosome level genome assembly of Anopheles stephensi

BioRxiv : the Preprint Server for Biology
A. R. ChidaSubhashini Srinivasan


Mosquito-borne diseases remain a major healthcare risk to growing economies like India. A chromosome-level quality reference genome of Anopheles stephensi, the vector causing malaria, is one of the prerequisites for successful management of malaria in India using state-of-the-art genetic technologies, such as gene editing or gene drive. Here, we describe a method to improve the publicly accessible assembly of the genomes of both Indian and Pakistani (SDA-500) strains of An. stephensi using a homology-based iterative approach. We have improved the assembly of one strain by using simulated mate-pair reads of incrementally increasing insert sizes from the other strain iteratively. The L50 for the Indian variety was improved from 37 to 9 after the iterations. From the scaffolds adding up to 214 Mb after the iterative approach, 180 Mb were placed onto chromosomes resulting in an assembly with an L50 of 2. The percent Ns (unspecified nucleotides A, C, G or T) for Indian strain remains low at 6.9 percent and based on the gene annotation/synteny, the genome is roughly more than 85% complete. There are 21,378 predicted proteins from IndV3s, of which 12,148 are validated using transcriptome and/or orthology to other proteomes. There are ...Continue Reading

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