Afiya Raziya Chida, Samathmika Ravi, Suvratha Jayaprasad, Kiran Paul, Jaysmita Saha, Chinjusha Suresh, Saurabh Whadgar, Naveen Kumar, Raksha Rao K, Chaitali Ghosh, Bibha Choudhary, Suresh Subramani, Subhashini 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 54 olfactory receptors (ORs) compared to 42 in An. funestus and 79 in An. gambiae, displaying wider variations in number of ORs across Anopheles genera. A limited whole genome sequencing of individuals to 30X coverage from India reveals a genetic diversity of 1 mutation every 68 bases, which is 10 times more than what is reported for An. stephensi. A comparative analysis of the genomes of three Anopheles species suggests switching of chromosomal arms while displaying limited inter-chromosomal gene flow.
