Although photographs of the BAC in situ hybridizations have been archived, the initial physical mapping of scaffolds was based on the assignment of BAC clones to lettered subdivisions in the polytene chromosome complement. This resulted in some ambiguity in physical map assignments and in orientation, particularly of the shorter scaffolds. In the initial MOZ1 assembly, 30 of the largest scaffolds (187,844,042 bp) were mapped and oriented and an additional 112 scaffolds were mapped but not oriented (45,266,526 bp), for a total of 84% of the assembly sequence having a formal map assignment. In some instances, more than one small scaffold mapped to the same lettered subdivision, in which case order and possibly orientation were assigned arbitrarily. The remaining 8845 unmapped scaffolds were arbitrarily assigned to an 'unmapped chromosome.' The MOZ1 assembly was the subject of the initial genome annotation described in Holt et al. (2002), and the assembly and associated annotation were displayed on the EBI/Sanger Ensembl Genome Browser on 29 May 2002.

The first update to the MOZ1 assembly, MOZ2 involved the results of a concerted effort to correct some of the ambiguities in scaffold map locations and orientations by manual analysis of the archived BAC chromosome hybridization photographs and by the hybridization of a small number of new BAC clones selected to resolve questions of scaffold orientation. The new AGP file, and early draft of which was first displayed on the A. gambiae genome poster published in the 4 October 2002 issue of Science, formed the basis of a new annotation and gene build displayed on 1 October 2003 (MOZ2) (Mongin et al. 2004). This assembly was also 278 Mb. The automated Ensembl gene-building system was used, repeated sequence elements and regions of low complexity were masked, coding regions were identified using BLAST and ESTs were mapped to the genome.

Genome Size (bp): 
Scaffold count: 
8 987
Release date: 
Wednesday, October 1, 2003


The Anopheles gambiae PEST strain was chosen for genome sequencing because it had both a fixed, standard chromosomal arrangement and a sex-linked pink eye mutation that could readily be used as an indicator of cross-colony contamination. The pink eye mutation originated in a colony called A. gambiae LPE established in 1951 at the London School of Hygiene and Tropical Medicine from mosquitoes collected in Lagos, Nigeria.

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 Downloads for this assembly