Why are there three Anopheles gambiae (PEST,M and S)


As of October 2015 (release VB-2015-10), VectorBase is showing two genome browsers for Anopheles gambiae: PEST and Pimperena (S). The former M assembly Mali-NIH is now available as Anopheles coluzzii given it now is recognized as a new species.

The genome sequences are very similar and they mainly differ by rearrangements of their genomes (inversions etc.). About 99.3% of PEST genes have at least one exon found in the Pimperena assembly and 98.8% of PEST genes have at least one exon found in the Mali-NIH assembly.

The PEST colony that was sequenced in 2001 (Holt et al 2002) currently serves as the An. gambiae reference genome. Because the M and S forms were not yet discovered at the time, laboratory crosses between M and S colonies used to generate PEST inadvertently resulted in an M-S chimeric background. For historical reasons and given the high level of gene conservation and synteny this is still labeled as the reference.

Although the PEST colony no longer exists, the Pimperena and Mali-NIH colonies are freely available from MR4. Because of the chimeric nature of this genome and the fact that the colony is no longer available, work is ongoing to change the reference to Pimperena via a collaboration between researchers at the University of Notre Dame. University of Wisconsin, and Virginia Tech. The timeline for this new reference is 2016.