Entamoeba histolytica (strain HM-1:IMSS), was the first human amoeba to have its genome sequenced, assembled and analyzed. Whole genome shotgun sequencing with small insert libraries was used to carry out sequencing to a 12.5-fold coverage. The sequencing project was a collaborative effort between JCVI (TIGR) and The Sanger Institute.

The exact number of chromosomes in E. histolytica is uncertain due to difficulties in condensing and resolving them by pulse-field gel electrophoresis. Approximately 9,938 predicted genes with an average size of 1.17 kb, comprise 49% of the genome. One third of this organism's predicted proteins (31.8%) do not have identifiable sequence homologues in other species.

The whole genome shotgun sequence data from E. histolytica strain HM-1:IMSS has been deposited in GenBank. The current version of the project (02) has the accession number AAFB02000000, consists of 1529 scaffolds DS571145-DS572673 and represents 8x coverage of the genome.

This sequencing project was completed by a collaboration between JCVI (TIGR) and the Sanger Institute.