title: New assembly, reannotation and analysis of the Entamoeba histolytica genome reveal new genomic features and protein content information.
abstract: BACKGROUND
  In order to maintain genome information accurately and relevantly, original genome annotations need to be updated and evaluated regularly. Manual reannotation of genomes is important as it can significantly reduce the propagation of errors and consequently diminishes the time spent on mistaken research. For this reason, after five years from the initial submission of the Entamoeba histolytica draft genome publication, we have re-examined the original 23 Mb assembly and the annotation of the predicted genes.
  
  
  RESULTS
  The evaluation of the genomic sequence led to the identification of more than one hundred artifactual tandem duplications that were eliminated by re-assembling the genome. The reannotation was done using a combination of manual and automated genome analysis. The new 20 Mb assembly contains 1,496 scaffolds and 8,201 predicted genes, of which 60% are identical to the initial annotation and the remaining 40% underwent structural changes. Functional classification of 60% of the genes was modified based on recent sequence comparisons and new experimental data. We have assigned putative function to 3,788 proteins (46% of the predicted proteome) based on the annotation of predicted gene families, and have identified 58 protein families of five or more members that share no homology with known proteins and thus could be entamoeba specific. Genome analysis also revealed new features such as the presence of segmental duplications of up to 16 kb flanked by inverted repeats, and the tight association of some gene families with transposable elements.
  
  
  CONCLUSIONS
  This new genome annotation and analysis represents a more refined and accurate blueprint of the pathogen genome, and provides an upgraded tool as reference for the study of many important aspects of E. histolytica biology, such as genome evolution and pathogenesis.
authors.affiliation: J. Craig Venter Institute, Rockville, Maryland, United States of America.
authors.forename: Hernan A
authors.initials: HA
authors.lastname: Lorenzi
authors.forename: Daniela
authors.initials: D
authors.lastname: Puiu
authors.forename: Jason R
authors.initials: JR
authors.lastname: Miller
authors.forename: Lauren M
authors.initials: LM
authors.lastname: Brinkac
authors.forename: Paolo
authors.initials: P
authors.lastname: Amedeo
authors.forename: Neil
authors.initials: N
authors.lastname: Hall
authors.forename: Elisabet V
authors.initials: EV
authors.lastname: Caler
mesh_terms: D002874:Chromosome Mapping; D019295:Computational Biology / Q000379:methods; D030541:Databases, Genetic; D004748:Entamoeba histolytica / Q000235:genetics*; D020440:Gene Duplication; D018503:Genome, Protozoan / Q000235:genetics*; D008390:Markov Chains; D011487:Protein Conformation; D015800:Protozoan Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D012091:Repetitive Sequences, Nucleic Acid; D017422:Sequence Analysis, DNA
chemical_list: D015800:Protozoan Proteins