The origins of apicomplexan sequence innovation
- James Wasmuth1,
- Jennifer Daub1,
- José Manuel Peregrín-Alvarez1,
- Constance Ann Marjory Finney2 and
- John Parkinson3,4
- 1 Hospital for Sick Children, Toronto;
- 2 McLaughlin-Rotman Centre for Global Health, University of Toronto;
- 3 Hospital for Sick Children
- E-mail: jparkin{at}sickkids.ca
Abstract
The Apicomplexa are a group of phylogenetically related parasitic protists that include Plasmodium, Cryptosporidium and Toxoplasma. Together they are a major global burden on human health and economics. To meet this challenge, several international consortia have generated vast amounts of sequence data for many of these parasites. Here we exploit these data to perform a systematic analysis of protein family and domain incidence across the phylum. A total of 87,736 protein sequences were collected from 15 apicomplexan species. These were compared to three protein databases, including the partial genome database, PartiGeneDB, which increases the breadth of taxonomic coverage. From these searches we constructed taxonomic profiles which reveal the extent of apicomplexan sequence diversity. Sequences without a significant match outside the phylum were denoted as apicomplexan-specialized. These were collated into 9,134 discrete protein families and placed in the context of the apicomplexan phylogeny, identifying the putative origin of each family. Most apicomplexan families were associated with an individual genus or species. Interestingly, many genera-specific innovations were associated with specialized host cell invasion and/or parasite survival processes. Contrastingly, those families reflecting more ancestral relationships were enriched in generalized housekeeping functions such as translation and transcription that have diverged within the apicomplexan lineage. Protein domain searches revealed 192 domains not previously reported in apicomplexans together with a number of novel domain combinations. We highlight domains that may be important to parasite survival.
Footnotes
-
- Received July 16, 2008.
- Accepted March 31, 2009.
- Copyright © 2009, Cold Spring Harbor Laboratory Press
