Jumbled Genomes: Missing Apicomplexan Synteny

Abstract

Whole-genome comparisons provide insight into genome evolution by informing on gene repertoires, gene gains/losses, and genome organization. Most of our knowledge about eukaryotic genome evolution is derived from studies of multicellular model organisms. The eukaryotic phylum Apicomplexa contains obligate intracellular protist parasites responsible for a wide range of human and veterinary diseases (e.g., malaria, toxoplasmosis, and theileriosis). We have developed an in silico protein-encoding gene based pipeline to investigate synteny across 12 apicomplexan species from six genera. Genome rearrangement between lineages is extensive. Syntenic regions (conserved gene content and order) are rare between lineages and appear to be totally absent across the phylum, with no group of three genes found on the same chromosome and in the same order within 25 kb up- and downstream of any orthologous genes. Conserved synteny between major lineages is limited to small regions in Plasmodium and Theileria/Babesia species, and within these conserved regions, there are a number of proteins putatively targeted to organelles. The observed overall lack of synteny is surprising considering the divergence times and the apparent absence of transposable elements (TEs) within any of the species examined. TEs are ubiquitous in all other groups of eukaryotes studied to date and have been shown to be involved in genomic rearrangements. It appears that there are different criteria governing genome evolution within the Apicomplexa relative to other well-studied unicellular and multicellular eukaryotes.

Parasite Calcineurin Regulates Host Cell Recognition and Attachment by Apicomplexans

“…and T. gondii have diverged substantially since descent from a last common ancestor (DeBarry and Kissinger, 2011). Nevertheless, these parasite species share many features in their styles of host cell invasion, including the use of secretory proteins for a specific and strong host cell attachment followed by an active process of intracellular entry (Carruthers and Tomley, 2008).…”

The kinomes of apicomplexan parasites

“…Since these genes lack orthologues outside of the Apicomplexa, they must either have been created de novo or have evolved beyond recognition. The genomes of the Apicomplexa are highly dynamic [110] and besides large gene gains and losses, they also include large genome rearrangements. Gene losses and genomic rearrangements complicate the detection of syntenic relationships across apicomplexan genomes, a useful measure in less dynamic genomes of the extent of divergence that has taken place since the species last shared a common ancestor.…”

“…Limited synteny is conserved only between Plasmodium spp. and Theileria and Babesia, which clusters haemosporidians and piroplasmids together, followed by Toxoplasma and Cryptosporidium [109,110]. However, synteny is only informative as to the overall conservation of genome structure, but not about orthologue conservation.…”

An evolutionary perspective on the kinome of malaria parasites

“…(c) Kinase gene architecture Another striking feature of Plasmodium evolution is the remarkably high rate of genomic rearrangement [97]. In protein kinase genes, this phenomenon contributes to variation in protein domain architecture.…”