Posts Tagged ‘genome evolution’

Pushing to the Limit

September 26th, 2010

Encephalitozoon intestinalisThe microsporidia are spore-forming unicellular fungal parasites, causing chronic, debilitating diseases to their animal hosts (human, insects, crustaceans, fish). These highly adapted fungi are characterized by a severe reduction, or even absence, of cellular components typical of eukaryotes such as mitochondria, Golgi apparatus and flagella. Lacking mitochondria and peroxysomes, these unicellular eukaryotes were first considered a deeply branching protist lineage, but they are now affiliated to the Fungi. These features previously recognized as primitive are instead highly derived adaptations to their obligate parasitic lifestyle (Corradi et al., 2009).

In the first issue of Nature Communications, Keeling’s group reports the genomic sequence of the microsporidian Encephalitozoon intestinalis. Its genome is extremely compacted with 2.3 Mbp — a 20% reduction from the  already severely reduced 2.9 Mbp genome of E. cuniculi. DNA was isolated from 500 million purified spores and used for Illumina sequencing, from which the entire genome was assembled de novo, resulting in an assembly of 137 scaffolds with an average coverage of 40×. The two species share a conserved gene content (~1,800 versus 2,000 protein-coding genes), order and density over most of their sequences. The majority of the size difference is due to gene loss, the protein-coding capacity of the two genomes is however very similar because most of the genes that are absent in E. intestinalis are duplicates of genes that were retained, or unidentified ORFs. Genome compaction is also reflected by reduced intergenic spacers and by the shortness of most putative proteins relative to their eukaryote orthologues. The exceptions are the subtelomeric regions, where E. intestinalis chromosomes are missing large gene blocks of sequence found in E. cuniculi. In the remaining gene-dense chromosome ‘cores’, the diminutive intergenic sequences and introns are actually more highly conserved than the genes themselves, suggesting that they have reached the limits of reduction for a fully functional genome … ‘getting rid of everything that is not essential for gene function’

Corradi N. et al. The complete sequence of the smallest known nuclear genome from the microsporidian Encephalitozoon intestinalis. Nature Communications 1, 78, doi:10.1038/ncomms1079

Katinka, M. D. et al. Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi . Nature 414, 450453 (2001).

Photo: Encephalitozoon intestinalis, ©

Genome Of Irish Potato Famine Pathogen Decoded

September 20th, 2009


A large international research team lead by Sophien Kamoun (Sainsbury Lab) and the Broad Institute (Brian Haas & Chad Nusbaum et al.) has decoded the genome of Phytophthora infestans that triggered the Irish potato famine in the mid-19th century and now threatens this season’s tomato and potato crops. This water mold, which is more closely related to the malaria parasite than to fungi, thrives in cool, wet weather, and can infect potatoes, tomatoes and other related plants, causing a “late blight” disease that can decimate entire fields in just a few days.

The genome sequence was reported in Nature. The genome of this fungus-like Oomycete — related to brown algae — is very large (~240 Mb; other species in the Phytophthora genus have less than 100 Mb). The genome analysis revealed a ‘two-speed’ genome, meaning that different parts of the genome are evolving at different rates. The pathogen can adapt rapidly to the plant immune system thanks to its genomic features including:

  • alternating repeat-rich (and gene-poor) regions and gene-dense regions;
  • gene-dense regions are shared among other Phytophthora species, preserved over millions of years of evolution, whereas the repeat-rich regions are undergoing relatively rapid changes;
  • The repeat-rich regions contain fewer genes compared to other genomic regions, yet those genes they do contain are enriched for those that play crucial roles in plant infection. The latter include small secreted proteins with a RXLR motif involved in the in planta targeting and CRN genes.

Further studies of these pathogenesis-related effectors will foster a deeper understanding of plant infection and help identify potential targets for environment-friendly protection treatments.

You can also listen to Sophien discuss his work in the September 10 issue Nature Podcast. He provides some good background and makes some suggestions as to how the genome can help with protecting potatoes.

Supernumerary chromosomes in a root-rot fungus

September 20th, 2009

lascaux_horseFungal interactions with plant roots are of major ecological and economic importance. They include beneficial interactions, such as the mutualistic mycorrhizal symbiosis, but also numerous detrimental interactions induced by soilborne pathogens. The root-rot pathogenic fungus Nectria haematococca, belonging to the ‘‘Fusarium solani species complex’’, is a common soil saprotroph and plant pathogen also causing opportunistic infections in animals, including man. F. solani is also damaging the prehistorical paintings of the caves at Lascaux. The ecological and host diversity of the fungus N. haematococca has been shown to be due in part to unique genes on different supernumerary chromosomes. These “extra” chromosomes are called “conditionally dispensable” (CD) chromosomes because while they are not required for axenic growth, they may allow isolates to have an expanded host range. The PDA1-CD chromosome carries a cluster of genes for pea pathogenicity. The 54 Mb genome of N. haematococca has been sequenced by the Joint Genome Institute and a paper in PLoS Genetics reports the major features of this genome. The current study reveals that it has one of the largest fungal genomes (15,707 genes), which may be related to its habitat diversity, and describes two additional supernumerary chromosomes. Two classes of genes were identified that have contributed to gene expansion: 1) lineage-specific genes (that are not found in other fungi), and 2) genes that are present as multiple copies in N. haematococca but commonly occur as a single copy in other fungi. Some of these genes have properties suggesting their acquisition by horizontal gene transfer. VanEtten and his colleagues showed that the three supernumerary chromosomes are different from the normal chromosomes; they contain more repeat sequences, are particularly enriched in unique and duplicated genes, and have a lower G+C content. In addition, the biochemical functions encoded by genes on these chromosomes suggest they may be involved in niche adaptation. The authors speculated that the dispensable nature and possession of habitat-determining genes by these chromosomes make them the biological equivalent of bacterial plasmids. It is likely advantageous for a root pathogen to be more competitive in the rhizosphere prior to its entry into the roots of its host.