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1.  The genome of the simian and human malaria parasite Plasmodium knowlesi 
Nature  2008;455(7214):799-803.
Plasmodium knowlesi is an intracellular malaria parasite whose natural vertebrate host is Macaca fascicularis (the ‘kra’ monkey); however, it is now increasingly recognized as a significant cause of human malaria, particularly in southeast Asia1,2. Plasmodium knowlesi was the first malaria parasite species in which antigenic variation was demonstrated3, and it has a close phylogenetic relationship to Plasmodium vivax​4, the second most important species of human malaria parasite (reviewed in ref. 4). Despite their relatedness, there are important phenotypic differences between them, such as host blood cell preference, absence of a dormant liver stage or ‘hypnozoite’ in P. knowlesi, and length of the asexual cycle (reviewed in ref. 4). Here we present an analysis of the P. knowlesi (H strain, Pk1(A+) clone5) nuclear genome sequence. This is the first monkey malaria parasite genome to be described, and it provides an opportunity for comparison with the recently completed P. vivax genome4 and other sequenced Plasmodium genomes6-8. In contrast to other Plasmodium genomes, putative variant antigen families are dispersed throughout the genome and are associated with intrachromosomal telomere repeats. One of these families, the KIRs9, contains sequences that collectively match over one-half of the host CD99 extracellular domain, which may represent an unusual form of molecular mimicry.
doi:10.1038/nature07306
PMCID: PMC2656934  PMID: 18843368
2.  The genome of the social amoeba Dictyostelium discoideum 
Eichinger, L. | Pachebat, J.A. | Glöckner, G. | Rajandream, M.-A. | Sucgang, R. | Berriman, M. | Song, J. | Olsen, R. | Szafranski, K. | Xu, Q. | Tunggal, B. | Kummerfeld, S. | Madera, M. | Konfortov, B. A. | Rivero, F. | Bankier, A. T. | Lehmann, R. | Hamlin, N. | Davies, R. | Gaudet, P. | Fey, P. | Pilcher, K. | Chen, G. | Saunders, D. | Sodergren, E. | Davis, P. | Kerhornou, A. | Nie, X. | Hall, N. | Anjard, C. | Hemphill, L. | Bason, N. | Farbrother, P. | Desany, B. | Just, E. | Morio, T. | Rost, R. | Churcher, C. | Cooper, J. | Haydock, S. | van Driessche, N. | Cronin, A. | Goodhead, I. | Muzny, D. | Mourier, T. | Pain, A. | Lu, M. | Harper, D. | Lindsay, R. | Hauser, H. | James, K. | Quiles, M. | Babu, M. Madan | Saito, T. | Buchrieser, C. | Wardroper, A. | Felder, M. | Thangavelu, M. | Johnson, D. | Knights, A. | Loulseged, H. | Mungall, K. | Oliver, K. | Price, C. | Quail, M.A. | Urushihara, H. | Hernandez, J. | Rabbinowitsch, E. | Steffen, D. | Sanders, M. | Ma, J. | Kohara, Y. | Sharp, S. | Simmonds, M. | Spiegler, S. | Tivey, A. | Sugano, S. | White, B. | Walker, D. | Woodward, J. | Winckler, T. | Tanaka, Y. | Shaulsky, G. | Schleicher, M. | Weinstock, G. | Rosenthal, A. | Cox, E.C. | Chisholm, R. L. | Gibbs, R. | Loomis, W. F. | Platzer, M. | Kay, R. R. | Williams, J. | Dear, P. H. | Noegel, A. A. | Barrell, B. | Kuspa, A.
Nature  2005;435(7038):43-57.
The social amoebae are exceptional in their ability to alternate between unicellular and multicellular forms. Here we describe the genome of the best-studied member of this group, Dictyostelium discoideum. The gene-dense chromosomes encode ~12,500 predicted proteins, a high proportion of which have long repetitive amino acid tracts. There are many genes for polyketide synthases and ABC transporters, suggesting an extensive secondary metabolism for producing and exporting small molecules. The genome is rich in complex repeats, one class of which is clustered and may serve as centromeres. Partial copies of the extrachromosomal rDNA element are found at the ends of each chromosome, suggesting a novel telomere structure and the use of a common mechanism to maintain both the rDNA and chromosomal termini. A proteome-based phylogeny shows that the amoebozoa diverged from the animal/fungal lineage after the plant/animal split, but Dictyostelium appears to have retained more of the diversity of the ancestral genome than either of these two groups.
doi:10.1038/nature03481
PMCID: PMC1352341  PMID: 15875012
3.  A Re-Annotation of the Saccharomyces Cerevisiae Genome 
Discrepancies in gene and orphan number indicated by previous analyses suggest that S. cerevisiae would benefit from a consistent re-annotation. In this analysis three new genes are identified and 46 alterations to gene coordinates are described. 370 ORFs are defined as totally spurious ORFs which should be disregarded. At least a further 193 genes could be described as very hypothetical, based on a number of criteria. It was found that disparate genes with sequence overlaps over ten amino acids (especially at the N-terminus) are rare in both S. cerevisiae and Sz. pombe. A new S. cerevisiae gene number estimate with an upper limit of 5804 is proposed, but after the removal of very hypothetical genes and pseudogenes this is reduced to 5570. Although this is likely to be closer to the true upper limit, it is still predicted to be an overestimate of gene number. A complete list of revised gene coordinates is available from the Sanger Centre (S. cerevisiae reannotation: ftp://ftp/pub/yeast/SCreannotation).
doi:10.1002/cfg.86
PMCID: PMC2447204  PMID: 18628908

Results 1-3 (3)