January 2013 archive

The probability of correctly resolving a split as an experimental design criterion in phylogenetics.

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The probability of correctly resolving a split as an experimental design criterion in phylogenetics.
Syst Biol. 2012 Oct;61(5):811-21
Authors: Susko E, Roger AJ
Abstract
We illustrate how rec…

Characterisation of full-length mitochondrial copies and partial nuclear copies (numts) of the cytochrome b and cytochrome c oxidase subunit I genes of Toxoplasma gondii, Neospora caninum, Hammondia heydorni and Hammondia triffittae (Apicomplexa: Sarcocystidae).

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Characterisation of full-length mitochondrial copies and partial nuclear copies (numts) of the cytochrome b and cytochrome c oxidase subunit I genes of Toxoplasma gondii, Neospora caninum, Hammondia heydorni and Hammondia triffittae (Apicomplexa: Sarcocystidae).

Parasitol Res. 2013 Jan 29;

Authors: Gjerde B

Abstract
Genomic DNA was extracted from three oocyst isolates of Hammondia triffittae from foxes and two oocyst isolates of Hammondia heydorni from dogs, as well as from cell culture-derived tachyzoites of Toxoplasma gondii (RH strain) and Neospora caninum (NC-Liverpool strain), and examined by PCR with primers targeting the cytochrome b (cytb) and the cytochrome c oxidase subunit I (cox1) genes in order to characterise both genes and, if possible, the remainder of the mitochondrial genome of these species. Several primers were designed and used in various combinations to amplify regions within and between both genes and to determine gene order. When certain forward primers targeting cytb were used in combination with certain reverse primers targeting cox1, two overlapping sequences were obtained for each species and isolate studied, which showed that a full-length copy of cytb was followed 36-37 bp downstream by a full-length copy of cox1, and these sequences are believed to represent the true mitochondrial genes and the gene order in the mitochondrial genome of the four species examined. The cytb of T. gondii, N. caninum, H. heydorni and H. triffittae comprised a total of 1,080 bp (359 amino acids) and used ATG and TAA as start and stop codon, respectively. The cox1 of these species also used TAA as stop codon, whereas the most likely start codon was ATG, resulting in a gene comprising 1,491 bp (496 amino acids). Pair-wise sequence comparisons based on either cytb or cox1 clearly separated T. gondii from N. caninum and both of these species from the two Hammondia species, whereas the latter two species were 100 % identical at cytb and shared 99.3 % identity at cox1. Phylogenetic analyses using the maximum-likelihood method confirmed these findings and placed T. gondii in a clade separate from the three other species and all four Toxoplasmatinae in a sister clade to Eimeria spp. PCR with other primers and/or primer pairs than those used to obtain the full-length mitochondrial genes yielded several types of about 1-1.5 kb long sequences, which comprised stretches of the primer-targeted genes at both ends and an intervening non-coding sequence of various length and composition. Thus, portions of cytb could be found both upstream and downstream from portions of cox1 and portions of the same gene could be found adjacent to each other (cytb→cox1; cox1→cytb; cytb→cytb; cox1→cox1). Sequence comparisons revealed that some of these gene fragments were truncated genes, whereas others included the putative start or stop codon of the full-length mitochondrial genes. From the nature of the gene fragments and/or their flanking sequences, they are assumed to be located on the chromosomes of the nuclear genome and to represent nuclear mitochondrial DNA segments (numts) or pseudogenes. In the four species examined, there were no nucleotide differences between the full-length mitochondrial copies of cytb and cox1 and their various incomplete nuclear counterparts. With a few exceptions, identical numt types and closely similar flanking sequences were obtained for all four species, which would indicate that the original transfer of these mitochondrial genes to the nuclear genome and/or the majority of any subsequent rearrangements of these gene fragments within the nuclear genome happened before the four species diverged. Yet, there were species-specific differences in the nucleotide composition of the nuclear gene fragments, identical to the differences in the mitochondrial genes, which would indicate that the incomplete nuclear copies of cytb and cox1 have been continuously updated during evolution to conform to their mitochondrial parent genes. The PCR-based findings of numts were further supported by Basic Local Alignment Search Tool (BLAST) searches against genome sequences of T. gondii and N. caninum using the concatenated mitochondrial cytb/cox1 sequences as queries. These searches revealed the presence of numerous numts of eighth distinct types in both species, with each one having a fixed starting and end point with respect to the nucleotide positions in the full-length mitochondrial genes. Four numt types were completely homologous between both species, whereas four other types differed with respect to their end point and/or the absence/presence of a 96-bp deletion. Each starting and end point was associated with a unique 100-200-bp long flanking sequence, which further revealed the presence of numts. For both species, the numt types and their various arrangements with respect to each other were identical or similar to those obtained by PCR in all four species examined. None of the identified numts covered a full-length gene, but together, the various numts covered the entire mitochondrial cytb and cox1 genes in an overlapping manner. In addition, they were fairly closely spaced on the chromosomes, and these features may explain why the nuclear copies were preferentially amplified to the exclusion of the true mitochondrial genes with most primers and primer pairs used in the present study. The possibility of a similar high prevalence of numts occurring in the nuclear genome of dinoflagellates is discussed.

PMID: 23358734 [PubMed – as supplied by publisher]

Postdoctoral position in Paris: Protist diversity and phylogeny in suboxic environments

  A postdoctoral contract of 1 year renewable up to 3 years is available in the “Microbial diversity and evolution” team at the institute of Ecology, Systematics and Evolution starting from September 2013 (dates are negotiable). The institute belongs to the French Research Council (CNRS) and the University of Paris-Sud, and is located at the …

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Evidence of purifying selection on merozoite surface protein 8 (MSP8) and 10 (MSP10) in Plasmodium spp.

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Evidence of purifying selection on merozoite surface protein 8 (MSP8) and 10 (MSP10) in Plasmodium spp.
Infect Genet Evol. 2012 Jul;12(5):978-86
Authors: Pacheco MA, Elango AP, Rahman AA, Fisher D, Collins W…

Comparative genome analysis of two Cryptosporidium parvum isolates with different host range.

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Comparative genome analysis of two Cryptosporidium parvum isolates with different host range.
Infect Genet Evol. 2012 Aug;12(6):1213-21
Authors: Widmer G, Lee Y, Hunt P, Martinelli A, Tolkoff M, Bodi K

Admixture and recombination among Toxoplasma gondii lineages explain global genome diversity.

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Admixture and recombination among Toxoplasma gondii lineages explain global genome diversity.

Proc Natl Acad Sci U S A. 2012 Aug 14;109(33):13458-63

Authors: Minot S, Melo MB, Li F, Lu D, Niedelman W, Levine SS, Saeij JP

Abstract
Toxoplasma gondii is a highly successful protozoan parasite that infects all warm-blooded animals and causes severe disease in immunocompromised and immune-naïve humans. It has an unusual global population structure: In North America and Europe, isolated strains fall predominantly into four largely clonal lineages, but in South America there is great genetic diversity and the North American clonal lineages are rarely found. Genetic variation between Toxoplasma strains determines differences in virulence, modulation of host-signaling pathways, growth, dissemination, and disease severity in mice and likely in humans. Most studies on Toxoplasma genetic variation have focused on either a few loci in many strains or low-resolution genome analysis of three clonal lineages. We use whole-genome sequencing to identify a large number of SNPs between 10 Toxoplasma strains from Europe and North and South America. These were used to identify haplotype blocks (genomic regions) shared between strains and construct a Toxoplasma haplotype map. Additional SNP analysis of RNA-sequencing data of 26 Toxoplasma strains, representing global diversity, allowed us to construct a comprehensive genealogy for Toxoplasma gondii that incorporates sexual recombination. These data show that most current isolates are recent recombinants and cannot be easily grouped into a limited number of haplogroups. A complex picture emerges in which some genomic regions have not been recently exchanged between any strains, and others recently spread from one strain to many others.

PMID: 22847430 [PubMed – indexed for MEDLINE]

Plasmodium cynomolgi genome sequences provide insight into Plasmodium vivax and the monkey malaria clade.

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Plasmodium cynomolgi genome sequences provide insight into Plasmodium vivax and the monkey malaria clade.
Nat Genet. 2012 Sep;44(9):1051-5
Authors: Tachibana S, Sullivan SA, Kawai S, Nakamura S, Kim HR, Goto…

An evolutionary perspective on the kinome of malaria parasites.

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An evolutionary perspective on the kinome of malaria parasites.
Philos Trans R Soc Lond B Biol Sci. 2012 Sep 19;367(1602):2607-18
Authors: Talevich E, Tobin AB, Kannan N, Doerig C
Abstract
Ma…

Symbiodinium transcriptomes: genome insights into the dinoflagellate symbionts of reef-building corals.

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Symbiodinium transcriptomes: genome insights into the dinoflagellate symbionts of reef-building corals.
PLoS One. 2012;7(4):e35269
Authors: Bayer T, Aranda M, Sunagawa S, Yum LK, Desalvo MK, Lindquist E, Co…

Structure of metaphase chromosomes: a role for effects of macromolecular crowding.

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Structure of metaphase chromosomes: a role for effects of macromolecular crowding.

PLoS One. 2012;7(4):e36045

Authors: Hancock R

Abstract
In metaphase chromosomes, chromatin is compacted to a concentration of several hundred mg/ml by mechanisms which remain elusive. Effects mediated by the ionic environment are considered most frequently because mono- and di-valent cations cause polynucleosome chains to form compact ~30-nm diameter fibres in vitro, but this conformation is not detected in chromosomes in situ. A further unconsidered factor is predicted to influence the compaction of chromosomes, namely the forces which arise from crowding by macromolecules in the surrounding cytoplasm whose measured concentration is 100-200 mg/ml. To mimic these conditions, chromosomes were released from mitotic CHO cells in solutions containing an inert volume-occupying macromolecule (8 kDa polyethylene glycol, 10.5 kDa dextran, or 70 kDa Ficoll) in 100 µM K-Hepes buffer, with contaminating cations at only low micromolar concentrations. Optical and electron microscopy showed that these chromosomes conserved their characteristic structure and compaction, and their volume varied inversely with the concentration of a crowding macromolecule. They showed a canonical nucleosomal structure and contained the characteristic proteins topoisomerase IIα and the condensin subunit SMC2. These observations, together with evidence that the cytoplasm is crowded in vivo, suggest that macromolecular crowding effects should be considered a significant and perhaps major factor in compacting chromosomes. This model may explain why ~30-nm fibres characteristic of cation-mediated compaction are not seen in chromosomes in situ. Considering that crowding by cytoplasmic macromolecules maintains the compaction of bacterial chromosomes and has been proposed to form the liquid crystalline chromosomes of dinoflagellates, a crowded environment may be an essential characteristic of all genomes.

PMID: 22540018 [PubMed – indexed for MEDLINE]