Jane Carlton PhD, Associate Professor; Adjunct Investigator, The Institute for Genome Research; Adjunct Research Associate, American Museum of Natural History

My Lab Group

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Comparative genomics is a large-scale approach to comparing genomes from two or more species, sub-species or strains of the same species, to discover the similaritites and differences between the genomes and to further understanding of the biology and evolution of the species, using a combination of bioinformatics, genomics, molecular evolution and molecular biology techniques.

The focus of the Carlton lab is on comparative genomics of eukaryotic parasites. In particular, we use bioinformatics and computational biology, in combination with genomics and wet-lab experiments, to study the evolution of whole genomes.

The parasitic protists that we study include species of the malaria parasite Plasmodium, and species of other apicomplexans such as Cryptosporidium. We also study species of trichomonad, lumenal parasites which cause a variety of diseases, e.g. human trichomoniasis which is caused by the sexually transmitted pathogen Trichomonas vaginalis.

Comparative Genomics of Plasmodium

More than eight species of Plasmodium are in the closing stages of sequencing, and draft sequences for four have been published, representing one of the largest datasets for a single eukaryotic pathogen (Table 1). The species are as follows: two species of human malaria parasite, P. falciparum and P. vivax; three species of rodent malaria P. berghei, P. chabaudi chabaudi and P. yoelii yoelii; a monkey malaria species P. knowlesi; a parasite of chimpanzees P. reichenowi; and a bird malaria parasite P. gallinaceum. In addition, several field isolates and additional lab clones of P. falciparum have recently been published [1]. Completion of sequencing, annotation and release of the data are expected for the majority of unpublished genomes over the next several years.

Table 1. Characteristics of eight Plasmodium genome datasets.
Abbreviations: NK: not known; In prep: in preparation; TIGR: The Institute for Genomic Research; Sanger: The Wellcome Trust Sanger Institute; U. S.: Stanford University. * an overestimate due to the partial nature of the genome data

We are taking advantage of this large amount of sequence data from a pathogen that is a serious threat to human health, and by using comparative genomics including evolutionary biology and population genetics, addressing broad questions that may be of relevance to other infectious diseases. For example:

• How does Plasmodium whole genome structure and organization evolve?
• How does this affect the biology of the parasite?
• How does selective constraint vary across Plasmodium chromosomes?
• What patterns or motifs can be identified by comparing non-coding regions of Plasmodium species?

The neglected pathogen Plasmodium vivax is of special interest to the Carlton group. The project to sequence the genome of the parasite is close to completion, and our lab are leading analysis of the sequence data with a view to publishing the completed project in the early part of 2007. A one-stop resource for the malaria research community with information on P. vivax malaria incidence, biology, history, genomics, outstanding research issues, resources and meetings is being maintained by the Carlton group at: http://www.vivaxmalaria.com

Genome Variation, Population Genetics and Association Mapping of Infectious Disease Organisms

The Carlton lab is also involved in the identification of polymorphic genetic markers in the genomes of infectious disease organisms, for genome diversity studies, population genetics, and association mapping of phenotypes such as drug resistance. For example, in collaboration with Dr. Xin-zhuan Su at NIH, we have undertaken a preliminary study of the genetic diversity of P. vivax, as a means of determining the type and frequency of repeats in the genome that might be used for genotyping studies, and as a preliminary comparative analysis with P. falciparum to determine if orthologous genes between malaria species are under the same selective constraints [6]. A 100 kb chromosome segment of P. vivax syntenic to P. falciparum chromosome 3 and containing 26 orthologous genes was sequenced from five P. vivax strains. Polymorphic tandem repeats (TRs) consisting of two to three imperfect repeating units of five nucleotides or greater, were found to be abundant, making them potentially useful as markers for population studies.

Agarose gel of five P. vivax microsatellites amplified from eight different lab isolates. Note the extreme polymorphism of the third microsatellite marker.

Subsequently, the whole genome sequence of P. vivax which is close to completion, has been scanned by members of my lab for microsatellites (MS). All MS have been amplified from eight P. vivax lab isolates, and are being used for several purposes: (1) to genotype chloroquine (CQ) resistant and CQ sensitive isolates for identification of CQ resistance gene(s) by association mapping; and (2) as markers to determine the population structure (linkage disequilibrium, diversity, population subdivision) of populations of P. vivax. Studies have already been published using some of these markers [7].

Comparative Genomics of Trichomonads

Parabasalids are a fascinating lineage of organisms several of which cause disease. Probably the most important in this regard are Trichomonas vaginalis, a sexually transmitted human pathogen, Trichomonas tenax an oral parasite, Pentatrichomonas hominis found in the intestine, and Tritrichomonas foetus, a cause of reproductive disease in cattle. T. vaginalis causes ~5 million cases of ‘trich’ in the U.S per year, and besides causing vaginitis, it is associated with increased risk of HIV-1 acquisition and a range of pregnancy-associated problems such as pre-term delivery of babies.

The paper describing the genome project of T. vaginalis [8] generated by TIGR with funding from the National Institute of Allergy and Infectious Diseases, NIH, is to be published in the January 12, 2007 edition of Science [9]. Now that a preliminary draft of the genome is complete, the Carlton lab is starting work on several aspects of trichomonad genomics: Sequencing of additional trichomonad isolates and species Development of polymorphic markers for population and diversity studies

We are currently looking for talented researchers to join our lab and be involved in
these studies. For additional information, please contact Dr. Jane Carlton.

Developing bioinformatics and research capability in endemic countries

Much of the Carlton lab research involves analyzing the genomes of tropical disease-causing parasites. This has led to many fruitful collaborations with scientists in developing country institutions:

The Carlton lab has hosted visiting scientists from several of these labs, while obtaining access to field study sites and parasite samples. Transferring scientific knowledge through teaching and research can only benefit those peoples who are ultimately at most risk from tropical diseases.

Selected Publications

1. Imwong M, Snounou G, Pukrittayakamee S, Tanomsing N, Kim JR, Nandy A, Guthmann JP, Nosten F, Carlton J, Looareesuwan S, Nair S, Sudimack D, Day NP, Anderson TJ, White NJ. Relapses of Plasmodium vivax Infection Usually Result from Activation of Heterologous Hypnozoites. J Infect Dis. 2007 Apr 1;195(7):927-33. Epub 2007 Feb 26.
2. Carlton JM, Hirt RP, Silva JC, et al.  Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis. Science. 2007 Jan 12;315(5809):207-12. Front cover article.
3. Carlton, J.M., Toward a malaria haplotype map. Nat Genet, 2007. 39(1): p. 5-6.
4. Eisen JA, Coyne RS, Wu M, Wu D, Thiagarajan M, Wortman JR, Badger JH, Ren Q, Amedeo P, Jones KM, Tallon LJ, Delcher AL, Salzberg SL, Silva JC, Haas BJ, Majoros WH, Farzad M, Carlton JM, Smith RK, Garg J, Pearlman RE, Karrer KM, Sun L, Manning G, Elde NC, Turkewitz AP, Asai DJ, Wilkes DE, Wang Y, Cai H, Collins K, Stewart BA, Lee SR, Wilamowska K, Weinberg Z, Ruzzo WL, Wloga D, Gaertig J, Frankel J, Tsao CC, Gorovsky MA, Keeling PJ, Waller RF, Patron NJ, Cherry JM, Stover NA, Krieger CJ, Del Toro C, Ryder HF, Williamson SC, Barbeau RA, Hamilton EP, Orias E. Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote. PLoS Biol. 2006 Sep;4(9):e286.
5. Gardner, M.J., N. Hall, E. Fung, O. White, M. Berriman, R.W. Hyman, J.M. Carlton, et al., Genome sequence of the human malaria parasite Plasmodium falciparum. Nature, 2002. 419(6906): p. 498-511.
6. Carlton, J., The Plasmodium vivax genome sequencing project. Trends Parasitol, 2003. 19(5): p. 227-31.
7. Carlton, J.M., S.V. Angiuoli, B.B. Suh, T.W. Kooij, M. Pertea, J.C. Silva, M.D. Ermolaeva, et al., Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. Nature, 2002. 419(6906): p. 512-9.
8. Hall, N., M. Karras, J.D. Raine, J.M. Carlton, T.W. Kooij, M. Berriman, L. Florens, et al., A comprehensive survey of the Plasmodium life cycle by genomic, transcriptomic, and proteomic analyses. Science, 2005. 307(5706): p. 82-6.
9. Feng, X., J.M. Carlton, D.A. Joy, J. Mu, T. Furuya, B.B. Suh, Y. Wang, et al., Single-nucleotide polymorphisms and genome diversity in Plasmodium vivax. Proc Natl Acad Sci U S A, 2003. 100(14): p. 8502-7.
10. Imwong, M., D. Sudimack, S. Pukrittayakamee, L. Osorio, J.M. Carlton, N.P. Day, N.J. White, et al., Microsatellite variation, repeat array length, and population history of Plasmodium vivax. Mol Biol Evol, 2006. 23(5): p. 1016-8.
11. Lyons, E.J. and J.M. Carlton, Mind the gap: bridging the divide between clinical and molecular studies of the trichomonads. Trends Parasitol, 2004. 20(5): p. 204-7.