Open Access Highly Accessed Research article

Comparative genomic analysis and phylogenetic position of Theileria equi

Lowell S Kappmeyer1, Mathangi Thiagarajan29, David R Herndon1, Joshua D Ramsay3, Elisabet Caler2, Appolinaire Djikeng4, Joseph J Gillespie56, Audrey OT Lau37, Eric H Roalson8, Joana C Silva6, Marta G Silva1, Carlos E Suarez1, Massaro W Ueti1, Vishvanath M Nene4, Robert H Mealey3, Donald P Knowles13 and Kelly A Brayton37*

Author Affiliations

1 Animal Disease Research Unit, Agricultural Research Service, USDA, Pullman, WA, 99164-7030, USA

2 J. Craig Venter Institute, Rockville, MD, 20850, USA

3 Department of Veterinary Microbiology & Pathology, Washington State University, Pullman, WA, 99164-7040, USA

4 International Livestock Research Institute, P.O. Box 30709, Nairobi, 00100, Kenya

5 Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, VA, 24061, USA

6 Institute for Genome Sciences and Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA

7 Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, 99164-7040, USA

8 School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA

9 Current address: Frederick National Lab for Cancer Research, Rockville, MD, 20852, USA

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BMC Genomics 2012, 13:603  doi:10.1186/1471-2164-13-603

Published: 9 November 2012

Additional files

Additional file 1:

Figure. Depiction of the T. equi apicoplast genome gene arrangement, showing unidirectional coding of genes. Known enzymes shown in red, ribosomal proteins in green, rRNA sequences in yellow, and groupings of tRNA molecules in blue. Location of conserved hypothetical (gray), and hypothetical (black) protein-encoding genes are shown by arrows or bars. Members of the three expanded gene families are marked with either “*”, “¡” or “^” to indicate similar genes. The molecule is depicted as linear, though not experimentally demonstrated to be either circular or linear.

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Additional file 2:

Table. Nuclear encoded genes potentially targeted to the apicoplast.

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Additional file 3:

Table. GPI anchored proteins predicted by GPI-SOM.

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Additional file 4:

Table. Transporter comparison B.bovis, T. equi, and T.parva.

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Additional file 5:

Table. 30 largest protein families.

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Additional file 6:

Figure. Alignment of EMA family sequences. Residues highlighted in yellow are conserved among all family members, and those in blue conserved among the majority of family members. Dashes represent gaps introduced to accommodate non-conserved stretches of sequence.

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Additional file 7:

Table. Proteins used in phylogenetic analysis.

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Additional file 8:

Figure. Phylogenetic trees. A: Most frequently recovered trees from maximum parsimony analysis of 150 polypeptides conserved among eight taxa, showing the number of times tree recovered out of 210 total topologies. Value above the line represents the number times that branch was recovered out of total times whole topology was recovered , and value below the line is percentage bootstrap support for that branch out of 1000 replicates. The bootstrap support for the individual MP trees was calculated for each individual dataset, and averages across all of the individual trees are presented. B: Single most parsimonious tree estimated from the concatenated dataset of the 150 polypeptides. Taxon codes are Cp: Cryptosporidium parvum, Tg: Toxoplasma gondii, Pf: Plasmodium falciparum, Pv: Plasmodium vivax, Bb: Babesia bovis, Te: Thieleria equi, Ta: Theileria annulata, Tp: Theileria parva. C: Trees estimated with maximum likelihood using six different models of amino acid substitution. Branch support was assessed with 1000 bootstrap pseudoreplications.

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