Open Access Highly Accessed Research article

High-resolution genotyping and mapping of recombination and gene conversion in the protozoan Theileria parva using whole genome sequencing

Sonal Henson1, Richard P Bishop1, Subhash Morzaria1, Paul R Spooner1, Roger Pelle1, Lucy Poveda2, Martin Ebeling3, Erich Küng3, Ulrich Certa3, Claudia A Daubenberger45 and Weihong Qi2*

Author Affiliations

1 International Livestock Research Institute, Nairobi, 00100, Kenya

2 Functional Genomics Center Zurich, UZH/ETHZ, Winterthurerstrasse 190, 8057, Zurich, Switzerland

3 F. Hoffmann-La Roche AG, Basel, 4070, Switzerland

4 Swiss Tropical and Public Health Institute, Socinstrasse 57, Basel, 4002, Switzerland

5 University of Basel, Peterplatz 1, Basel, 4003, Switzerland

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BMC Genomics 2012, 13:503  doi:10.1186/1471-2164-13-503

Published: 23 September 2012

Additional files

Additional file 1: Figure S5:

Unmapped and unaligned regions in the sequenced genomes. Chromosomes 1 to 4 are arranged from left to right. Strains are lined up from top to bottom, where the strain name is indicated at the beginning of each track. Positions of the 27 loci encoding products previously known as immune-relevant [10] are shown in orange using the “Loci” track. M: Marikebuni. MM: MugugaMarikebuni; MU: MugugaUganda. U: Uganda.

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Additional file 2: Table S3:

Genes unmapped to T. parva Muguga reference genome in each strain. ‘M’ indicates mapped and ‘UM’ indicates unmapped in the strain.

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Additional file 3: Table S5:

Genotyping results of MugugaMarikebuni.

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Additional file 4: Table S6:

Genotyping results of MugugaUganda.

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Additional file 5: Figure S1:

Comparison of crossover events detected using SNP markers with those identified using VNTR markers [10]. Chromosomes 1 to 4 are arranged from left to right. Identified CO events in each progeny strain are lined up from top to bottom, where the strain name is indicated at the beginning of each track. Colour transitions between blue and red indicate CO events. MugugaMarikebuni (MM) and MugugaUganda (MU) were the two recombinant clones analyzed in our study. All other clones were crosses of Muguga and Marikebuni, which were analyzed with VNTR markers as described in [10].

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Additional file 6: Table S1:

Crossover (CO) breakpoints and sizes of associated gene conversions (GC) in the progeny strains.

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Additional file 7: Figure S2:

Detection of crossover events when varying the sliding window size. (A) Number of SNPs as the sliding window size. Tested sizes were 7, 11, 15, 19 and 23 SNPs, respectively. (B) Absolute physical distance as the sliding window size. Tested sizes were 1, 2, 3, 4, 5, 6 Kb, respectively. In both figures, chromosomes 1 to 4 are arranged from left to right. Identified CO events in each progeny strain using different window sizes are lined up from top to bottom, where the strain name and the window size are indicated at the beginning of each track. Color transitions between blue and red indicate CO events. Due to limited resolution, a few CO events of very short sizes are not visible, including the CO breakpoint of 1 Kb on chromosome 4 at the position of 1.797 Mb in MugugaMarikebuni, which was detected by the window size of 7 SNPs, as well as the CO breakpoints on chromosome 1 at positions around 1.1 Mb in MugugaMarikebuni, which were detected by all window sizes but only visible for windows of physical distances. MM: MugugaMarikebuni; MU: MugugaUganda.

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Additional file 8: Table S2:

Non-crossover breakpoints in the progeny strains.

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Additional file 9: Figure S6:

Number of recombination events by chromosome sizes. MM: MugugaMarikebuni. MU: MugugaUganda. CO: cross over event. NCO: non-cross over event. TOT: all recombination events (COs plus NCOs).

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Additional file 10: Figure S3:

Distribution of Ka/Ks ratios by intra-species polymorphism analysis. Red bars represent histograms of Ka/Ks ratios. Blue curves are normal distribution curves fit to the corresponding histograms. The top four graphs were based on BLAT alignment of Muguga mRNAs to de novo assemblies, bottom four were to mapped assemblies.

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Additional file 11: Figure S4:

Ka/Ks ratios by Fisher exact test P-values. Vertical lines represent the means of Ka/Ks ratios. Horizontal lines represent the cut-off P-value (0.05). The top four graphs were based on BLAT alignment of Muguga mRNAs to de novo assemblies, bottom four were to mapped assemblies.

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Additional file 12: Table S4:

Genes potentially under positive selection by intra-species polymorphism analysis.

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Additional file 13:

Supplementary information on Material and Methods.

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Additional file 1: Figure S7:

Alleles around recombination breakpoints and definitions of breakpoint boundaries. One example for each breakpoint type was shown: (A) Simple CO breakpoints without associated gene conversions. Around these breakpoints, markers had the following characteristics: start with at least 15 continuous alleles of p1, followed by at least 15 continuous alleles of p2 (or 15 p2 alleles followed by 15 p1 alleles, for simplicity we use the p1 to p2 change as an example). The p1 allele frequencies would be 15/15, 14/15, 13/15, . . ., 1/ 15, 0/15 (which corresponded to a 15/15 p2 allele frequency). Thus the size of the breakpoint would be the length of the 15 p1 alleles plus the distance to the first p2 allele, as indicated by the yellow bars. (B) Complex breakpoints with gene conversions. Markers around these break points start with 15 continuous p1 alleles (p1 allele frequency of 15/15, followed by 1 to 14 p2 alleles, then 1to 14 p1 alleles, . . ., until it reaches a track of at lease 15 continuous p2 alleles so the p1 allele frequency reaches 15/15). (C) NCO breakpoints. NCO breakpoints were strictly defined as a region consisting of 3 to 14 contiguous markers with one parental allele type, flanked by longer stretches of markers with the other parental allele type. Muguga alleles are shown in red, while Uganda alleles in blue. Yellow bars indicate the boundaries of breakpoints, where the allele frequency changes from 100% of one parent to 100% of the other parent. For each marker, such allele frequency was calculated using the sliding window method described in materials and methods.

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