<<comment>> Raw nuclear DNA Sequence

1. <<comment>> Raw nuclear DNA Sequence RepeatMasker <<comment>> 426,440 EST of apicomplexa TRF Repeat masking <<comment>> Chromosome I 690 curated gene models RepeatScout <<comment>> 1.2% of repeat sequences (75 kbp) <<comment>> Uniprot BLAT Chromosome I 690 curated gene models Abinitio gene detection GeneWise Protein alignments EST2Genome EST2Genome EST Alignments SNAP GAZE <<comment>> 5,419 gene models <<comment>> 1,426 gene models <<comment>> 44,545 EST have been aligned Figure S1

2. <<comment>> 1,426 gene models <<comment>> Raw nuclear DNA Sequence <<comment>> 3,923 gene models EST/Prot mapping Snap detection Automatic detection GlimmerHMM BlastX homology saturation GAZE <<comment>> Similar to MegaBlast Delete CDS without homology overlapping CDS with homology Gene selection Create CDS presenting homology and delete overlapping CDS without homologies Figure S2 Delete in frame introns (mostly from GAZE) Create intron to cover all ORFs in frames presenting BLASTX alignments from homologues <<comment>> Gene fusion event is evaluated Gene structure Split CDS with BLASTX alignment corresponding to different homologues Calculate start codon position by comparison with three best homologues <<comment>> Homologues should have conserved ATG position Translate CDS in amino acids sequence Best bidirectionnal hit and KEGG ID identification <<comment>> Annotated DNA Sequence 3,513 gene models

3. A. B. C. D. E. Figure S3

4. A. Tandem repeats CRMP GAPDH Gap Ia Ib Chromosome I 0 500 1000 1300 Kbp N1-15 CEN REP FBA IIIa IIIc IIIb CEN B. Chromosome III rDNA N1-15 FBA IIa IIb Chromosome II CEN Ia Ib Chromosome I 0 1000 2000 3000 Kbp CEN REP Figure S4

5. Bmldh Bmtpk cDNA cDNA gDNA gDNA RT- RT- RT+ RT+ 1000 bp - Figure S5

6. A 95 100 100 LDH-like MDH 100 MDH-like LDH of apicomplexa 100 100 100 100 95 84 98 82 LDH 92 100 96 0.2 88 84 100 100 Figure S6A

7. B 100 88 90 Eukaryota 97 89 90 100 Bacteria 100 Bartonella 91 Figure S6B