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Table 2 Loci encoding well-characterized peptide products, which contain SNPs between the Serengeti-transformed stock and reference Muguga strain. Variants were also found in 47 hypothetical proteins (Additional file 2: Table S2)

From: The genomes of three stocks comprising the most widely utilized live sporozoite Theileria parva vaccine exhibit very different degrees and patterns of sequence divergence

Locus Tag /2005 Locus Tag IDa Product Name TM Domainsb Protein Localization / Confidencec Serengeti-transformed SNPsd Kiambu5 SNPse
Syn Nsyn Syn Nsyn
TP01_0011 TpMuguga_01g00011f ABC transporter 11 _ / 2 9 11 ≥66f ≥14f
TP02_0016 TpMuguga_02g00016f ABC transporter 13 _ / 2 2 2 ≥21f ≥7f
TP02_0017 TpMuguga_02g00017f ABC transporter 12 _ / 3 19 17 ≥11f ≥8f
TP02_0940 TpMuguga_02g00940f ABC transporter 12 _ / 1 1   ≥0f ≥0f
TP02_0951 TpMuguga_02g00951f ABC transporter 11 _ / 1 44 37 ≥9f ≥2f
TP03_0007 TpMuguga_03g00007f ABC transporter 11 _ / 1 7 4 ≥11f ≥9f
TP03_0864 TpMuguga_03g00864 ABC transporter 13 _ / 2 5 3 10 6
TP04_0021 TpMuguga_04g00021f ABC transporter 13 _ / 1 10 24 ≥43f ≥23f
TP02_0449 TpMuguga_02g00449 DNA replication factor CDT1 like 0 _ / 2 4    1
TP02_0448 TpMuguga_02g00448 F-box-like/WD repeat-containing protein TBL1XR1 0 _ / 1   1   1
TP03_0280 TpMuguga_03g00280 Papain family cysteine protease 1 _ / 2 12 7 1 1
TP04_0278 TpMuguga_04g00278 Translation initiation factor IF-2 1 S / 2 4 8   5
TP04_0279 TpMuguga_04g00279 Translation initiation factor IF-2 1 S / 2 1 3   
TP04_0280 TpMuguga_04g00280f Translation initiation factor IF-2 1 S / 1 1 3 ≥2f ≥2f
  1. aLocus Tag Identifiers according to the updated whole genome gene structural re-annotation
  2. bNumber of transmembrane domains
  3. cProtein localization predictions based on TargetP: C = chloroplast; M = mitochondrion; S = Secretory pathway; _ = Any other location. Prediction confidence: 1 = max; 5 = min
  4. dSNPs between the Serengeti-transformed isolate and the reference Muguga isolate. Both synonymous (Syn) and non-synonymous (Nsyn) SNP counts are shown
  5. eSNPs between Kiambu5 and the reference Muguga isolate
  6. fThis genes coding sequence(s) had at least one position with <10x mapping coverage in the Kiambu5 stock, and thus there is likely more variation in the actual sequence