Additional file 1 of Re-annotation of the Theileria parva genome refines 53% of the proteome and uncovers essential components of N-glycosylation, a conserved pathway in many organisms
Creators: name: Tretina, Kyle
name: Pelle, Roger
name: Orvis, Joshua
name: Hanzel T. Gotia
name: Olukemi O. Ifeonu
name: Kumari, Priti
name: Palmateer, Nicholas C.
name: Shaikh B. A. Iqbal
name: Fry, Lindsay M.
name: Vishvanath M. Nene
name: Daubenberger, Claudia A.
name: Bishop, Richard P.
name: Silva, Joana C.
Publisher: name: figshare
Year: 2020
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: FOS: Biological sciences

description: Additional file 1: Supplemental Figure S1. Architecture of the Theileria parva Muguga genome and associated new structural annotation and RNAseq expression data. Supplemental Figure S2. Updated gene annotation efforts in the Theileria parva genome reveal the existence of many genes that overlap adjacent genes at either UTR or CDS sequences. Supplemental Figure S3. RNA-seq reads that map to introns in the Theileria parva Muguga genome support the existence of genes where a subset of introns are not spliced. Supplemental Figure S4. Histogram of mRNA length across all annotated transcripts in the current T. parva Muguga annotation. Supplementary Fig.ure S5. Types of transcription initiated in Theileria parva. Supplemental Figure S7. The expression distribution of three selected gene families in T. parva Muguga (SVSP = subtelomeric variable secreted protein gene family; Tpr = T. parva repeat gene family; TashAT = Theileria annulata schizont AT hook gene family). Supplementary Figure S8. Theileria PIN1 is an example of a parasite-secreted protein that plays a role in host transformation. Supplemental Figure S9. The expression N-glycosylation pathway components in the sporozoite and schizont life cycle stages of T. parva Muguga. Supplemental Figure S10. A representation of the relative weights of each evidence in each EVM prediction tested. Supplemental Figure S11. The percentage of validated genes, or coding exons correctly predicted by EVM with each evidence combination. Supplemental Figure S12. A comparison of the prediction accuracy of each gene predictor used in this study. Supplemental Table S1. RNAseq read counts, length and GC content of each T. parva chromosome. Supplemental Table S2. A comparison of genome characteristics of T. parva Muguga to several other piroplasms and Plasmodium falciparum 3D7. Supplemental Table S3. A list of the expression levels (RPKM = reads per kilobase of transcript per million reads) of known T. parva antigens. Supplemental Table S4. A list of the most highly-expressed genes in the T. parva schizont RNAseq dataset. Supplemental Table S5. A table of key T. parva genes with reads per kilobase of transcript per million reads of zero. (Tp = Theileria parva Muguga; Pf = Plasmodium falciparum 3D7). Supplemental Table S6. A description of the top 20 largest multi-gene families defined by OrthoMCL in T. parva Muguga and their conservation in T. annulata (Ta), T. orientalis (To), and T. equi (Te), as defined by Jaccard-filtered clusters of orthologous genes. Supplemental Table S7. Summary of the top-ranked Phyre2 hits for each proposed Alg homolog discussed in this study. Supplemental Table S8. The exon distribution of the validation and training sets used for gene prediction.