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The coding potential of the transcripts was evaluated as follows: transcripts over 200 nucleotide long that had not been previously annotated in genome version 1.6 were selected and analyzed for their coding potential using the CNCI program (https://github.com/www-bioinfo-org/CNCI) and Rfam database.
The C-terminal domains have been previously annotated in NCBI and were confirmed using NCBI's CDD.
None of the prioritized germline variants had been previously annotated in Mitomap and may, therefore, deserve further investigation.
Notably, Arp2 and Arp3 homologues have been previously annotated in both the Plasmodium and Cryptosporidium genome databases (PfArp3: CAD51790, PfArp2: CpArp364, Cpand3: EAK88375, and CpArp2, EAK88162).
Most of these genes (28/31) have been previously annotated in the literature as either cell cycle regulated and/or critical for cell cycle progression.
One important region highly relevant to immune response, the Swine Leukocyte Antigen Complex (MHC), has been previously annotated in detail [ 50] and will not be discussed here.
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In rice, 475 Pack-MuLEs in Chromosome 1 and 10 were previously annotated in detail [39].
Our group has recently produced a T. brucei flagellar proteome [7] as well as a PFR proteome generated using comparative proteomics that consists of 30 high confidence proteins including 20 that were previously annotated in the genome as hypothetical [18].
The ompA homolog was previously annotated in P. luminescens.
Two cysteine proteases were previously annotated in the P. falciparum genome database.
Genes with known roles in meiosis based on evidence in well-studied model systems (e.g. yeast, mouse, and nematodes) were previously annotated in monogononts [ 31].
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