The nucleotide sequence of the granulin gene of Choristoneura fumiferana granulovirus (CfGV) was determined. The gene encodes a protein of 248 amino acids with a predicted Mr of 29.299 kDa. The granulin genes of Trichoplusia ni, Pieris brassicae and Cryptophlebia leucotreta granuloviruses showed homologies ranging from 76.7-80.5% for nucleotide sequences and 84.2-88.3% for amino acid sequences when compared to CfGV. The secondary structure of CfGV granulin protein, including the hydrophilic (polar) and hydrophobic (basic) regions, was predicted and found to be similar to other granulins. A very late baculovirus promoter motif, ATAAG, was found within the putative promoter region of the CfGV granulin gene.

A gene located immediately upstream of the granulin gene of Choristoneura fumiferana (ChfuGV) granulovirus was identified, sequenced and named ORF891. The determined, putative open reading frame (ORF) of 891 bp encodes an estimated 34.6 kDa protein. The 5' end transcript of the gene was mapped and analysed. A putative promoter region organization of ChfuGV ORF891 contains a consensus late baculovirus promoter element, TAAG, and two putative early TATA boxes similar to the promoters of ORF909 of Cryptophlebia leucotreta granulovirus (ClGV). Sequence comparisons of ChfuGV ORF891 with ClGV ORF909 and Cydia pomonella granulovirus (CpGV) ORF124R showed respective homologies of 60.9 and 63.9% for nucleotides and 46.3% and 49.3% for amino acids. Homology of ChfuGV ORF891 with ME53 ORF of Autographa californica multicapsid nucleopolyhedrovirus (AcMNPV) was 68.2% for nucleotides but a total lack of homology for amino acid sequences. Two zinc finger motifs are also associated with ChfuGV ORF891.

Toxoplasma gondii is a significant zoonotic protist pathogen that infects up to 1/3 of the human population. This apicomplexan parasite contains three genome sequences: nuclear (63 Mb); plastid organellar, ptDNA (35 kb); and mitochondrial organellar, mtDNA (5.9 kb of non-repetitive sequence). We find that the nuclear genome contains a significant amount of NUMTs (nuclear DNA of mitochondrial origin) and NUPTs (nuclear DNA of plastid origin) that are continuously acquired and represent a significant source of intraspecific genetic variation. NUOT (nuclear DNA of organellar origin) accretion has generated 1.6% of the extant T. gondii ME49 nuclear genome; the highest fraction ever reported in any organism. NUOTs are primarily found in organisms that retain the non-homologous end-joining repair pathway. Significant movement of organellar DNA was experimentally captured via amplicon sequencing of a CRISPR-induced double-strand break in non-homologous end-joining repair competent, but not ku80 mutant, Toxoplasma parasites. Comparisons with Neospora caninum, a species that diverged from Toxoplasma ~28 MY ago, revealed that the movement and fixation of 5 NUMTs predates the split of the two genera. This unexpected level of NUMT conservation suggests evolutionary constraint for cellular function. Most NUMT insertions reside within (60%) or nearby genes (23% within 1.5 kb) and reporter assays indicate that some NUMTs have the ability to function as cis-regulatory elements modulating gene expression. Together these findings portray a role for organellar sequence insertion in dynamically shaping the genomic architecture and likely contributing to adaptation and phenotypic changes in this important human pathogen.