Assignment of whether protein pairs were orthologous, homologous, paralogous,
or unrelated was assessed manually on an individual basis. Data and evidence
supporting protein similarity are provided in Supplementary Table 1.
EdU/BrdU double labelling.
Parasites labelled with 10 mM EdU and BrdU were
fixed in Methacarn (6:3:1 methanol:chloroform:glacial acetic acid) or processed
for in situ hybridization. After a 45-min 2N HCl treatment, EdU was detected and
parasites were processed for anti-BrdU immunofluorescence (anti-BrdU 1:500,
clone MoBU, Invitrogen). We observed no crossreactivity between this antibody
and EdU.
To quantify the level of BrdU/EdU overlap and measure centre-to-centre distances
between nuclei, three-dimensional confocal stacks from EdU/BrdUlabelled
animals were re-sampled to give isotropic voxels, and subjected to
Gaussian filtering and background-subtraction. Labelled nuclei were segmented
with Imaris (Bitplane Inc.) using parameters empirically determined to minimize
the need for manual corrections; typically, fewer than 5% of the total nuclei
required correction. The three-dimensional coordinates of the nuclei were
exported and analysed with MATLAB. Overlapping EdU- and BrdU-labelled
nuclei were defined as nuclei with centre-to-centre distances ,1 nuclear size
(,4 mm). Statistical analyses were performed in Origin (OriginLab).