Table 1. Presence of pseudogenes in representative families of duplicated genes of Trichomonas.
protein family | average length in aa | family size | assembly boundary | genes with stops or FSa | truncated genesb | percentage of pseudogenesc |
Dynein heavy chain family protein | 3937 | 22 | 1 | 0 | 1 | 5% |
transmembrane adenylyl cyclases | 1550 | 123 | 12 | 56 | 4 | 46% |
cyclic nucleotide phosphodiesterase | 1134 | 41 | 2 | 1 | 7 | 18% |
Clan SB, family S8, subtilisin-like serine peptidase | 868 | 31 | 6 | 2 | 2 | 16% |
Adaptin N terminal region family protein | 811 | 51 | 2 | 3 | 1 | 6% |
ABC transporter family protein | 614 | 64 | 7 | 11 | 8 | 32% |
Dolichol-phosphate-mannose-protein mannosyltransferase | 479 | 31 | 0 | 1 | 1 | 6% |
major facilitator superfamily protein | 403 | 48 | 1 | 9 | 1 | 21% |
Clan CA, family C1, cathepsin L-like cysteine peptidase | 286 | 44 | 2 | 1 | 6 | 17% |
small Rab GTPase | 203 | 184 | 3 | 3 | 3 | 3% |
small GTP-binding protein | 193 | 39 | 0 | 1 | 2 | 5% |
ADP-ribosylation factor | 181 | 24 | 0 | 2 | 0 | 8% |
FS: frame shift.
truncated genes: those whose length is between 30% to 70% of the length of a complete gene.
pseudogenes: those containing stops and/or frame shifts and/or truncations that cannot be explained by assembly issues.