Table 1 RNA-seq sample descriptions and metrics
Sample | Replicates | Host/location | Description | Main developmental process | Specific developmental processes | No. of genes expressed (% totala) | Comparison | No. of up-regulatedb (% of expressed genes) | GOIc |
|---|---|---|---|---|---|---|---|---|---|
Larvae | 3 × apx. 550 pooled S2–S3 Larvae | Beetle (Tribolium spp.)/haemocoel | 5-day old, mid-metamorphosis Larvae | Cysticercoid morphogenesis | Specification of primary body axes (AP/DV/LR) involving differentiation of juvenile worm and cyst-/tail-forming poles. Nascent nerve-muscle development in cyst and juvenile poles (e.g. rostellar apparatus, suckers) | 10,257 (83%) | Larvae cf. Whole Adult | 2266 (18%) | 72 |
Whole Adult | 3 × whole, gravid worms | Mouse (Mus musculus)/bile duct | Whole, gravid worms | Strobilar and sexual development | (encompassing all processes below) | 10,139 (82%) | Whole Adult cf. Larvae | 3087 (30%) | n/a |
Scolex-Neck | 1 × 13, 1 × 14, 1 × 43 pooled scolex + neck pieces (~ 0.5 cm each) |  | Scolex and ‘neck’ (including a variable number of nascent segments) | Proglottisation and strobilation | Formation of nascent segments and proglottids; cellular integration into existing muscle, nerve and excretory systems | 9564 (77%) | Scolex-Neck cf. Mid/Scolex-Neck cf. End | 1052 (11%)/812 (8%) | 61/49 |
Mid | 1 × 11, 1 × 12, 1 × 15 pooled pieces (~ 2.5 cm each) |  | Segments with mature proglottids | Sexual maturation | Gametogenesis and maturation of female system; fertilisation | 10,170 (82%) | Mid cf. Scolex-Neck/Mid cf. End | 2066 (20%)/457 (4.5%) | 60/16 |
End | 1 × 11, 1 × 12, 1 × 17 pooled pieces (~ 2.5 cm each) |  | Sub-terminal, gravid segments | Egg and embryo maturation | Embryogenesis; proglottid senescence | 10,095 (82%) | End cf. Scolex-Neck/End cf. Mid | 1440 (14%)/924 (9%) | 22/18 |