Table 7. Comparison among reference transcriptomes in the identification of differentially expressed genes (DEGs) between L. madurae copepodites and adult females among transcripts encoding for “giant” proteins, voltage-gated sodium channels and circadian system proteins.
Transcripts were identified as DEGs using a Benjamini-Hochberg corrected p-value <0.05.
| Target proteins | ||||||
|---|---|---|---|---|---|---|
| Transcript | Reference transcriptomes | |||||
| Protein name | Trinity identification # | “Full” | “Pred.genes” | “Full-CDS” | “Pred.genes-CDS” | |
| “Giants” | ||||||
| Twitchin X20 | TR75346|c7_g2_i1 | - | - | - | - | |
| Titin | TR27483|c2_g1_i1 | - | - | - | - | |
| Dynein heavy chain5 | TR79107|c1_g1_i1 | - | - | - | - | |
| Nesprin-1 | TR75290|c0_g1_i1 | YES | YES | YES | YES | |
| Dystonin | TR39786|c3_g2_i1 | - | - | - | - | |
| Fibrillin-1 | TR81357|c0_g1_i1 | YES | YES | YES | YES | |
| Nesprin-1 | TR75299|c4_g1_i1 | - | - | - | - | |
| Voltatge-gated sodium channel | ||||||
| NaV1.1 | TR7852|c0_g1_i1 | - | - | - | - | |
| TR7852|c0_g1_i2 | - | X | - | X | ||
| TR7852|c0_g1_i3 | YES | X | YES | X | ||
| TR7852|c0_g1_i4 | YES | X | YES | X | ||
| TR7852|c0_g1_i5 | - | X | - | X | ||
| TR7852|c0_g1_i6 | - | X | - | X | ||
| TR7852|c0_g1_i7 | - | X | - | X | ||
| NaV1.2 | TR7852|c0_g2_i1 | YES | YES | YES | YES | |
| TR7852|c0_g2_i2 | - | X | - | X | ||
| NaV2 | TR65477|c0_g1_i1 | - | X | - | X | |
| TR65477|c0_g1_i2 | - | - | - | - | ||
| TR68660|c0_g0_i1 | - | X | - | X | ||
| TR68660|c0_g0_i2 | - | - | - | - | ||
| TR25803|c0_g1_i1 | - | - | - | - | ||
| Circadian system | ||||||
| Clock (CLK) | Labma-CLK | TR80374|c0_g1_i1 | - | - | - | - |
| Cryptochrome 2 (CRY2) | Labma-CRY2 | TR24805|c1_g1_i4 | YES | X | YES | X |
| Labma-CRY2 | TR24805|c1_g1_i12 | - | X | YES | X | |
| Labma-CRY2 | TR24805|c1_g1_i11 | YES | X | YES | X | |
| Labma-CRY2 | TR24805|c1_g1_i10 | - | X | - | X | |
| Labma-CRY2 | TR24805|c1_g1_i9 | YES | X | YES | X | |
| Labma-CRY2 | TR24805|c1_g1_i8 | YES | X | YES | X | |
| Labma-CRY2 | TR24805|c1_g1_i7 | YES | X | YES | X | |
| Labma-CRY2 | TR24805|c1_g1_i6 | - | YES | - | YES | |
| Labma-CRY2 | TR24805|c1_g1_i5 | - | X | - | X | |
| Labma-CRY2 | TR24805|c1_g1_i3 | YES | X | YES | X | |
| Labma-CRY2 | TR24805|c1_g1_i2 | YES | X | YES | X | |
| Labma-CRY2 | TR24805|c1_g1_i1 | YES | X | YES | X | |
| Cycle (CYC) | Labma-CYC-v1 | TR40651|c0_g1_i4 | - | X | - | X |
| Labma-CYC-v1 | TR40651|c0_g1_i1 | - | - | YES | - | |
| Labma-CYC-v2a | TR40651|c0_g1_i3 | YES | X | YES | X | |
| Labma-CYC-v2b | TR40651|c0_g1_i5 | YES | X | YES | X | |
| Labma-CYC-v3 | TR40651|c0_g1_i2 | YES | X | YES | X | |
| Labma-CYC-v4 | TR40651|c0_g1_i7 | - | X | - | X | |
| Labma-CYC-v4 | TR40651|c0_g1_i6 | - | X | - | X | |
| Period (PER) | Labma-PER-v1 | TR32117|c1_g1_i2 | YES | YES | YES | YES |
| Labma-PER-v2 | TR32117|c1_g1_i1 | YES | X | YES | X | |
| Timeless (TIM) | Labma-TIM-v1 | TR9084|c2_g1_i4 | YES | - | YES | - |
| Labma-TIM-v2 | TR9084|c2_g1_i3 | - | X | YES | X | |
| Labma-TIM-v3 | TR9084|c2_g1_i2 | YES | X | YES | X | |
| Labma-TIM-v4 | TR9084|c2_g1_i1 | YES | X | YES | X | |
| Casein kinase IIα (CKIIα) | Labma-CKIIα | TR16899|c1_g1_i1 | - | - | - | - |
| Casein kinase IIβ (CKIIβ) | Labma-CKIIβ | TR61463|c0_g1_i1 | - | - | - | - |
| Clockwork orange (CWO) | Labma-CWO-v1 | TR54681|c0_g1_i3 | YES | YES | YES | YES |
| Labma-CWO-v1 | TR54681|c0_g1_i2 | YES | X | YES | X | |
| Labma-CWO-v2 | TR54681|c0_g1_i1 | YES | X | YES | X | |
| Doubletime (DBT) | Labma-DBT-I | TR25584|c0_g3_i1 | - | - | - | - |
| Labma-DBT-II-v1 | TR13652|c3_g1_i1 | - | YES | - | YES | |
| Labma-DBT-II-v2 | TR13652|c3_g1_i2 | - | X | - | X | |
| Labma-DBT-III-v1 | TR84098|c0_g1_i2 | - | X | - | X | |
| Labma-DBT-III-v1 | TR84098|c0_g1_i1 | - | X | - | X | |
| Labma-DBT-III-v2 | TR84098|c0_g1_i4 | - | - | - | - | |
| Labma-DBT-III-v2 | TR84098|c0_g1_i3 | - | X | - | X | |
| Jetlag (JET) | Labma-JET | TR56999|c0_g1_i3 | YES | X | YES | X |
| Labma-JET | TR56999|c0_g1_i2 | - | YES | - | YES | |
| Labma-JET | TR56999|c0_g1_i1 | YES | X | YES | X | |
| PAR-domain protein 1 (PDP1) | Labma-PDP1-I-v1 | TR26154|c2_g1_i2 | - | - | - | - |
| Labma-PDP1-I-v2 | TR26154|c2_g1_i1 | - | - | - | - | |
| Labma-PDP1-II | TR81334|c0_g4_i2 | - | X | - | X | |
| Labma-PDP1-II | TR81334|c0_g4_i1 | - | YES | - | YES | |
| Labma-PDP1-III | TR85690|c1_g2_i3 | - | - | - | - | |
| Labma-PDP1-III | TR85690|c1_g2_i2 | - | X | - | X | |
| Labma-PDP1-III | TR85690|c1_g2_i1 | YES | X | YES | X | |
| Labma-PDP1-IV | TR40313|c4_g1_i2 | - | - | - | - | |
| Labma-PDP1-IV | TR40313|c4_g1_i1 | YES | X | YES | X | |
| Protein phosphatase 1 (PP1) | Labma-PP1-I | TR8331|c4_g1_i1 | - | - | - | - |
| Labma-PP1-II | TR44262|c1_g1_i1 | - | - | - | - | |
| Labma-PP1-III | TR58187|c0_g1_i1 | - | - | - | - | |
| Labma-PP1-IV | TR43009|c0_g1_i1 | - | - | - | - | |
| Protein phosphatase 2A (PP2A)–Microtubule star (MTS) | Labma-MTS-I | TR69087|c4_g1_i1 | - | - | - | - |
| Labma-MTS-II | TR6003|c0_g1_i1 | - | - | - | - | |
| PP2A –Twins (TWS) | Labma-TWS-I | TR47276|c5_g1_i1 | - | - | YES | YES |
| Labma-TWS-II | TR55093|c0_g1_i1 | - | - | - | - | |
| PP2A –Widerborst (WDB) | Labma-WDB-v1 | TR25971|c2_g2_i2 | - | - | - | - |
| Labma-WDB-v2 | TR25971|c2_g2_i1 | - | X | - | X | |
| Shaggy (SGG) | Labma-SGG-I | TR76551|c2_g2_i2 | - | - | - | - |
| Labma-SGG-I | TR76551|c2_g2_i1 | - | X | - | X | |
| Labma-SGG-II-v1 | TR80377|c0_g1_i2 | - | - | - | - | |
| Labma-SGG-II-v2 | TR69087|c4_g1_i1 | - | - | - | - | |
| Supernumerary limbs (SLIMB) | Labma-SLIMB-v1 | TR55609|c6_g1_i2 | - | - | - | - |
| Labma-SLIMB-v2 | TR55609|c6_g1_i1 | - | X | - | X | |
| Vrille (VRI) | Labma-VRI | TR41378|c1_g1_i2 | - | X | - | X |
| Labma-VRI | TR41378|c1_g1_i1 | YES | YES | YES | YES | |
| Cryptochrome 1 (CRY1) | Labma-CRY1 | TR53226|c0_g1_i1 | - | - | - | YES |
| Pigment dispersing hormone (PDH) | Labma-prepro-PDH-v1 | TR22949|c0_g1_i2 | - | YES | - | YES |
| Labma-prepro-PDH-v2 | TR22949|c0_g1_i1 | - | X | - | X | |
| PDH receptor (PDHR) | Labma-PDHR | TR69493|c0_g1_i1 | - | - | - | - |
Legend
- Transcript present in the reference transcriptome but not differentially expressed
YES Transcript present in the reference transcriptome and differentially expressed
X Transcript not present in the reference transcriptome
In bold Transcripts resulting differentially expressed in all 4 reference transcriptomes