A first look at population differences at qPCR primer sites for three population of Olympia oysters
Plate 1 (samwhite_112381) included, BMP2, CARM, HSPb11, and PGEEP4. At the bottom is a full list of qPCR primers.
BMP2
Limited coverage
CARM
Better coverage
conflicts were ambigs (ie S,W,R)
HSPb11
Missed qPCR primer (R did not seem to work)
PGEEP4
Nothing assembled – everything under 100 bp.
Plate 2 (samwhite_112404) included, H2A, H2AV, p291N, CRAF, GABABR, GRB2, H3-3
H2A
comp23253_c0_seq1
One primer not covered
H2AV
comp25000_c0_seq1
Not much coverage
p291N
comp22144_c0_seq1
Not much coverage
CRAF
comp25313_c0_seq1
Decent coverage, only conflict = ambig, SNP!
SNP
GABABR
comp19002_c0_seq1
Great coverage, did find some SNPs. Missed qPCR primer
SNPs
GRB2
comp10127_c0_seq1
Not great coverage
H3-3
comp19571_c0_seq1
List of QPCR Primers
| QPCR Primer | sequence | Protein |
|---|---|---|
| HSP70c_FWD | AGGAAAGGTCGGGAGAGGAA | Heat shock 70 kDa protein 12A |
| HSP70c_REV | ACCTCGGACTTTGGACGAAC | Heat shock 70 kDa protein 12A |
| p29ING4_FWD | TACCTTTGGGCTTCACCGTC | Inhibitor of growth protein 4 (p29ING4) |
| p29ING4_REV | GTCCATCACACACCCCTCAG | Inhibitor of growth protein 4 (p29ING4) |
| CerS2_FWD | TTGTCGGTCTCCTCCTGCTA | Ceramide synthase 2 (CerS2) (LAG1 longevity assurance homolog 2) |
| CerS2_REV | CCGTCTTCTGAGCCATCGTT | Ceramide synthase 2 (CerS2) (LAG1 longevity assurance homolog 2) |
| GABABR1_FWD | CCGAGGAGGACACGAAACTC | Gamma-aminobutyric acid type B receptor subunit 1 (GABA-B receptor 1) (GABA-B-R1) (GABA-BR1) (GABABR1) (Gb1) |
| GABABR1_REV | CGGACAGGTTCTGGATTCCG | Gamma-aminobutyric acid type B receptor subunit 1 (GABA-B receptor 1) (GABA-B-R1) (GABA-BR1) (GABABR1) (Gb1) |
| HSP70d_FWD | TTTGTCTCACCGGCTTTGTG | Heat shock 70 kDa protein 6 (Heat shock 70 kDa protein B’) |
| HSP70d_REV | GACATGAGACCAAAGACGCC | Heat shock 70 kDa protein 6 (Heat shock 70 kDa protein B’) |
| THRa_FWD | GACACTATCCTCACTCGGCG | Thyroid hormone receptor alpha (Nuclear receptor subfamily 1 group A member 1) |
| THRa_REV | GGGTGCCGAGTAAACAAGGA | Thyroid hormone receptor alpha (Nuclear receptor subfamily 1 group A member 1) |
| Defensin_FWD | TCTAGCGGAGTTTGTTGGGG | Big defensin |
| Defensin_REV | ATGGCTGTCGGAGGAGGATT | Big defensin |
| GRB2_FWD | AACTTTGTCCACCCAGACGG | Growth factor receptor-bound protein 2 (Adapter protein GRB2) (Protein Ash) (SH2/SH3 adapter GRB2) |
| GRB2_REV | CCAGTTGCAGTCCACTTCCT | Growth factor receptor-bound protein 2 (Adapter protein GRB2) (Protein Ash) (SH2/SH3 adapter GRB2) |
| H3.3_FWD | CACGCTCTCCTCGAATCCTC | Histone H3.3 |
| H3.3_REV | AAGTTGCCTTTCCAGCGTCT | Histone H3.3 |
| H2A.V_FWD | TGCTTTCTGTGTGCCCTTCT | Histone H2A.V (H2A.F/Z) (Fragment) |
| H2A.V_REV | TATCACACCCCGTCACTTGC | Histone H2A.V (H2A.F/Z) (Fragment) |
| H2A_FWD | GCTGGGGTTTTTCTGGGTCT | Histone H2A |
| H2A_REV | GGAACTACGCCGAGAGAGTG | Histone H2A |
| Hspb11_FWD | ATGTTTCCTGGTCTCCGTCA | Heat shock protein beta-11 (Hspb11) (Placental protein 25) (PP25) |
| Hspb11_REV | CATCAACGCCAGGGGAACTT | Heat shock protein beta-11 (Hspb11) (Placental protein 25) (PP25) |
| GDF-8_FWD | CCGTGGATGTCGCAGAAAGA | Growth/differentiation factor 8 (GDF-8) (Myostatin) (Myostatin-1) (zfMSTN-1) (Myostatin-B) |
| GDF-8_REV | CTGCTTTCTCCGTCCCCTTT | Growth/differentiation factor 8 (GDF-8) (Myostatin) (Myostatin-1) (zfMSTN-1) (Myostatin-B) |
| HSP70b_FWD | AAGTACCTTGGGGAGCTTGC | Heat shock 70 kDa protein 12B |
| HSP70b_REV | TCCACAGACTTTCCTCCCCA | Heat shock 70 kDa protein 12B |
| GRP-78_FWD | GAGAAACCACGCAGGGAGAA | 78 kDa glucose-regulated protein (GRP-78) (Heat shock 70 kDa protein 5) (Immunoglobulin heavy chain-binding protein) (BiP) |
| GRP-78_REV | CATCAGCATCGAAGGCAACG | 78 kDa glucose-regulated protein (GRP-78) (Heat shock 70 kDa protein 5) (Immunoglobulin heavy chain-binding protein) (BiP) |
| CARM1_FWD | TGGTTATCAACAGCCCCGAC | Histone-arginine methyltransferase CARM1 (EC 2.1.1.-) (EC 2.1.1.125) (Coactivator-associated arginine methyltransferase 1) (Protein arginine N-methyltransferase 4) |
| CARM1_REV | GTTGTTGACCCCAGGAGGAG | Histone-arginine methyltransferase CARM1 (EC 2.1.1.-) (EC 2.1.1.125) (Coactivator-associated arginine methyltransferase 1) (Protein arginine N-methyltransferase 4) |
| BMP-2_FWD | TGAAGGAACGACCAAAGCCA | Bone morphogenetic protein 2 (BMP-2) (Bone morphogenetic protein 2A) (BMP-2A) |
| BMP-2_REV | TCCGGTTGAAGAACCTCGTG | Bone morphogenetic protein 2 (BMP-2) (Bone morphogenetic protein 2A) (BMP-2A) |
| PGE/EP4_FWD | ACAGCGACGGACGATTTTCT | Prostaglandin E2 receptor EP4 subtype (PGE receptor EP4 subtype) (PGE2 receptor EP4 subtype) (Prostanoid EP4 receptor) |
| PGE/EP4_REV | ATGGCAGACGTTACCCAACA | Prostaglandin E2 receptor EP4 subtype (PGE receptor EP4 subtype) (PGE2 receptor EP4 subtype) (Prostanoid EP4 receptor) |
| CRAF1_FWD | AGCAGGGCATCAAACTCTCC | TNF receptor-associated factor 3 (EC 6.3.2.-) (CD40 receptor-associated factor 1) (CRAF1) (TRAFAMN) |
| CRAF1_REV | ACAAGTCGCACTGGCTACAA | TNF receptor-associated factor 3 (EC 6.3.2.-) (CD40 receptor-associated factor 1) (CRAF1) (TRAFAMN) |
| NFKBina_FWD | GATGGCGGTGCATGTGTTAG | NF-kappa-B inhibitor alpha (I-kappa-B-alpha) (IkB-alpha) (IkappaBalpha) (REL-associated protein pp40) |
| NFKBina_REV | CGAGGAGAACCTTGTGCAGT | NF-kappa-B inhibitor alpha (I-kappa-B-alpha) (IkB-alpha) (IkappaBalpha) (REL-associated protein pp40) |
| PGRP-S_FWD | GAGACTTCACCTCGCACCAA | Peptidoglycan recognition protein 1 (Peptidoglycan recognition protein short) (PGRP-S) |
| PGRP-S_REV | AACTGGTTTGCCCGACATCA | Peptidoglycan recognition protein 1 (Peptidoglycan recognition protein short) (PGRP-S) |
| TLR2.1_FWD | ACAAAGATTCCACCCGGCAA | Toll-like receptor 2 type-1 |
| TLR2.1_REV | ACACCAACGACAGGAAGTGG | Toll-like receptor 2 type-1 |
| GDF-8b_FWD | AACTGATTCTGCTCGTCGCA | Growth/differentiation factor 8 (GDF-8) (Myostatin) |
| GDF-8b_REV | TGTTCTTCCACCCACCACTG | Growth/differentiation factor 8 (GDF-8) (Myostatin) |
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