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) |
