Comprehensive Transcriptome Study to Develop Molecular Resources of the Copepod Calanus sinicus for Their Potential Ecological Applications

Table 5

Single nucleotide polymorphism (SNP) markers derived from the transcriptome of Calanus  sinicus.

Locus	Putative function	SNP type	Primer sequence (5′-3′)	𝐻𝑜	𝐻𝑒	Minor allele and frequency
CsSNP01	Heat shock protein 40	G/A	AS1: GCGGGCAGGGCGGCATGATGGAATGGACGGAACGGAG; AS2: GCGGGCATGATGGAATGGACGGAATGTAA; CR: CCTAAGCTGGCAAATGGATCATC	0.156	1.257	A; 0.423
CsSNP02	Cytosolic heat shock protein 90 kda	G/T	AS1: GCGGGCAGGGCGGCCCTGATCTTGTCCAGAGCAGCG; AS2: GCGGGCCCTGATCTTGTCCAGAGCATAT; CR: GAAATATTTCTGAGAGAACTCATC	0.333	0.282	G; 0.250
CsSNP03	Heat shock protein 70	C/T	AS1: GCGGGCAGGGCGGCTCCATCCTCACTATTGAAGACGGC; AS2: GCGGGCTCCATCCTCACTATTGAAGATAGT; CR: CAAGATGAGTGTCTCCACTGGTGG	0.500	0.523	T; 0.452
CsSNP04	Ferritin	G/T	AS1: GCGGGCAGGGCGGCCCACTCAGCCAGCTCATCACGG; AS2: GCGGGCCCACTCAGCCAGCTCATCATAT; CR: GGCTCATCAACACCTTCAACAAC	0.194	0.325	G; 0.338
CsSNP05	10 kda heat shock protein	C/T	AS1: GCGGGCAGGGCGGCGGATGAAGGATCCACTCTCCGCC; AS2: GCGGGCGGATGAAGGATCCACTCTCTACT; CR: GAGTCGTGGTGGCTGTTGGACC	0.822	0.522	T; 0.375
CsSNP06	Prophenoloxidase	G/A	AS1: GCGGGCAGGGCGGCCAGTACCCCATCTTTACTCTGCTG; AS2: GCGGGCCAGTACCCCATCTTTACTCTATTA; CR: ATTAGCTATTGACCAAATGGAAATC	0.098	0.475	A; 0.163
CsSNP07	Selenium- dependent salivary glutathione peroxidase	G/A	AS1: GCGGGCAGGGCGGCCCGTACTGGCCAGCCATACCGG; AS2: GCGGGCCCGTACTGGCCAGCCATATAGA; CR: ATCAGCATAGGTTCAACAGAAGAG	0.125	0.225	G; 0.221
CsSNP08	Selenium-dependent glutathione peroxidase	G/A	AS1: GCGGGCAGGGCGGCTCGGCCTGGAAATGGGTGCGAG; AS2: GCGGGCTCGGCCTGGAAATGGGTTAGAA; CR: TTTGCTTCCACCTTATCGAACATC	0.246	0.325	A; 0.223
CsSNP09	Superoxide dismutase	G/A	AS1: GCGGGCAGGGCGGCAAAGTCAGAGGAACCATTACGCTG; AS2: GCGGGCAAAGTCAGAGGAACCATTACAATA; CR: TCCTTCCAATAACACGGACGTGCC	0.056	0.468	A; 0.200
CsSNP10	Ferritin heavy subunit	C/T	AS1: GCGGGCAGGGCGGCCATTTCTTGGAGGAACAGGTAGGC; AS2: GCGGGCCATTTCTTGGAGGAACAGGTATAT; CR: CATCTCCACTCTGGTAAGCAAGTCC	0.083	0.475	C; 0.324
CsSNP11	Lysosomal aspartic protease precursor	C/T	AS1: GCGGGCAGGGCGGCGATGGACCCACGCTATGACCGGC; AS2: GCGGGCGATGGACCCACGCTATGACCAGT; CR: GCATCCATATAATTAGACAGTGG	0.500	0.482	T; 0.265
CsSNP12	Catalase	C/T	AS1: GCGGGCAGGGCGGCTATGAATGGATATGGATCCCGC; AS2: GCGGGCTATGAATGGATATGGATCACAT; CR: GATGGGCTCATTGTCTGCATTC	0.250	0.335	C; 0.188
CsSNP13	Trypsin	C/T	AS1: GCGGGCAGGGCGGCCTGCACGAAGCAATGCTGTCGAC; AS2: GCGGGCCTGCACGAAGCAATGCTGTTAAT; CR: AGGGGTCTTTGTAGTTTGGATCTC	0.833	0.501	T; 0.415
CsSNP14	Zwilch-like protein	C/T	AS1: GCGGGCAGGGCGGCTGGAGGCTTTTAGCCTGGAGGCC; AS2: GCGGGCTGGAGGCTTTTAGCCTGGATACT; CR: GACCACAGCATGTCCGTGAAGTCC	0.778	0.516	C; 0.425
CsSNP15	Broad-complex core protein isoform 6	C/T	AS1: GCGGGCAGGGCGGCTATACCTTCCTCCAGAGGCCGCC; AS2: GCGGGCTATACCTTCCTCCAGAGGCTACT; CR: GTCAGTGTATTTCACACCCTTGAG	0.223	0.212	T; 0.325
CsSNP16	V-Type proton Atpase 116 kda subunit	C/T	AS1: GCGGGCAGGGCGGCTATACCTTCCTCCAGAGGCCGCC; AS2: GCGGGCTATACCTTCCTCCAGAGGCTACT; CR: GTCAGTGTATTTCACACCCTTGAG	0.456	0.487	C; 0.212

GC tails are underlined, and additional deliberate mismatches are boxed. AS1 and AS2: allele-specific primers; CR: common reverse primer; 𝐻_𝑜: observed heterozygosity; 𝐻_𝑒: expected heterozygosity.