Table 2 List of the 62 C. ensifolium genic-SSR primers including their unigenes annotation
Name | Product size (bp) | SSR | SSR location | Primer | Homologs in non-redundant database (accession in Genebank) | GO annotation | KOG annotation | KEGG annotation | Allele number | PIC |
|---|---|---|---|---|---|---|---|---|---|---|
SSR01 | 400-500 | (AC)8 | utr5 | F: AACGCCATGTCCAATACCC | PREDICTED: probable transcription factor KAN2-like (XP_002278005.2) | GO: 0003677 | KOG1601 | NULL | 5 | 0.552 |
| Â | Â | Â | Â | R: GGAGGGCTTATTTGCAGCG | Â | Â | Â | Â | Â | Â |
SSR02 | 300-400 | (AC)8 | utr5 | F: CTCCTTCAAGCTTCTGCCC | PREDICTED: histone-lysine N-methyltransferase, H3 lysine-9, H3 lysine-27, H4 lysine-20 and cytosine specific SUVH2 (XP_002282386.1) | GO: 0042393 | NULL | NULL | NA | NA |
| Â | Â | Â | Â | R: GACCGCAGCGTTAATGACC | Â | Â | Â | Â | Â | Â |
SSR03 | 400-500 | (AC)8 | utr3 | F: CTCGGTTCATTTGCAGCCC | PREDICTED: mitochondrial import receptor subunit TOM20 (XP_002269795.1) | GO: 0045040 | NULL | NULL | 7 | 0.690 |
| Â | Â | Â | Â | R: GGGTGGGTATGGCGAAATC | Â | Â | Â | Â | Â | Â |
SSR04 | 400-500 | (AC)8 | utr3 | F: AGAATCTGCCAACCCTTGATAC | NULL | NULL | NULL | NULL | 6 | 0.657 |
| Â | Â | Â | Â | R: GCAGATGCCAGTTAGAATGGG | Â | Â | Â | Â | Â | |
SSR05 | 1000 | (AC)8 | utr3 | F: AGAACTGCAGGTGTGAAGC | PREDICTED: protein CbbY, chromosomal-like isoform 1 (XP_003574671.1) | GO: 0016787 | NULL | NULL | 3 | 0.125 |
| Â | Â | Â | Â | R: GGCTTGAAGTGGCGATAACC | Â | Â | Â | Â | Â | |
SSR06 | 600 | (AC)9 | utr3 | F: GCGTCTGCTGAAACGATGG | Putative steroid 22-alpha-hydroxylase (AAN60994.1) | GO: 0016020 | KOG0157 | K09587 | 2 | 0.063 |
| Â | Â | Â | Â | R: AAACAGCGCCTGTCATTCC | Â | Â | Â | Â | Â | Â |
SSR07 | 300-400 | (AC)9 | utr3 | F: ACGCTGCATCCCATTTCAC | PREDICTED: uncharacterized protein LOC100243361 (XP_002276849.2) | GO: 0008987 | NULL | K03517 | 4 | 0.180 |
| Â | Â | Â | Â | R: CAGTCTGTTGAGGAAGCCG | Â | Â | Â | Â | Â | Â |
SSR08 | 100-200 | (AC)10 | utr3 | F: TGCTGGAATACATGCGAGAC | Predicted protein (XP_002298559.1) | GO: 0023014 | KOG0610 | Â | 14 | 0.753 |
| Â | Â | Â | Â | R: GTTTGCCGAAGCCAGTGC | Â | Â | Â | Â | Â | Â |
SSR11 | 600 | (AG)10 | utr3 | F: AACTGACAAGCATCTGCAAG | Uncharacterized protein LOC100273319 precursor (NP_001141232.1) | GO: 0005774 | NULL | NULL | 6 | 0.477 |
| Â | Â | Â | Â | R: CTGCTGCATTGGCCTTACC | Â | Â | Â | Â | Â | Â |
SSR12 | 300 | (AG)11 | utr5 | F: TCAGCCGAGGTTAGTATACGG | PREDICTED: phosphatidylinositol-4-phosphate 5-kinase 9-like (XP_002265706.1) | GO: 0016020 | KOG0229 | K00889 | NA | NA |
| Â | Â | Â | Â | R: CTTGCCATCTCAGCAGTCG | Â | Â | Â | Â | Â | Â |
SSR13 | 400-500 | (AG)11 | utr5 | F: GCTGCTGCTTGGTGGAAAC | Predicted protein (XP_002317724.1) | GO: 0005488 | NULL | NULL | 6 | 0.343 |
| Â | Â | Â | Â | R: GCGCTCGTTGTATGGCTTG | Â | Â | Â | Â | Â | Â |
SSR14 | 300 | (AG)11 | utr5 | F: CACAGCAGCTCACAATCCTG | Unnamed protein product (CBI20568.3) | GO: 0006099 | KOG1257 | K00029 | 8 | 0.467 |
| Â | Â | Â | Â | R: TACAGCCCTGTTTACCGCC | Â | Â | Â | Â | Â | Â |
SSR15 | 100-200 | (AG)11 | utr3 | F: CCTTCTCTCCGCGTACCAG | PREDICTED: uncharacterized protein LOC100825549 (XP_003558805.1) | GO: 0005783 | NULL | NULL | 4 | 0.339 |
| Â | Â | Â | Â | R: CTTCGGTTGGCGTTTAGGG | Â | Â | Â | Â | Â | Â |
SSR16 | 300-400 | (AG)11 | utr5 | F: GCCCACAGCAATCCATCTG | PE repeat family protein (XP_003014087.1) | NULL | NULL | NULL | 7 | 0.348 |
| Â | Â | Â | Â | R: GCAGTCGAAGAAACCGTGG | Â | Â | Â | Â | Â | Â |
SSR17 | 400 | (AG)11 | utr5 | F: GGATCACCAACAGCATGGG | Transcription factor (ADG57844.1) | GO: 0003677 | NULL | K09060 | 4 | 0.417 |
| Â | Â | Â | Â | R: TCCACCAAGAGCAAGGATG | Â | Â | Â | Â | Â | Â |
SSR18 | 300 | (AG)11 | utr5 | F: TGAAACGGTTGGCTCTAGTTC | Conserved hypothetical protein (XP_002527260.1) | NULL | NULL | NULL | 13 | 0.519 |
| Â | Â | Â | Â | R: AGCAAGCACTGACCTGAAAC | Â | Â | Â | Â | Â | |
SSR21 | 300-500 | (GT)8 | utr3 | F: TGGGCGACAGATCGAGTTC | Hypothetical protein OsJ_08996 (EAZ25197.1) | NULL | NULL | NULL | 15 | 0.794 |
| Â | Â | Â | Â | R: ACATGGACCACAGCATTCC | Â | Â | Â | Â | Â | Â |
SSR22 | 200-300 | (GT)9 | utr3 | F: TATGCGTCTCTCCCAACCG | 14-3-3-like protein B-like(ACQ45020.1) | GO: 0019904 | KOG0841 | K06630 | 10 | 0.572 |
| Â | Â | Â | Â | R: AAGCTAGTGGCCTTTGGTG | Â | Â | Â | Â | Â | Â |
SSR23 | 100-200 | (GT)10 | utr3 | F: CGGCGATCGATTTATGAGCC | PREDICTED: beta-amylase 1, chloroplastic isoform 1 (XP_002285569.1) | GO: 0005634 | NULL | K01177 | NA | NA |
| Â | Â | Â | Â | R: CGATACTCCTCAATGTCGTGG | Â | Â | Â | Â | Â | |
SSR24 | 200-300 | (GT)11 | utr5 | F: TCGGTAACCTGTTGCAAGG | PREDICTED: flavin-containing monooxygenase YUCCA6-like (XP_003550114.1) | GO: 0050661 | NULL | K11816 | 2 | 0.063 |
| Â | Â | Â | Â | R: ACCTGTGAAGCTACCAGAC | Â | Â | Â | Â | Â | Â |
SSR25 | 100-250 | (GT)11 | utr3 | F: GAATCTCTCGCACCCGAAG | Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B, putative (XP_002528338.1) | GO: 0006536 | NULL | K02434 | NA | NA |
| Â | Â | Â | Â | R: TGGACAACATCAAGTGACGC | Â | Â | Â | Â | Â | |
SSR26 | 100-250 | (AAG)7 | utr3 | F: GCTTTATGCGACATCTGCG | Unnamed protein product (CBI25980.3) | GO: 0005634 | KOG1901 | NULL | 11 | 0.638 |
| Â | Â | Â | Â | R: CGTCGGTTCCATGCACATC | Â | Â | Â | Â | Â | Â |
SSR27 | 500-600 | (AGC)5 | utr3 | F: CTGCCTTCACAGCTAATGCC | Os04g0512400 (NP_001053298.1) | GO: 0046872 | NULL | NULL | 3 | 0.313 |
| Â | Â | Â | Â | R: GCATGCTTGGACGCTGAAC | Â | Â | Â | Â | Â | Â |
SSR29 | 200-300 | (AGC)6 | utr3 | F: AGCAAACGGCAAGTCATGG | RING finger protein 113A, putative (XP_002522169.1) | GO: 0016020 | NULL | K13127 | 2 | 0.033 |
| Â | Â | Â | Â | R: ATTCGACTACCAGCCGGAC | Â | Â | Â | Â | Â | Â |
SSR30 | 200-300 | (AGG)5 | utr3 | F: AAACGAAGGGCTGGAAGTC | NULL | NULL | NULL | NULL | 9 | 0.486 |
| Â | Â | Â | Â | R: TTTGACATCGGGAAGTGGC | Â | Â | Â | Â | Â | Â |
SSR31 | 100-200 | (AGG)5 | utr5 | F: GGGATGCATAGACCTTTCGC | Protein MSF1, putative (XP_002535293.1) | GO: 0005739 | KOG3336 | NULL | 2 | 0.033 |
| Â | Â | Â | Â | R: CAGGTTCAACGGCATCGTG | Â | Â | Â | Â | Â | Â |
SSR32 | 1000-1100 | (AGG)5 | utr3 | F: CTCCGGCCTCTGGTTACTC | PREDICTED: HVA22-like protein j (XP_002281038.1) | NULL | KOG1726 | NULL | 7 | 0.601 |
| Â | Â | Â | Â | R: AGTGATGAGGCTTGGACCG | Â | Â | Â | Â | Â | Â |
SSR34 | 700-900 | (AGG)6 | utr5 | F: GAGAGGGAATTGCAGTGGC | Hypothetical protein (BAI68347.1) | NULL | NULL | NULL | 6 | 0.696 |
| Â | Â | Â | Â | R: ACCGAGCTAGCACTTCATC | Â | Â | Â | Â | Â | Â |
SSR35 | 700-900 | (ATC)5 | utr5 | F: AGAGTGATTGTCCAGCTCCG | PREDICTED: diacylglycerol kinase-like (XP_003534537.1) | GO: 0009395 | NULL | K07029 | 4 | 0.475 |
| Â | Â | Â | Â | R: TGCCTCTCTGGTGATGTCC | Â | Â | Â | Â | Â | Â |
SSR36 | 400-500 | (ATC)5 | utr3 | F: AGTATTGGACCCTCCAGGC | NULL | NULL | NULL | NULL | 5 | 0.536 |
| Â | Â | Â | Â | R: AGAGGATCATGGTGTTAGGC | Â | Â | Â | Â | Â | |
SSR37 | 200-300 | (ATC)5 | utr5 | F: GGCCTAGCCAGCCCTTC | NULL | NULL | NULL | NULL | 3 | 0.205 |
| Â | Â | Â | Â | R: ATTTGGATCGCACAAGCGG | Â | Â | Â | Â | Â | Â |
SSR38 | 200-300 | (ATC)6 | utr3 | F: TAGCCCATGCCAGTGTTCC | LOC100285373 (NP_001151738.1) | GO: 0007165 | NULL | NULL | 3 | 0.149 |
| Â | Â | Â | Â | R: AACTGCCACAAGAGAAGGC | Â | Â | Â | Â | Â | Â |
SSR39 | 1000-1100 | (ATC)6 | utr3 | F: ACAGACTGCCACCTGTTCC | unnamed protein product (CBI38283.3) | GO: 0008234 | KOG1870 | K11835 | 5 | 0.401 |
| Â | Â | Â | Â | R: GCCTGCCTTTGCTCCTTG | Â | Â | Â | Â | Â | Â |
SSR40 | 400 | (ATC)6 | utr5 | F: ACAAGCATCATCCCAAATTCC | PREDICTED: probably inactive leucine-rich repeat receptor-like protein kinase At2g25790-like (XP_002267653.1) | GO: 0007165 | NULL | NULL | NA | NA |
| Â | Â | Â | Â | R: GCAGAAACTGGAGCTTGCC | Â | Â | Â | Â | Â | Â |
SSR42 | 200-300 | (CCG)5 | utr5 | F: GACGACATATCGCGTTCGG | unnamed protein product (CBI18667.3) | GO: 0003779 | KOG0160 | NULL | 6 | 0.564 |
| Â | Â | Â | Â | R: CTCAGCCACACCCAAGAGG | Â | Â | Â | Â | Â | Â |
SSR43 | 500 | (CCG)5 | utr5 | F: GGAGCTGCATACGCAAGTG | glycinebetaine/proline transporter (BAJ07206.1) | GO: 0015193 | NULL | NULL | 7 | 0.572 |
| Â | Â | Â | Â | R: AGCTTCTCACTGCCTCCAG | Â | Â | Â | Â | Â | Â |
SSR44 | 300-400 | (CCG)5 | utr5 | F: CGTCGACTCCTCGAGATCC | predicted protein (BAJ93650.1) | GO: 0046872 | NULL | NULL | NA | NA |
| Â | Â | Â | Â | R: GCGTTAGCAGCAGTCTTGG | Â | Â | Â | Â | Â | Â |
SSR45 | 400-500 | (CCG)5 | utr5 | F: GCCTTACACATCCCTTCCAAC | unnamed protein product (CBI33381.3) | GO: 0005515 | KOG0550 | NULL | 5 | 0.338 |
| Â | Â | Â | Â | R: TGCCTGCTGATAGTTTGCC | Â | Â | Â | Â | Â | Â |
SSR46 | 200-300 | (CCG)6 | utr5 | F: CCTTCGTGGACTCAACAGC | hypothetical protein SORBIDRAFT_01g031510 (XP_002465065.1) | NULL | NULL | NULL | 2 | 0.063 |
| Â | Â | Â | Â | R: TCTCGTGCAGGAATCGGTC | Â | Â | Â | Â | Â | Â |
SSR47 | 400-500 | (CCG)6 | utr3 | F: GCAGGTGTCCTCATCGGAG | CONSTANS-like protein (ADN97077.1) | GO: 0005622 | KOG1601 | NULL | NA | NA |
| Â | Â | Â | Â | R: CTCCGGCTAACTCCATCCC | Â | Â | Â | Â | Â | Â |
SSR49 | 300 | (CCG)7 | utr3 | F: AGAGGGCCACCTGCTTTC | predicted protein (XP_002312577.1) | NULL | KOG1863 | NULL | 6 | 0.549 |
| Â | Â | Â | Â | R: GCCAATTGCCAGATGGACG | Â | Â | Â | Â | Â | Â |
SSR52 | 400-500 | (CCT)4 | utr5 | F: AAGAGGCACTGCAAGACCC | hypothetical protein SORBIDRAFT_01g031070 (XP_002465040.1) | NULL | NULL | NULL | 8 | 0.378 |
| Â | Â | Â | Â | R: CGTTCCAGCAACCCATAGC | Â | Â | Â | Â | Â | Â |
SSR53 | 100-200 | (CCT)4 | utr5 | F: GCTGAAGGTTCCGGTCCTC | PREDICTED: uncharacterized protein LOC100830480 (XP_003580351.1) | NULL | NULL | NULL | 8 | 0.700 |
| Â | Â | Â | Â | R: TCCGCCTCTTTAAGCCGAC | Â | Â | Â | Â | Â | Â |
SSR54 | 200-300 | (CCT)4 | utr5 | F: ATCTTCCCTCCACATCGGC | hypothetical protein MTR_1g083540 (XP_003591171.1) | GO: 0005886 | NULL | NULL | 5 | 0.422 |
| Â | Â | Â | Â | R: TGGAGAAGAGTCGACCAGC | Â | Â | Â | Â | Â | Â |
SSR55 | 200-300 | (CCT)4 | utr5 | F: TGGAATGGTTCTAGGGCTTC | hypothetical protein (CCA65980.1) | NULL | NULL | NULL | 2 | 0.323 |
| Â | Â | Â | Â | R: CCACTGGTACCCTCCTTGG | Â | Â | Â | Â | Â | Â |
SSR56 | 900-1000 | (CCT)5 | utr5 | F: TGCTTCATTGTTGGAGGCG | predicted protein (XP_002324427.1) | GO: 0008643 | KOG0254 | NULL | 5 | 0.315 |
| Â | Â | Â | Â | R: AGTGGACGGAGAGTCAAGC | Â | Â | Â | Â | Â | Â |
SSR59 | 200-300 | (CGG)5 | utr3 | F: GTTTCCAACGGTCAGCTCG | leucine-rich repeat transmembrane protein kinase family protein (NP_177007.1) | GO: 0005524 | NULL | NULL | 3 | 0.432 |
| Â | Â | Â | Â | R: GTGATGTGGTAGCATCGCC | Â | Â | Â | Â | Â | Â |
SSR60 | 200-300 | (CGG)5 | utr5 | F: TACGGTTTCGACCAGCCTC | Unnamed protein product (CBI41056.3) | GO: 0005634 | KOG0265 | K10143 | 4 | 0.203 |
| Â | Â | Â | Â | R: CCATGCAGATCGGGCAAAG | Â | Â | Â | Â | Â | Â |
SSR62 | 300-400 | (CGG)6 | utr5 | F: GGTGGGTTAGACCAGCTCC | Hypothetical protein OsI_29809 (EAZ07555.1) | GO: 0005634 | NULL | NULL | 6 | 0.570 |
| Â | Â | Â | Â | R: TCCTCAAGGCAAAGCTCCC | Â | Â | Â | Â | Â | Â |
SSR63 | 100-200 | (CGG)6 | utr5 | F: CTTCCTCCACCTGGATCGC | Uncharacterized protein LOC100277474(NP_001144494.1) | GO: 0008270 | NULL | NULL | 4 | 0.308 |
| Â | Â | Â | Â | R: CTGCCGATCAATCCGAGAC | Â | Â | Â | Â | Â | Â |
SSR64 | 400-500 | (CGG)6 | utr3 | F: CGCTCAAAGAGATGGCACG | Os01g0226200 (NP_001042462.1) | NULL | NULL | NULL | 11 | 0.627 |
| Â | Â | Â | Â | R: TAGTACGGCGCTGCTTGAG | Â | Â | Â | Â | Â | Â |
SSR66 | 300-400 | (CGG)7 | utr3 | F: CATCTTCCTTGCCCGATGC | PREDICTED: pentatricopeptide repeat-containing protein At5g42310, mitochondrial (XP_002272226.1) | NULL | KOG4197 | NULL | 4 | 0.126 |
| Â | Â | Â | Â | R: CCCGCCAAATTTCGAGACC | Â | Â | Â | Â | Â | Â |
SSR68 | 100-200 | (GAT)5 | utr3 | F: CCAGATCGAATGGCTACGC | Hypothetical protein VITISV_010525 (CAN79523.1) | GO: 0003723 | NULL | NULL | 4 | 0.211 |
| Â | Â | Â | Â | R: CAAGGAGCTCGTCGAAGG | Â | Â | Â | Â | Â | Â |
SSR69 | 200-300 | (GAT)5 | utr5 | F: GTTTAGGCTAGCAGTGCGG | NULL | NULL | NULL | NULL | 3 | 0.149 |
| Â | Â | Â | Â | R: TGAGAACGTAGTGAAGTTGCC | Â | Â | Â | Â | Â | |
SSR70 | 200-300 | (GAT)7 | utr3 | F: CCCAACGCAGAACGATAGC | NULL | NULL | NULL | NULL | 5 | 0.529 |
| Â | Â | Â | Â | R: CGGTGGCACAAATGGAACG | Â | Â | Â | Â | Â | Â |
SSR71 | 400-500 | (GGT)5 | utr5 | F: GCATCGAAACCACTGTCGC | Hypothetical protein SORBIDRAFT_09g018170 (XP_002439663.1) | NULL | NULL | NULL | 2 | 0.262 |
| Â | Â | Â | Â | R: CCCTAGCCGGAGTCTCAAC | Â | Â | Â | Â | Â | Â |
SSR73 | 100-200 | (GGT)5 | utr3 | F: GGACACAATGGAGACGAAGG | T4.15 (CCH50976.1) | GO: 0044238 | NULL | NULL | 16 | 0.863 |
| Â | Â | Â | Â | R: TGCATGAAACCACATGGC | Â | Â | Â | Â | Â | Â |
SSR75 | 400-500 | (GTT)6 | utr3 | F: GCCTTTGACCATTCCGTGC | Mitogen-activated protein kinase 1 (AEQ28763.1) | GO: 0043622 | KOG0660 | K04371 | 2 | 0.118 |
| Â | Â | Â | Â | R: GGCCGCCATGAGTAAGAAC | Â | Â | Â | Â | Â | Â |
SSR76 | 500-600 | (GTT)6 | utr5 | F: AGACAGAGAGTCCCTAAAGGC | NULL | NULL | NULL | NULL | 7 | 0.519 |
| Â | Â | Â | Â | R: CAGGGATGTTAAGTGGGCTG | Â | Â | Â | Â | Â | |
SSR77 | 300-400 | (GTT)6 | utr3 | F: TTTGTGGCAGTGGAAAGCG | NULL | NULL | NULL | NULL | 5 | 0.470 |
| Â | Â | Â | Â | R: TGATACCAATGGCAAGGCG | Â | Â | Â | Â | Â | Â |
SSR79 | 200-300 | (GTT)6 | utr5 | F: AGGATTCATGTAGCCGACCTC | Hypothetical protein OsI_35425 (EEC67831.1) | NULL | NULL | K10728 | 2 | 0.207 |
| Â | Â | Â | Â | R: TCCCTGAAGGAGGCAAACC | Â | Â | Â | Â | Â | Â |
SSR80 | 400-500 | (GTT)7 | utr3 | F: GCACCCAGCTTGTTTGAGG | NULL | NULL | NULL | NULL | 8 | 0.626 |
| Â | Â | Â | Â | R: CCCATACATTACAGGCAAGC | Â | Â | Â | Â | Â | |