Isolation and Characterization of Novel Genomic and EST-SSR Markers in Coreoperca whiteheadi Boulenger and Cross-Species Amplification
Abstract
:1. Introduction
2. Results and Discussion
3. Experimental Section
4. Conclusions
Acknowledgments
References
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Screening step | Number and percentage |
---|---|
Sequenced clones | 90 |
Redundant clones | 30 (33.33%) |
Unique clones | 60 (66.67%) |
SSR clones | 49 (81.67%) |
Primer design | 31 |
Polymorphic markers | 7 |
Locus | Gene Bank | Repeat motif | Primer sequence(5′-3′) | Na (size range, bp) | Ta (°C) | HO | He | PIC | P-HWE |
---|---|---|---|---|---|---|---|---|---|
EST-SSR | |||||||||
CW399 | JX503464 | (CA)10N(CA)10 | F: ATTTGCATTCGAGGTCATC | 4 (104–136) | 55 | 1.0000 | 0.7118 | 0.6464 | 0.4512 |
R: CAGATACATCATGGTGTCCTT | |||||||||
CW403 | JX503460 | (GT)5N(TG)6 | F: CTGAATTTGAATTGTCTGGA | 5 (180–263) | 55 | 1.0000 | 0.7574 | 0.7063 | 0.0002 * |
R: ACACACGCTGACACTATTTC | |||||||||
CW411 | JX503452 | (TG)12 | F: CAACTAATCATCACAGCCCA | 4 (86–116) | 58 | 0.9688 | 0.7039 | 0.6383 | 0.0101 |
R: GCTCCATACTGTACTCATTACCA | |||||||||
CW416 | JX503447 | (AC)13N(CA)8(CT)8 | F: GACCAAAGATTTCAAGGAGT | 5 (185–250) | 55 | 0.5000 | 0.6736 | 0.6155 | 0.3571 |
R: AGTACAAAGATAGAGGGATGTG | |||||||||
CW372 | JX503491 | (AC)11N(AC)5 | F: ATCACACACTCGCAACATTC | 4 (164–225) | 60 | 0.9688 | 0.7257 | 0.6620 | 0.0029 |
R: GTAAAGGGGTCGTATGTCGT | |||||||||
CW376 | JX503487 | (CAG)9 | F: CTTGGACCTGAACCTGGA | 3 (250–283) | 58 | 0.9063 | 0.6066 | 0.5299 | 0.9911 |
R: CCACCAACACCTACTCCCTAT | |||||||||
CW460 | JX503403 | (GT)9N(TC)5 | F: AATGGGACCACCCCTCTTGT | 3 (232–268) | 55 | 1.0000 | 0.6344 | 0.5540 | 0.0000 * |
R: GGGGAAGGATGAGGAGTTTG | |||||||||
CW426 | JX503437 | (GT)13(GA)18 | F: TTTGAATCCTCCACTTGTA | 3 (139–171) | 54 | 0.8125 | 0.6652 | 0.5813 | 0.9815 |
R: ATGTAGTCCGAAGCAGAAG | |||||||||
CW461 | JX503402 | (TC)14 | F: CGCGTCCGATCTGTTTTACC | 3 (178–194) | 55 | 0.9375 | 0.6647 | 0.5799 | 0.0041 |
R: AAGCTGCTCTTTCATCTCGTCA | |||||||||
CW745 | JX503388 | (TG)18 | F: AAGAGTGCGGAAGACGAGG | 4 (103–137) | 55 | 1.0000 | 0.7257 | 0.6632 | 0.0120 |
R: ACAACCCAACCACCACCAA | |||||||||
CW467 | JX503396 | (TCA)5 | F: TGGTCTCCGCACAACATCAT | 5 (238–300) | 55 | 1.0000 | 0.6920 | 0.6182 | 0.0000 * |
R: CCAGATCCACATCCCTTCAC | |||||||||
Mean | 3.9 | 0.9176 | 0.6874 | 0.6177 | |||||
G-SSR | |||||||||
FC124 | JX449121 | (TCC)6 | F: CCAACGCAGCAACATTTCTA | 4 (185–222) | 60 | 0.5313 | 0.6344 | 0.5755 | 0.5555 |
R: TGACAAGCAGAAGAGGAGGC | |||||||||
FC133 | JX449126 | (TCC)9 | F: GAGTCAGCAGAAGGGAACCA | 4 (101–121) | 62 | 1.0000 | 0.7431 | 0.6829 | 0.0034 |
R: GGGACTGGGACTAACACTTC | |||||||||
FC137 | JX449130 | (TG)20 | F: CCCTCTCTGTTGTCTTGGCT | 6 (65–108) | 62 | 0.6563 | 0.6205 | 0.5841 | 0.2640 |
R: GTCTACTCCCTAACCCCAGT | |||||||||
FC139 | JX449132 | (AGG)5 | F: GTGCTCCAACCAGACAGAGG | 4 (74–92) | 60 | 0.9063 | 0.6141 | 0.5422 | 0.0003 * |
R: AACTTGTTGCTCTTCATCCA | |||||||||
FC154 | JX449140 | (CCT)8 | F: AGCCACGACTGTTTAGATGA | 3 (197–241) | 60 | 0.3750 | 0.6146 | 0.5242 | 0.0421 |
R: AGAGTGCTCCAGTCCACAGT | |||||||||
FC161 | JX449144 | (GGA)4 | F: CAGGAGATGAGGGTGACA | 3 (308–472) | 60 | 0.4250 | 0.4766 | 0.4658 | 0.0261 |
R: GAGGAGGGAGATACAGAAGC | |||||||||
FC163 | JX449146 | (GAG)6 | F: GTGTTGAAGGTGTGGAGGTG | 3 (187–230) | 58 | 0.8438 | 0.6592 | 0.5743 | 0.0109 |
R: GTCTGTTTGGAAGGAATG | |||||||||
Mean | 3.8 | 0.6339 | 0.5804 | 0.5213 |
Locus | Repeat motif | Primer sequence (5′-3′) | Expected size (bp) | Ta (°C) | Na | Gene Bank | |
---|---|---|---|---|---|---|---|
F: | R: | ||||||
CW370 | (TG)14 | CTTATTGGCTATGTGGTGCT | GTCCCTTTCTCTCTGTTTACTTC | 280–380 | 58 | 5/-- | JX503493 |
CW372 | (AC)11N(AC)5 | ATCACACACTCGCAACATTC | GTAAAGGGGTCGTATGTCGT | 160–220 | 60 | 6/4 | JX503491 |
CW375 | (GT)17 | TCTGTACCACCTGAGCGTTC | TCCTGTTTATGCTCCACGAC | 130–160 | 60 | 4/-- | JX503488 |
CW376 | (CAG)9 | CTTGGACCTGAACCTGGA | CCACCAACACCTACTCCCTAT | 260–305 | 58 | 4/3 | JX503487 |
CW379 | (TC)12N(CT)5 | GGTCATACCTGGTGTAGTCACT | ATTACCCAGAAGCACTAGCAT | 170–212 | 58 | 4/-- | JX503484 |
CW380 | (CCA)6N(TCA)7 | CCTCTGCGCTAACTAACA | CTTCTCCAGCTTCTTCAAAC | 147–201 | 55 | 4/-- | JX503483 |
CW382 | (AC)5N(TG)14N(GT)5 | GAAGCAACACAGCCAGAAGAGG | TTCCACGGCGTCTCCAAC | 350–410 | 60 | 3/-- | JX503481 |
CW389 | (AC)22N(AC)5N(TG)5 | TAACAGACAAAACCTGGACT | ATGGCTCCTGGTATTTAGTG | 280–350 | 58 | 5/-- | JX503474 |
CW390 | (AC)12 | CAACAATGAGAACCCACAGA | CAGCAAAGAGCAGAGTTGTA | 217–280 | 58 | 5/-- | JX503473 |
CW392 | (AAT)5 | GATAATACTGCTGAGCAAGTC | TCATCACACTCAGTAGCAAC | 220–310 | 58 | 3/-- | JX503471 |
CW395 | (CA)11 | CACAGAAGTGAACCGACA | CAACAGTCTTGACAATCTCTCT | 200–250 | 55 | 5/-- | JX503468 |
CW398 | (CA)6N(CA)14N(CA)5 | ACAGTTTGACGGAGTGTAAC | ACTTCAGACAAGCAAATGTG | 147–230 | 58 | 5/-- | JX503465 |
CW399 | (CA)10N(CA)10 | ATTTGCATTCGAGGTCATC | CAGATACATCATGGTGTCCTT | 90–155 | 55 | 5/4 | JX503464 |
CW403 | (GT)5N(TG)6 | CTGAATTTGAATTGTCTGGA | ACACACGCTGACACTATTTC | 190–260 | 55 | 4/5 | JX503460 |
CW408 | (ATC)11 | GCATTAGGGACATTAGGTACTC | GCCATGTTTCAGTTCAGGTA | 125–210 | 58 | 4/-- | JX503455 |
CW411 | (TG)12 | CAACTAATCATCACAGCCCA | GCTCCATACTGTACTCATTACCA | 100–171 | 58 | 5/4 | JX503452 |
CW412 | (AC)18 | ACATCGAGACTACTGGAAGG | CATCAATTACTTGGTCTCCAT | 170–210 | 55 | 4/-- | JX503451 |
CW413 | (TTGT)5 | AGGTGTGAACTATAAGTAGCACG | ACTCCACTGGCTACACACAT | 123–170 | 60 | 3/-- | JX503450 |
CW416 | (AC)13N(CA)8(CT)8 | GACCAAAGATTTCAAGGAGT | AGTACAAAGATAGAGGGATGTG | 180–210 | 55 | 4/5 | JX503447 |
CW425 | (TCT)6 | TCATAGCTCCGCCTACACCA | CAGCGACGCACCAGCAAAA | 170–300 | 56 | 5/-- | JX503438 |
CW426 | (GT)13(GA)18 | TTTGAATCCTCCACTTGTA | ATGTAGTCCGAAGCAGAAG | 130–255 | 54 | 8/3 | JX503437 |
CW429 | (CA)20 | TCACTAAGATGATTGCTGC | TGACTACTGTTGTGATGGG | 200–310 | 54 | 5/-- | JX503434 |
CW432 | (GT)20 | ATATTCCAGTGGGTTTTACTTACA | GCTAGCCTCCCTCCCTTA | 200–250 | 57 | 4/-- | JX503431 |
CW437 | (AATA)5 | CACATATTAACAAGTCAGCGTGAG | ATGGCTTTGAGTTCTGAGACGA | 210–270 | 55 | 4/-- | JX503426 |
CW443 | (TGA)8 | AACTGTTGGTGGTGATGAGGG | GATCGTGTTGGAAAGAATGTCG | 160–220 | 55 | 5/-- | JX503420 |
CW447 | (AC)12 | GCTGGTTCTGGCTCTGGTC | TATAAGGAATGTGAGGGTCTGG | 200–280 | 57 | 3/-- | JX503416 |
CW454 | (TG)13 | ATCCATCCAGGTTCAAGTGC | TCAATCTTCTCTTTATTGACCACAT | 280–355 | 55 | 5/-- | JX503409 |
CW457 | (TTA)5N(TG)6 | CTGACTCATGCTGCATATTGTGA | GCCAGGGTGCAATTAAGTGT | 242–309 | 55 | 4/-- | JX503406 |
CW460 | (GT)9N(TC)5 | AATGGGACCACCCCTCTTGT | GGGGAAGGATGAGGAGTTTG | 210–260 | 55 | 3/3 | JX503403 |
CW461 | (TC)14 | CGCGTCCGATCTGTTTTACC | AAGCTGCTCTTTCATCTCGTCA | 170–200 | 55 | 3/3 | JX503402 |
CW465 | (CTG)7 | CTGACAGGCAGAAGGTAGCA | ATTTAGCAGAGCTTTGACCC | 180–280 | 55 | 4/-- | JX503398 |
CW467 | (TCA)5 | TGGTCTCCGCACAACATCAT | CCAGATCCACATCCCTTCAC | 220–290 | 55 | 5/5 | JX503396 |
CW740 | (GT)9T(TG)12 | AGACATCCCAATGTGGCAGAA | ACGCAAGACAAGCCATACGTG | 210–300 | 55 | 4/-- | JX503393 |
CW745 | (TG)18 | AAGAGTGCGGAAGACGAGG | ACAACCCAACCACCACCAA | 107–160 | 55 | 4/4 | JX503388 |
CW754 | (AC)23 | AGAATGGTCAAACTCCTGCAA | ATCACTATTTACCACGTACACTCGA | 160–275 | 55 | 6/-- | JX503379 |
CW757 | (ACC)7 | CTAGGACGCTTCCAAACTGG | GGGAGAAAGGGTAGCAGAGG | 250–300 | 58 | 4/-- | JX503376 |
CW759 | (CA)13N(CA)8 | TGGGCGACGGCTTAGAAAG | TATCGAGTGAATCATTGGAATCG | 250–330 | 54 | 3/-- | JX503374 |
Mean | 4.3/3.8 |
© 2012 by the authors; licensee Molecular Diversity Preservation International, Basel, Switzerland. This article is an open-access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/3.0/).
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Tian, C.; Liang, X.; Yang, M.; Zheng, H.; Dou, Y.; Cao, L. Isolation and Characterization of Novel Genomic and EST-SSR Markers in Coreoperca whiteheadi Boulenger and Cross-Species Amplification. Int. J. Mol. Sci. 2012, 13, 13203-13211. https://doi.org/10.3390/ijms131013203
Tian C, Liang X, Yang M, Zheng H, Dou Y, Cao L. Isolation and Characterization of Novel Genomic and EST-SSR Markers in Coreoperca whiteheadi Boulenger and Cross-Species Amplification. International Journal of Molecular Sciences. 2012; 13(10):13203-13211. https://doi.org/10.3390/ijms131013203
Chicago/Turabian StyleTian, ChangXu, XuFang Liang, Min Yang, HeZi Zheng, YaQi Dou, and Liang Cao. 2012. "Isolation and Characterization of Novel Genomic and EST-SSR Markers in Coreoperca whiteheadi Boulenger and Cross-Species Amplification" International Journal of Molecular Sciences 13, no. 10: 13203-13211. https://doi.org/10.3390/ijms131013203