Novel Microsatellite Markers of Meretrix petechialis and Cross-species Amplification in Related Taxa (Bivalvia: Veneroida)
Abstract
:1. Introduction
2. Results
2.1. Microsatellite Marker Isolation and Polymorphism Analyses
2.2. Genetic Variability of Meretrix petechialis Populations
2.3. Cross-Species Amplification
3. Discussion
4. Experimental Section
4.1. Sample Collection
4.2. Library Construction and Sequencing
4.3. Primer Design and Genotyping
4.4. Statistical Analysis
5. Conclusions
Acknowledgments
References
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Primer name | Core sequence | Primer (5′→3′) | Annealing temp. | Amplicon size | No. Allele | Ho | He | GenBank accession No. | |
---|---|---|---|---|---|---|---|---|---|
Mp01-nfrdi | (AC)34 | F R | GACCGCGATCGTATACAAGTCCC TCCGTGCATGTGTGCCTATATCC | 48 | 179–199 | 4 | 0.372 | 0.306 | JX017338 |
Mp02-nfrdi | (AC)14 | F R | CATGGGAAGCAGGCGGTTTGTTG ACATACGTGTGCGCATGCGTGTG | 52 | 102–164 | 9 | 0.327 | 0.287 | JX017339 |
Mp03-nfrdi | (AC)29 | F R | TCGTATACAAGTCCCGGTCCTGG TCCGTGCATGTGTGCCTATATCC | 50 | 149–155 | 2 | 0.118 | 0.111 | JX017340 |
Mp04-nfrdi | (AC)24 | F R | GGATTCCAGTTTAGCCCTCTC TATACACAGCGCAAGGTGAAC | 52 | 246–286 | 13 | 0.244 | 0.218 | JX017341 |
Mp05-nfrdi | (AC)28 | F R | CCATATTTGACAGCAGTTTCGTC CAAAGTATCGCCTGAACCTGAC | 50 | 78–92 | 6 | 0.369 | 0.34 | JX017342 |
Mp06-nfrdi | (AC)11 | F R | ACAGGACCTGATCGTGAACAC CAGGCCGAGTGCAGAAGTGGA | 50 | 168–196 | 2 | 0.14 | 0.13 | JX017343 |
Mp07-nfrdi | (AC)31 | F R | GTATACAAGTCCCGGTCCTGT CATCCGTGCATGTGTGCCTAT | 48 | 103–173 | 5 | 0.675 | 0.455 | JX017344 |
Mp08-nfrdi | (AC)37 | F R | TATAGTTCGGACGGACATGGACA GCCCAAGAGTTGAACATCAGGTT | 48 | 129–227 | 43 | 0.603 | 0.594 | JX017345 |
Mp09-nfrdi | (GT)5CT(GT)7 CT(GT)3 | F R | ACATACGTGTGCGCATGCATGTG GCAGGCGGTTTGGCTGGCAGGTC | 58 | 209–267 | 6 | 0.394 | 0.381 | JX017346 |
Mp10-nfrdi | (AC)10 | F R | AGGACCTGATCCTGAACACAC TCTGCATGACTGTCTGTCTCC | 48 | 188 | 1 | - | - | JX017347 |
Mp11-nfrdi | (GT)11 | F R | CCGAGTGCAGAAGAGGAACACAC CACACAGGACCTGATCGTGAACA | 48 | 118 | 1 | - | - | JX017348 |
Mp12-nfrdi | (AC)35 | F R | ACAGACCAAACCATCCTTATCCC CTATTTTCAAGCCAGGCAGAATG | 50 | 93 | 1 | - | - | JX017349 |
Mp13-nfrdi | (AC)8 | F R | TTAACCCGGCCACCCACCTATAC CGTATTTGTGCGCATGCGTGTGC | 50 | 83 | 1 | - | - | JX017350 |
Mp14-nfrdi | (GT)10 | F R | GCAGCAGGCCGAGTGCAGAAG CGTTGGGGCACCGCGACCACA | 48 | 165 | 1 | - | - | JX017351 |
Mp15-nfrdi | (GT)11TT(GT)16 (AT)2(GT)2GA(GT)9 | F R | GCCTATATCTGCGTATGTGCATC AGGGGACCGCGATCGTATACAAG | 48 | 112 | 1 | - | - | JX017352 |
Microsatellite loci | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
Pop. | Mp01-nfrdi | Mp02-nfrdi | Mp03-nfrdi | Mp04-nfrdi | Mp05-nfrdi | Mp06-nfrdi | Mp07-nfrdi | Mp08-nfrdi | Mp09-nfrdi | Means | |
GC | N | 35 | 35 | 35 | 34 | 33 | 35 | 35 | 35 | 35 | 34.7 |
Na | 3 | 5 | 2 | 7 | 2 | 2 | 2 | 18 | 3 | 5.3 | |
AR | 2.8 | 4.6 | 2.0 | 6.5 | 2.0 | 2.0 | 2.0 | 15.7 | 2.8 | 4.9 | |
R | 179–199 | 102–136 | 149–155 | 246–286 | 78–92 | 168–196 | 143–173 | 129–205 | 209–247 | ||
Ho | 0.400 | 0.286 | 0.114 | 0.353 | 0.303 | 0.057 | 0.714 | 0.543 | 0.571 | 0.372 | |
He | 0.330 | 0.260 | 0.109 | 0.319 | 0.261 | 0.056 | 0.466 | 0.549 | 0.467 | 0.365 | |
FIS | −0.212 | −0.097 | −0.045 | −0.107 | −0.161 | −0.015 | −0.533 * | 0.011 | −0.224 | −0.084 | |
MA | N | 58 | 57 | 58 | 58 | 58 | 58 | 58 | 58 | 57 | 57.8 |
Na | 2 | 6 | 2 | 8 | 2 | 2 | 3 | 26 | 4 | 6.7 | |
AR | 2.0 | 4.9 | 2.0 | 5.5 | 2.0 | 2.0 | 2.5 | 16.9 | 3.0 | 5.2 | |
R | 179–199 | 102–164 | 149–155 | 246–280 | 78–92 | 168–196 | 103–173 | 129–227 | 209–267 | ||
Ho | 0.431 | 0.263 | 0.138 | 0.345 | 0.379 | 0.155 | 0.603 | 0.586 | 0.333 | 0.355 | |
He | 0.341 | 0.243 | 0.130 | 0.308 | 0.331 | 0.144 | 0.430 | 0.651 | 0.309 | 0.374 | |
FIS | −0.264 | −0.084 | −0.065 | −0.119 | −0.146 | −0.075 | −0.403 * | 0.099 | −0.078 | −0.051 | |
Mean all pops. | N | 46.5 | 46 | 46.5 | 46 | 45.5 | 46.5 | 46.5 | 46.5 | 46 | |
Na | 2.5 | 5.5 | 2 | 7.5 | 2 | 2 | 2.5 | 22 | 3.5 | ||
AR | 2.4 | 4.8 | 2 | 6 | 2 | 1.9914 | 2.3 | 16.3 | 2.9 | ||
R | 179–199 | 102–164 | 149–155 | 246–286 | 78–92 | 168–196 | 103–173 | 129–227 | 209–267 | ||
Ho | 0.386 | 0.275 | 0.126 | 0.349 | 0.341 | 0.106 | 0.659 | 0.565 | 0.452 | ||
He | 0.336 | 0.252 | 0.119 | 0.314 | 0.296 | 0.1 | 0.448 | 0.6 | 0.388 | ||
FIS | −0.238 | −0.091 | −0.055 | −0.113 | −0.154 | −0.045 | −0.468 * | −0.055 | −0.151 |
Taxonomy | Veneridae | Psammobiidae | Mactridae | Corbiculidae | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Species | Meretrix petechialis | Meretrix lousoria | Gomphina veneriformis | Cyclina sinensis | Ruditapes philippinarum | Nuttallia japonica | Mactra chinensis | Mactra veneriformis | Tresus keenae | Corbicula japonica | Corbicula leana | Corbicula fluminea | Corbicula colorata | Transferability * |
Number of Individuals | 95 | 7 | 2 | 2 | 9 | 3 | 1 | 2 | 1 | 2 | 2 | 4 | 2 | |
Mp01-nfrdi | 179–199 | 179 | - | 91–139 | - | 179–199 | - | - | - | - | 77 | - | 83 | 41.7 (16.7) |
Mp02-nfrdi | 102–164 | - | 132 | 64–124 | 112–306 | 222 | - | 146 | 146–150 | 276–334 | 242–300 | 82–178 | 82 | 83.3 (50.0) |
Mp03-nfrdi | 149–155 | 149 | - | 143 | 117 | - | - | 65 | - | - | - | - | - | 33.3 (0) |
Mp04-nfrdi | 246–286 | - | - | - | - | - | - | - | - | - | - | - | - | 0/0 |
Mp05-nfrdi | 78–92 | 78–92 | - | 82–332 | - | 112 | - | 214 | - | 108 | - | 96 | - | 50.0 (16.7) |
Mp06-nfrdi | 168–196 | 168 | 126–296 | 126–298 | 72–122 | 126–140 | 196 | 82–228 | 164 | 98 | 166 | - | 132 | 91.7 (33.3) |
Mp07-nfrdi | 103–173 | 143–173 | - | 91–111 | - | 67 | - | - | - | - | 155–175 | - | 93 | 41.7 (25.0) |
Mp08-nfrdi | 129–227 | - | 87–123 | 89–99 | 137–245 | 159–161 | 169–253 | - | 215 | 101 | 243–245 | 111–135 | 245 | 83.3 (58.3) |
Mp09-nfrdi | 209–267 | - | - | - | - | - | - | - | - | - | - | - | - | 0/0 |
Mp10-nfrdi | 188 | 188 | 196 | 192–198 | 94–108 | - | 110–178 | 182 | 112 | 266–270 | - | 100–166 | - | 75.0 (41.7) |
Mp11-nfrdi | 118 | - | 132–138 | - | - | 132–146 | 156 | - | 94–178 | - | - | - | 138 | 41.7 (25.0) |
Mp12-nfrdi | 93 | - | 65–111 | 93 | 95–123 | - | - | 121–161 | - | - | - | - | - | 33.3 (25.0) |
Mp13-nfrdi | 83 | - | 71 | - | 65–87 | 115–215 | 91–219 | 91–139 | 199 | - | 105 | 83 | - | 66.7 (33.3) |
Mp14-nfrdi | 165 | - | 157 | 157 | 129–131 | 75 | - | 101 | - | - | - | - | 239–243 | 50.0 (16.7) |
Mp15-nfrdi | 112 | 76–112 | - | - | 102 | - | - | 222 | - | - | - | 126–350 | - | 33.3 (16.7) |
Transferability * | - | 46.7 (20.0) | 53.0 (26.7) | 66.7 (40.0) | 60 (46.7) | 60.0 (33.3) | 33.3 (20.0) | 60.0 (20.0) | 40.0 (13.3) | 33.3 (13.3) | 40.0 (20.0) | 40.0 (26.7) | 46.7 (6.7) |
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Kang, J.-H.; Kim, B.-H.; Park, J.-Y.; Lee, J.-M.; Jeong, J.-E.; Lee, J.-S.; Ko, H.-S.; Lee, Y.-S. Novel Microsatellite Markers of Meretrix petechialis and Cross-species Amplification in Related Taxa (Bivalvia: Veneroida). Int. J. Mol. Sci. 2012, 13, 15942-15954. https://doi.org/10.3390/ijms131215942
Kang J-H, Kim B-H, Park J-Y, Lee J-M, Jeong J-E, Lee J-S, Ko H-S, Lee Y-S. Novel Microsatellite Markers of Meretrix petechialis and Cross-species Amplification in Related Taxa (Bivalvia: Veneroida). International Journal of Molecular Sciences. 2012; 13(12):15942-15954. https://doi.org/10.3390/ijms131215942
Chicago/Turabian StyleKang, Jung-Ha, Byeng-Hak Kim, Jung-Youn Park, Jung-Mi Lee, Ji-Eun Jeong, Jun-Sang Lee, Hyun-Sook Ko, and Yong-Seok Lee. 2012. "Novel Microsatellite Markers of Meretrix petechialis and Cross-species Amplification in Related Taxa (Bivalvia: Veneroida)" International Journal of Molecular Sciences 13, no. 12: 15942-15954. https://doi.org/10.3390/ijms131215942