Development and Characterization of New Single Nucleotide Polymorphism Markers from Expressed Sequence Tags in Common Carp (Cyprinus carpio)
Abstract
:1. Introduction
2. Results and Discussion
3. Experimental Section
3.1. Detection and Annotation of Putative SNPs
3.2. Validation and Characterization of SNPs
3.3. Data Analysis
4. Conclusions
Supplementary Materials
Acknowledgements
References
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Cluster ID | Primers designed | Length (bp, anticipative/actual) | Number of SNPs (putative/validated) | New SNPs in exon/intron | Annotation |
---|---|---|---|---|---|
Cyprinus_Cluster7873.seq.Contig1 | 7873-1 | 180/388 | 1/0 | 14/32(5) a | extracellular space |
7873-2 | 196/313 | 1/0 | 4/0 | ||
Cyprinus_Cluster7877.seq.Contig1 | 7877 | 163/250 | 6/1 | 0/0 | malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) activity |
Cyprinus_Cluster7885.seq.Contig1 | 7885 | 215/215 | 1/0 | 1(2)/− | actin binding |
Cyprinus_Cluster7889.seq.Contig1 | 7889 | 319/822 | 1/0 | 0/0 | cornified envelope |
Cyprinus_Cluster7892.seq.Contig1 | 7892 | 253/377 | 4/1 | 0/0 | structural constituent of ribosome |
Cyprinus_Cluster7895.seq.Contig1 | 7895-2 | 157/954 | 1/0 | 2/11(5) | cerebroside-sulfatase activity |
Cyprinus_Cluster7896.seq.Contig1 | 7896 | 448/450 | 1/0 | 1/− | nucleus |
Cyprinus_Cluster7898.seq.Contig1 | 7898 | 238/238 | 0/0 | 13/− | creatine kinase activity |
Cyprinus_Cluster7909.seq.Contig1 | 7909 | 533/533 | 2/0 | 13/− | N.A. b |
Cyprinus_Cluster7918.seq.Contig1 | 7918 | 278/550 | 1/1 | 1/0 | cathepsin H activity |
Cyprinus_Cluster7921.seq.Contig1 | 7921 | 164/319 | 1/0 | 1/2 | N.A. |
Cyprinus_Cluster7927.seq.Contig1 | 7927 | 322/322 | 1/1 | 1/− | N.A. |
Cyprinus_Cluster7929.seq.Contig1 | 7929 | 222/1433 | 1/0 | 1/13(3) | 3-hydroxyanthranilate 3,4-dioxygenase activity |
Cyprinus_Cluster7933.seq.Contig1 | 7933 | 429/1016 | 1/1 | 34(1)/55(18) | glutathione transferase activity |
Cyprinus_Cluster7943.seq.Contig1 | 7943 | 402/405 | 4/0 | 1(2)/− | N.A. |
Cyprinus_Cluster7944.seq.Contig1 | 7944 | 298/298 | 4/0 | 5/− | GTPase activity |
Cyprinus_Cluster7947.seq.Contig1 | 7947 | 236/419 | 2/1 | 2/3 | lysozyme activity |
Cyprinus_Cluster7953.seq.Contig1 | 7953 | 347/347 | 1/1 | 7/− | serine-type endopeptidase inhibitor activity |
Cyprinus_Cluster7955.seq.Contig1 | 7955 | 240/357 | 3/0 | 0/0 | actin binding |
Cyprinus_Cluster7957.seq.Contig1 | 7957 | 354/1428 | 5/0 | 2/17(2) | fructose-bisphosphate ldolase activity |
Cyprinus_Cluster7961.seq.Contig1 | 7961 | 222/418 | 2/1 | 21/26(5) | external side of plasma membrane |
Cyprinus_Cluster7969.seq.Contig1 | 7969 | 217/216 | 4/4 | 7/− | antigen binding |
Cyprinus_Cluster7974.seq.Contig1 | 7974 | 215/443 | 6/0 | 1/5 | N.A. |
Cyprinus_Cluster7980.seq.Contig1 | 7980-2 | 211/529 | 7/0 | 1/13(1) | l-lactate dehydrogenase activity |
Cyprinus_Cluster7986.seq.Contig1 | 7986-2 | 191/404 | 1/0 | 4/17 | binding |
Cyprinus_Cluster7988.seq.Contig1 | 7988 | 184/324 | 1/0 | 16/30(2) | receptor activity |
Cyprinus_Cluster7990.seq.Contig1 | 7990 | 273/1301 | 2/1 | (2)/3 | ubiquitin-protein ligase activity |
Cyprinus_Cluster7992.seq.Contig1 | 7992 | 139/139 | 1/0 | 1/− | adenyl-nucleotide exchange factor activity |
Cyprinus_Cluster8000.seq.Contig1 | 8000 | 419/709 | 2/0 | 2/3 | glucose-6-phosphatase activity |
Cyprinus_Cluster8001.seq.Contig1 | 8001 | 376/1412 | 2/1 | 2/4(2) | N.A. |
Cyprinus_Cluster8008.seq.Contig1 | 8008 | 233/1715 | 2/1 | 0/0 | integral to membrane |
Cyprinus_Cluster8009.seq.Contig1 | 8009-2 | 213/412 | 3/1 | 3/3 | calcium ion binding |
Cyprinus_Cluster8011.seq.Contig1 | 8011 | 303/302 | 2/0 | 2/− | thyroxine 5′-deiodinase activity |
Cyprinus_Cluster8012.seq.Contig1 | 8012 | 203/203 | 2/0 | 1(1)/0 | N.A. |
Cyprinus_Cluster8013.seq.Contig1 | 8013 | 260/257 | 5/1 | 1/0 | N.A. |
Cyprinus_Cluster8017.seq.Contig1 | 8017 | 313/1384 | 3/0 | (1)/6 | regulation of progression through cell cycle |
Cyprinus_Cluster8021.seq.Contig1 | 8021 | 447/656 | 8/0 | 6/1 | N.A. |
Cyprinus_Cluster8025.seq.Contig1 | 8025 | 318/875 | 2/2 | 0/7 | steroid binding |
Cyprinus_Cluster8034.seq.Contig1 | 8034 | 327/327 | 2/0 | 2/− | bisphosphoglycerate mutase activity |
Cyprinus_Cluster8041.seq.Contig1 | 8041 | 173/329 | 1/0 | 0/2 | cytoplasm |
Cyprinus_Cluster8048.seq.Contig1 | 8048 | 256/989 | 2/0 | 1/0 | dolichyl-diphosphooligosaccharide-protein glycotransferase activity |
Cyprinus_Cluster8050.seq.Contig1 | 8050-1 | 179/179 | 1/0 | 6(1)/− | signal transducer activity |
Cyprinus_Cluster8052.seq.Contig2 | 8052cg2 | 286/792 | 1/1 | 13/53(15) | l-lactate dehydrogenase activity |
Cyprinus_Cluster8123.seq.Contig1 | 8123 | 428/428 | 7/3 | 6/0 | mitochondrion |
Cyprinus_Cluster8142.seq.Contig1 | 8142 | 420/420 | 7/3 | 1/0 | N.A. |
Cyprinus_Cluster8184.seq.Contig1 | 8184 | 413/413 | 3/0 | 12/0 | N.A. |
Total | 47 | 13,213/27,010 | 121/26 | 202(10)/306(58) | - |
Transitions | Transversions | Multiple | |||||
---|---|---|---|---|---|---|---|
A/G | C/T | A/C | A/T | G/C | GT | ||
In exons | 64 | 81 | 27 | 18 | 19 | 18 | 1C/G/T |
In introns | 88 | 68 | 29 | 55 | 26 | 39 | 1A/G/T |
In complete sequences | 152 | 149 | 56 | 73 | 45 | 55 | 2 |
Loci | Allele Frequencies | He | Ho | PIC | p-value |
---|---|---|---|---|---|
CC a 7892G > A | 0.355(A)/0.645(G) | 0.464 | 0.342 | 0.403 | 0.15446 |
CC7953C > G | 0.263(G)/0.737(C) | 0.393 | 0.526 | 0.313 | 0.04006 |
CC7943G > A | 0.316(A)/0.684(G) | 0.438 | 0.474 | 0.339 | 0.71678 |
CC7909-1G > A | 0.355(A)/0.645(G) | 0.464 | 0.500 | 0.353 | 0.73065 |
CC7909-2T > C | 0.145(C)/0.855(T) | 0.251 | 0.237 | 0.217 | 0.57020 |
CC7909-3A > G | 0.25(G)/0.75(A) | 0.380 | 0.395 | 0.305 | 1.00000 |
CC7909-4A > T | 0.145(T)/0.855(A) | 0.251 | 0.237 | 0.217 | 0.56984 |
CC7909-5T > C | 0.145(C)/0.856(T) | 0.251 | 0.237 | 0.217 | 0.56926 |
CC7909-6G > C | 0.145(C)/0.857(G) | 0.251 | 0.237 | 0.217 | 0.56908 |
CC7909-7T > A | 0.092(A)/0.908(T) | 0.169 | 0.079 | 0.153 | 0.01852 |
CC7909-8A > G | 0.079(G)/0.921(A) | 0.147 | 0.105 | 0.135 | 0.19207 |
CC7909-9T > A | 0.066(A)/0.934(T) | 0.125 | 0.079 | 0.115 | 0.13050 |
CC7909-10T > C | 0.224(C)/0.776(T) | 0.352 | 0.184 | 0.287 | 0.00768 |
CC7909-11T > C | 0.092(C)/0.908(T) | 0.169 | 0.079 | 0.153 | 0.01862 |
CC7909-12T > A | 0.092(A)/0.909(T) | 0.169 | 0.079 | 0.153 | 0.01853 |
CC7909-13T > C | 0.368(C)/0.632(T) | 0.472 | 0.158 | 0.357 | 0.00003 |
CC7969-1G > T | 0.053(T)/0.947(G) | 0.101 | 0.053 | 0.095 | 0.07912 |
CC7969-2C > A | 0.290(A)/0.710(C) | 0.417 | 0.158 | 0.327 | 0.00030 |
CC7969-3C > G | 0.111(G)/0.889(C) | 0.200 | 0.111 | 0.178 | 0.04048 |
CC7969-4A > G | 0.167(G)/0.833(A) | 0.282 | 0.333 | 0.239 | 0.55952 |
CC7969-5A > C | 0.236(C)/0.764(A) | 0.366 | 0.472 | 0.296 | 0.15560 |
CC7969-6A > G | 0.236(G)/0.764(A) | 0.366 | 0.472 | 0.296 | 0.15479 |
CC7969-7T > G | 0.236(G)/0.764(T) | 0.366 | 0.472 | 0.296 | 0.15639 |
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Zhu, C.; Cheng, L.; Tong, J.; Yu, X. Development and Characterization of New Single Nucleotide Polymorphism Markers from Expressed Sequence Tags in Common Carp (Cyprinus carpio). Int. J. Mol. Sci. 2012, 13, 7343-7353. https://doi.org/10.3390/ijms13067343
Zhu C, Cheng L, Tong J, Yu X. Development and Characterization of New Single Nucleotide Polymorphism Markers from Expressed Sequence Tags in Common Carp (Cyprinus carpio). International Journal of Molecular Sciences. 2012; 13(6):7343-7353. https://doi.org/10.3390/ijms13067343
Chicago/Turabian StyleZhu, Chuankun, Lei Cheng, Jingou Tong, and Xiaomu Yu. 2012. "Development and Characterization of New Single Nucleotide Polymorphism Markers from Expressed Sequence Tags in Common Carp (Cyprinus carpio)" International Journal of Molecular Sciences 13, no. 6: 7343-7353. https://doi.org/10.3390/ijms13067343