Multiplex PCR and Sequence Analysis to Investigate Genetic Diversity of Fasciola Isolates from Cattle and Sheep in Turkey
Abstract
:1. Introduction
2. Materials and Methods
2.1. Collection of Adult Fasciola spp. Samples
2.2. Genomic DNA Isolation
2.3. Amplification of Pepck by Multiplex PCR
2.4. Amplification of nad1 by PCR
2.5. DNA Sequence Analysis
2.6. Haplotype Analysis
3. Results
3.1. Multiplex PCR Data
3.2. nad1 Sequence Analysis
3.3. Haplotype Analysis, Nucleotide Polymorphism, and Diversity and Neutrality Indices
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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n | hn | hd ± SD | πd ± SD | Tajima’s D | p Value | Fu’s Fs | p Value | FLD | p Value | FLF | p Value |
---|---|---|---|---|---|---|---|---|---|---|---|
50 | 47 | 0.997 ± 0.005 | 0.02423 ± 0.00159 | −0.43557 | p > 0.10 | −35.537 | 0.000 | 0.76537 | p > 0.10 | 0.38471 | p > 0.10 |
n | hn | hd ± SD | πd ± SD | Tajima’s D | p Value | Fu’s Fs | p Value | FLD | p Value | FLF | p Value |
---|---|---|---|---|---|---|---|---|---|---|---|
49 | 43 | 0.986 ± 0.011 | 0.02810 ± 0.00220 | −0.62751 | p > 0.10 | −22.700 | 0.000 | 1.23614 | p > 0.10 | 0.65299 | p > 0.10 |
Number | Haplotype Name | Isolate No. | Isolate Codes (Accession No.) |
---|---|---|---|
1 | Hap01 | 1 | [FHC01-ON640928] |
2 | Hap02 | 1 | [FHC02-ON640929] |
3 | Hap03 | 1 | [FHC03-ON640930] |
4 | Hap04 | 1 | [FHC04-ON640931] |
5 | Hap05 | 1 | [FHC05-ON640932] |
6 | Hap06 | 1 | [FHC06-ON640933] |
7 | Hap07 | 1 | [FHC07-ON640934] |
8 | Hap08 | 1 | [FHC08-ON640935] |
9 | Hap09 | 3 | [FHC09-ON640936 FHC42-ON640969 FHS24-ON641001] |
10 | Hap10 | 1 | [FHC10-ON640937] |
11 | Hap11 | 1 | [FHC11-ON640938] |
12 | Hap12 | 1 | [FHC12-ON640939] |
13 | Hap13 | 1 | [FHC13-ON640940] |
14 | Hap14 | 1 | [FHC14-ON640941] |
15 | Hap15 | 1 | [FHC15-ON640942] |
16 | Hap16 | 1 | [FHC16-ON640943] |
17 | Hap17 | 1 | [FHC17-ON640944 FHS15-ON640992 FHS27-ON641004] |
18 | Hap18 | 1 | [FHC18-ON640945] |
19 | Hap19 | 1 | [FHC19-ON640946] |
20 | Hap20 | 1 | [FHC20-ON640947] |
21 | Hap21 | 1 | [FHC21-ON640948] |
22 | Hap22 | 1 | [FHC22-ON640949] |
23 | Hap23 | 1 | [FHC23-ON640950] |
24 | Hap24 | 1 | [FHC24-ON640951] |
25 | Hap25 | 1 | FHC25-ON640952] |
26 | Hap26 | 9 | [FHC26-ON640953 FHC31-ON640958 FHC46-ON640973 FHS36-ON641013 FHS38-ON641015 FHS43-ON641020 FHS45-ON641022 FHS46-ON641023 FHS48-ON641025] |
27 | Hap27 | 1 | [FHC27-ON640954] |
28 | Hap28 | 1 | [FHC28-ON640955] |
29 | Hap29 | 1 | [FHC29-ON640956] |
30 | Hap30 | 1 | [FHC30-ON640957] |
31 | Hap31 | 1 | [FHC32-ON640959] |
32 | Hap32 | 1 | [FHC33-ON640960] |
33 | Hap33 | 1 | [FHC34-ON640961] |
34 | Hap34 | 1 | [FHC35-ON640962] |
35 | Hap35 | 1 | [FHC36-ON640963] |
36 | Hap36 | 1 | [FHC37-ON640964] |
37 | Hap37 | 1 | [FHC38-ON640965] |
38 | Hap38 | 1 | [FHC39-ON640966] |
39 | Hap39 | 1 | [FHC40-ON640967] |
40 | Hap40 | 1 | [FHC41-ON640968] |
41 | Hap41 | 1 | [FHC43-ON640970] |
42 | Hap42 | 1 | [FHC44-ON640971] |
43 | Hap43 | 1 | [FHC45-ON640972] |
44 | Hap44 | 1 | [FHC47-ON640974] |
45 | Hap45 | 1 | [FHC48-ON640975] |
46 | Hap46 | 1 | [FHC49-ON640976] |
47 | Hap47 | 1 | [FHC50-ON640977] |
48 | Hap48 | 1 | [FHS01-ON640978] |
49 | Hap49 | 1 | [FHS02-ON640979] |
50 | Hap50 | 1 | [FHS03-ON640980] |
51 | Hap51 | 1 | [FHS04-ON640981] |
52 | Hap52 | 1 | [FHS05-ON640982] |
53 | Hap53 | 1 | [FHS06-ON640983] |
54 | Hap54 | 1 | [FHS7-ON640984] |
55 | Hap55 | 1 | [FHS8-ON640985] |
56 | Hap56 | 1 | [FHS9-ON640986] |
57 | Hap57 | 1 | [FHS10-ON640987] |
58 | Hap58 | 1 | [FHS11-ON640988] |
59 | Hap59 | 1 | [FHS12-ON640989] |
60 | Hap60 | 1 | [FHS13-ON640990] |
61 | Hap61 | 1 | [FHS14-ON640991] |
62 | Hap62 | 1 | [FHS16-ON640993] |
63 | Hap63 | 1 | [FHS17-ON640994] |
64 | Hap64 | 1 | [FHS18-ON640995] |
65 | Hap65 | 1 | [FHS19-ON640996] |
66 | Hap66 | 1 | [FHS20-ON640997] |
67 | Hap67 | 1 | [FHS21-ON640998] |
68 | Hap68 | 1 | [FHS22-ON640999] |
69 | Hap69 | 1 | [FHS23-ON641000] |
70 | Hap70 | 1 | [FHS25-ON641002] |
71 | Hap71 | 1 | [FHS26-ON641003] |
72 | Hap72 | 1 | [FHS28-ON641005] |
73 | Hap73 | 1 | [FHS29-ON641006] |
74 | Hap74 | 1 | [FHS30-ON641007] |
75 | Hap75 | 1 | [FHS31-ON641008] |
76 | Hap76 | 1 | [FHS32-ON641009] |
77 | Hap77 | 1 | [FHS33-ON641010] |
78 | Hap78 | 1 | [FHS34-ON641011] |
79 | Hap79 | 1 | [FHS35-ON641012] |
80 | Hap80 | 1 | [FHS37-ON641014] |
81 | Hap81 | 1 | [FHS39-ON641016] |
82 | Hap82 | 1 | [FHS40-ON641017] |
83 | Hap83 | 1 | [FHS41-ON641018] |
84 | Hap84 | 1 | [FHS42-ON641019] |
85 | Hap85 | 1 | [FHS44-ON641021] |
86 | Hap86 | 1 | [FHS47-ON641024] |
87 | Hap87 | 1 | [FHS49-ON641026] |
n | hn | hd ± SD | πd ± SD | Tajima’s D | p Value | Fu’s Fs | p Value | FLD | p Value | FLF | p Value |
---|---|---|---|---|---|---|---|---|---|---|---|
99 | 87 | 0.991 ± 0.005 | 0.02661 ± 0.00148 | −0.85844 | p > 0.10 | −33.441 | 0.000 | 1.00700 | p > 0.10 | 0.26059 | p > 0.10 |
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Uzun, V.; Celik, F.; Simsek, S.; Kesik, H.K.; Kilinc, S.G.; Zhang, X.; Ahmed, H.; Cao, J. Multiplex PCR and Sequence Analysis to Investigate Genetic Diversity of Fasciola Isolates from Cattle and Sheep in Turkey. Pathogens 2022, 11, 1235. https://doi.org/10.3390/pathogens11111235
Uzun V, Celik F, Simsek S, Kesik HK, Kilinc SG, Zhang X, Ahmed H, Cao J. Multiplex PCR and Sequence Analysis to Investigate Genetic Diversity of Fasciola Isolates from Cattle and Sheep in Turkey. Pathogens. 2022; 11(11):1235. https://doi.org/10.3390/pathogens11111235
Chicago/Turabian StyleUzun, Veysel, Figen Celik, Sami Simsek, Harun Kaya Kesik, Seyma Gunyakti Kilinc, Xiaocheng Zhang, Haroon Ahmed, and Jianping Cao. 2022. "Multiplex PCR and Sequence Analysis to Investigate Genetic Diversity of Fasciola Isolates from Cattle and Sheep in Turkey" Pathogens 11, no. 11: 1235. https://doi.org/10.3390/pathogens11111235