In Silico Evaluation of the Haplotype Diversity, Phylogenetic Variation and Population Structure of Human E. granulosus sensu stricto (G1 Genotype) Sequences
Abstract
:1. Introduction
2. Materials and Methods
2.1. Data Collection
2.2. Alignment and Phylogenetic Analysis
2.3. Haplotype Analysis and Networking
3. Results
3.1. Polymorphism and Haplotype Analysis
3.2. Haplotype Network
3.3. Phylogenetic Tree
3.4. Gene Flow, Diversity and Neutrality Analysis
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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mt-CO1 | mt-ND1 | ||||
---|---|---|---|---|---|
Origin | No. of Isolates | Accession Numbers | Origin | No. of Isolates | Accession Numbers |
China | 43 | DQ356874-75-76-77-78-79-80/83, KJ628328-29-30-31-32-33-34-35, AB688602-03-04-05-06-07-08-09-10-11/13-14-15-16-17-18-19, MH050608-09-10-11-12-13-14-15-16-17 | Uzbekistan | 43 | MN696570/72/76-77-78-79-80-81-82-83-84-85-86-87-88-89-90-91-92-93-94-95-96-98-99, MN696600-01-02-03-04/06-07-08-09-10-11-12-13/15/19-20-21-22 |
Tunisia | 13 | MG672264-65-66-67-68-69-70-71-72-73-74-75-76 | Algeria | 20 | MG672128, KT316342, KR349038-39-40-41-42-43-44, MG672282/84-85-86-87-88-89-90-91-92-93 |
Pakistan | 12 | MK229295-96-97/99, MK229301-02/04/13/15/17-18-19 | China | 17 | AY572548, KJ556993-94, EU072111-12-13-14, MH050620-21-22-23-24-25-26-27-28-29 |
Mongolia | 12 | MG672254-55, AB893242-43-44-45-46-47-48-49-50-51 | Peru | 14 | JF946597-98-99, JF946600-01-02-03-04-05-06-07-08-09/24, |
Algeria | 12 | MG672128, MG672283-84-85-86-87-88-89-90-91-92-93 | Tunisia | 13 | MG672264-65-66-67-68-69-70-71-72-73-74-75-76 |
Turkey | 10 | EU006783, GU951512-13, MG886833-34-35-36-37-38-39 | Iran | 9 | KT284349, MG672245, JF836800-01-02-03, JF836797-98-99 |
Iran | 9 | KR337817, MW350099, MT073987, MG672245, MH025946-47, JQ250810/12/15 | Slovenia | 6 | MT239133-34-35/38/40/42 |
Russia | 9 | AB777904/07-08, AB688136-37-38-39-40-41 | Spain | 4 | KU925413-14, MG672129/37 |
Spain | 4 | MG672129/37, KU925413-14, | Iraq | 3 | FJ226756, MN231833-34 |
Finland | 3 | MG672132, KY766884, KU925429 | Finland | 3 | MG672132, KY766884, KU925429 |
India | 2 | JX854029-30 | Mongolia | 2 | MG672254-55 |
Morocco | 1 | EF367266 | Poland | 2 | KT780298- KT780300 |
Romania | 1 | MG672138 | Romania | 1 | MG672138 |
Kazakhstan | 1 | MG672257 | Kazakhstan | 1 | MG672257 |
Italy | 1 | MG672135 | Italy | 1 | MG672135 |
Morocco | 1 | EF367298 |
Haplotype Name | No. of Isolate | Accession Numbers |
---|---|---|
Hap01 | 2 | KJ628335-China, KJ628331-China |
Hap02 | 1 | KR337817-Iran |
Hap03 | 79 | GU951513-Turkey, GU951512-Turkey, JX854029-India, MG886839-Turkey, MG886838-Turkey, MG886837-Turkey, MG886836-Turkey, MG886835-Turkey, MG886834-Turkey, MG886833-Turkey, DQ356883-China, MW350099-Iran, MT073987-Iran, MK229301-Pakistan, MK229296-Pakistan, MH050617-China, MH050615-China, MH050614-China, MH050612-China, MH050609-China, MH050608-China, MH025946-Iran, KJ628334-China, KJ628333-China, KJ628332-China, KJ628330-China, KJ628329-China, AB688617-China, AB688616-China, AB688614-China, AB688611-China, AB688610-China, AB688609-China, AB688608-China, AB688607-China, AB688603-China, AB688602-China, JQ250815-Iran, AB893250-Mongolia, AB893249-Mongolia, AB893248-Mongolia, AB893247-Mongolia, AB893245-Mongolia, AB893244-Mongolia, AB893243-Mongolia, AB777908-Russia, AB777907-Russia, AB777904-Russia, AB688141-Russia, AB688136-Russia, MG672293-Algeria, MG672292-Algeria, MG672291-Algeria, MG672289-Algeria, MG672288-Algeria, MG672287-Algeria, MG672285-Algeria, MG672284-Algeria, MG672283-Algeria, MG672276-Tunisia, MG672275-Tunisia, MG672274-Tunisia, MG672272-Tunisia, MG672270-Tunisia, MG672269-Tunisia, MG672268-Tunisia, MG672266-Tunisia, MG672265-Tunisia, MG672264-Tunisia, MG672257-Kazakhstan, MG672254-Mongolia, MG672245-Iran, MG672135-Italy, MG672132-Finland, MG672129-Spain, MG672128-Algeria, KY766884-Finland, KU925429-Finland, KU925413-Spain |
Hap04 | 1 | EU006783-Turkey |
Hap05 | 2 | JX854030-India, MH050610-China |
Hap06 | 2 | MK229304-Pakistan, MK229299-Pakistan |
Hap07 | 1 | DQ356880-China |
Hap08 | 1 | DQ356879-China |
Hap09 | 2 | DQ356878-China, AB688604-China |
Hap10 | 12 | DQ356877-China, MK229302-Pakistan, MK229297-Pakistan, MH050611-China, JQ250812-Iran, JQ250810-Iran, AB893246-Mongolia, AB688140-Russia, AB688139-Russia, MG672290-Algeria, MG672267-Tunisia, MG672255-Mongolia |
Hap11 | 2 | DQ356876-China, DQ356875-China |
Hap12 | 1 | DQ356874-China |
Hap13 | 2 | MK229319-Pakistan, MK229313-Pakistan |
Hap14 | 3 | MK229318-Pakistan, AB688618-China, MG672286-Algeria |
Hap15 | 1 | MK229317-Pakistan |
Hap16 | 1 | MK229315-Pakistan |
Hap17 | 1 | MK229295-Pakistan |
Hap18 | 2 | MH050616-China, AB688606-China |
Hap19 | 1 | MH050613-China |
Hap20 | 1 | EF367266-Morocco |
Hap21 | 1 | MH025947-Iran |
Hap22 | 1 | KJ628328-China |
Hap23 | 1 | AB688619-China |
Hap24 | 1 | AB688615-China |
Hap25 | 1 | AB688613-China |
Hap26 | 1 | AB688605-China |
Hap27 | 1 | AB893251-Mongolia |
Hap28 | 1 | AB893242-Mongolia |
Hap29 | 1 | AB688138-Russia |
Hap30 | 1 | AB688137-Russia |
Hap31 | 1 | MG672273-Tunisia |
Hap32 | 1 | MG672271-Tunisia |
Hap33 | 1 | MG672138-Romania |
Hap34 | 2 | MG672137-Spain, KU925414-Spain |
Haplotype Name | No. of Isolate | Accession Numbers |
---|---|---|
Hap01 | 83 | KU925413-Spain, EU072111-China, FJ226756-Iraq, KT284349-Iran, JF836803-Iran, JF836802-Iran, JF836801-Iran, JF836799-Iran, JF836797-Iran, MN696622-Uzbekistan, MN696621-Uzbekistan, MN696620-Uzbekistan, MN696619-Uzbekistan, MN696606-Uzbekistan, MN696596-Uzbekistan, MN696591-Uzbekistan, MN696583-Uzbekistan, MN696572-Uzbekistan, MN696570-Uzbekistan, JF946609-Peru, JF946608-Peru, JF946607-Peru, JF946606-Peru, JF946605-Peru, JF946604-Peru, JF946603-Peru, JF946602-Peru, JF946601-Peru, JF946600-Peru, JF946599-Peru, JF946598-Peru, JF946597-Peru, KR349044-Algeria, KR349042-Algeria, KR349038-Algeria, MT239138-Slovenia, MT239133-Slovenia, KT780300-Poland, KT780298-Poland, JF946624-Peru, MH050629-China, MH050628-China, MH050626-China, MH050625-China, MH050622-China, MH050621-China, MH050620-China, KJ556994-China, KJ556993-China, MN231834-Iraq, EF367298-Morocco, MG672293-Algeria, MG672292-Algeria, MG672291-Algeria, MG672289-Algeria, MG672288-Algeria, MG672287-Algeria, MG672285-Algeria, MG672284-Algeria, MG672283-Algeria, MG672276-Tunisia, MG672275-Tunisia, MG672274-Tunisia, MG672273-Tunisia, MG672272-Tunisia, MG672271-Tunisia, MG672270-Tunisia, MG672268-Tunisia, MG672267-Tunisia, MG672266-Tunisia, MG672265-Tunisia, MG672264-Tunisia, MG672257-Kazakhstan, MG672255-Mongolia, MG672254-Mongolia, MG672245-Iran, MG672138-Romania, MG672135-Italy, MG672132-Finland, MG672129-Spain, MG672128-Algeria, KY766884-Finland, KU925429-Finland |
Hap02 | 1 | EU072114-China |
Hap03 | 2 | EU072113-China, JF836798-Iran |
Hap04 | 2 | EU072112-China, AY572548-China |
Hap05 | 15 | JF836800-Iran, MN696613-Uzbekistan, MN696612-Uzbekistan, MN696610-Uzbekistan, MN696609-Uzbekistan, MN696607-Uzbekistan, MN696599-Uzbekistan, MN696598-Uzbekistan, MN696590-Uzbekistan, MN696589-Uzbekistan, MN696587-Uzbekistan, MN696585-Uzbekistan, MN696584-Uzbekistan, MN696582-Uzbekistan, MN696581-Uzbekistan |
Hap06 | 1 | MN696615-Uzbekistan |
Hap07 | 2 | MN696611-Uzbekistan, MN696608-Uzbekistan |
Hap08 | 1 | MN696604-Uzbekistan |
Hap09 | 1 | MN696603-Uzbekistan |
Hap10 | 1 | MN696602-Uzbekistan |
Hap11 | 1 | MN696601-Uzbekistan |
Hap12 | 1 | MN696600-Uzbekistan |
Hap13 | 1 | MN696595-Uzbekistan |
Hap14 | 1 | MN696594-Uzbekistan |
Hap15 | 1 | MN696593-Uzbekistan |
Hap16 | 1 | MN696592-Uzbekistan |
Hap17 | 1 | MN696588-Uzbekistan |
Hap18 | 1 | MN696586-Uzbekistan |
Hap19 | 1 | MN696580-Uzbekistan |
Hap20 | 1 | MN696579-Uzbekistan |
Hap21 | 1 | MN696578-Uzbekistan |
Hap22 | 1 | MN696577-Uzbekistan |
Hap23 | 1 | MN696576-Uzbekistan |
Hap24 | 1 | KT316342-Algeria |
Hap25 | 1 | KR349043-Algeria |
Hap26 | 2 | KR349041-Algeria, MG672286-Algeria |
Hap27 | 2 | KR349040-Algeria, MG672290-Algeria |
Hap28 | 2 | KR349039-Algeria, MG672269-Tunisia |
Hap29 | 1 | MT239142-Slovenia |
Hap30 | 1 | MT239140-Slovenia |
Hap31 | 1 | MT239135-Slovenia |
Hap32 | 1 | MT239134-Slovenia |
Hap33 | 1 | MH050627-China |
Hap34 | 1 | MH050624-China |
Hap35 | 1 | MH050623-China |
Hap36 | 1 | MN231833-Iraq |
Hap37 | 2 | MG672137-Spain KU925414-Spain |
n | H | hd ± SD | πd ± SD | Tajima’s D | p Value | Fu’s Fs | p Value | FLD | p Value | FLF | p Value | |
---|---|---|---|---|---|---|---|---|---|---|---|---|
mt-CO1 | 133 | 34 | 0.640 ± 0.048 | 0.00255 ± 0.00031 | −2.47269 | *. p < 0.01 | −49.797 | 0.000 | −3.97170 | p < 0.02 | −4.03871 | p < 0.02 |
mt-ND1 | 140 | 37 | 0.639 ± 0.047 | 0.00611 ± 0.00147 | −2.80355 | *. p < 0.001 | −31.231 | 0.000 | −8.50154 | p < 0.02 | −7.14019 | p < 0.02 |
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Selcuk, M.A.; Celik, F.; Kesik, H.K.; Gunyakti Kilinc, S.; Ahmed, H.; Jiang, N.; Simsek, S.; Cao, J. In Silico Evaluation of the Haplotype Diversity, Phylogenetic Variation and Population Structure of Human E. granulosus sensu stricto (G1 Genotype) Sequences. Pathogens 2022, 11, 1346. https://doi.org/10.3390/pathogens11111346
Selcuk MA, Celik F, Kesik HK, Gunyakti Kilinc S, Ahmed H, Jiang N, Simsek S, Cao J. In Silico Evaluation of the Haplotype Diversity, Phylogenetic Variation and Population Structure of Human E. granulosus sensu stricto (G1 Genotype) Sequences. Pathogens. 2022; 11(11):1346. https://doi.org/10.3390/pathogens11111346
Chicago/Turabian StyleSelcuk, Muhammed Ahmed, Figen Celik, Harun Kaya Kesik, Seyma Gunyakti Kilinc, Haroon Ahmed, Nan Jiang, Sami Simsek, and Jianping Cao. 2022. "In Silico Evaluation of the Haplotype Diversity, Phylogenetic Variation and Population Structure of Human E. granulosus sensu stricto (G1 Genotype) Sequences" Pathogens 11, no. 11: 1346. https://doi.org/10.3390/pathogens11111346