Population Diversity Analysis Provide Insights into Provenance Identification of Dendrobium catenatum
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Collection and DNA Extraction
2.2. RAD Library Development and Sequencing
2.3. SNP Calling
2.4. Phylogenetic Tree Construction
2.5. Population Structure Analyses
2.6. Genetic Diversity and Differentiation
3. Results
3.1. Sequence Data Quality
3.2. Genetic Diversity
3.3. Phylogenetic Tree
3.4. Population Structure
3.5. Genetic Relationships
3.6. Genetic Differentiation
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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Sample Name | Location | Specimen Code | Population Code | Individual Number |
---|---|---|---|---|
D. catenatum | Guangze, Fujian Province | Z.J. Liu 10572 | FJGZTP01 | 5 |
Liancheng, Fujian Province | Z.J. Liu 10583 | FJLCTP02 | 4 | |
Pingjiang, Hunan Province | Z.J. Liu 10580 | HNPJTP04 | 5 | |
Yiyang, Hunan Province | Z.J. Liu 10582 | HNYYTP05 | 5 | |
Yuanling, Hunan Province | Z.J. Liu 10578 | HNYLTP06 | 5 | |
Xinning, Hunan Province | Z.J. Liu 9506 | HNXNTP36 | 3 | |
Lipu, Guangxi Province | Z.J. Liu 10574 | GXLPTP07 | 5 | |
Gongcheng, Guangxi Province | Z.J. Liu 9497 | GXGCTP09 | 4 | |
Xing’an, Guangxi Province | Z.J. Liu 9518 | GXXATP10 | 5 | |
Lishui, Zhengjiang Province | Z.J. Liu 9520 | ZJLSTP12 | 5 | |
Wuyi, Zhengjiang Province | Z.J. Liu 9511 | ZJWYTP32 | 5 | |
Quzhou, Zhengjiang Province | Z.J. Liu 9510 | ZJQZTP13 | 5 | |
Yanshan, Jiangxi Province | Z.J. Liu 10576 | JXQSTP14 | 5 | |
Xiushui, Jiangxi Province | Z.J. Liu 10573 | JXXSTP15 | 4 | |
Huichang, Jiangxi Province | Z.J. Liu 10581 | JXHCTP16 | 5 | |
Xingguo, Jiangxi Province | Z.J. Liu 9517 | JXXGTP17 | 4 | |
Nanxiong, Guangdong Province | Z.J. Liu 10584 | GDNXTP19 | 5 | |
Heyuan, Guangdong Province | Z.J. Liu 10585 | GDHYTP20 | 4 | |
Shaoguan, Guangdong Province | Z.J. Liu 9504 | GDSGTP22 | 5 | |
Qujing, Yunnan Province | Z.J. Liu 10579 | YNQJTP24 | 4 | |
Wangzishan, Yunnan Province | Z.J. Liu 7462 | WZSTP34 | 4 | |
Xianning, Hubei Province | Z.J. Liu 9514 | HBXNTP25 | 5 | |
Sandu, Guizhou Province | Z.J. Liu 11147 | GZSDTP29 | 4 | |
Dushan, Guizhou Province | Z.J. Liu 11148 | GZDSTP30 | 4 | |
D. huoshanense | Huangshan, Anhui Province | Z.J. Liu 9508 | AHHSHS26 | 5 |
Longhushan, Jiangxi Province | Z.J. Liu 9500 | JXLHSHS28 | 5 |
Taxon | Population | AP | HO | HE | π | FIS | Tajima’s D |
---|---|---|---|---|---|---|---|
D. catenatum | 0.0992 | 0.1575 | 0.1584 | 0.3836 | |||
FJGZTP01 | 3254 | 0.0786 | 0.0969 | 0.1165 | 0.0725 | 0.6534 | |
FJLCTP02 | 1934 | 0.0729 | 0.0833 | 0.099 | 0.0496 | 0.3964 | |
HNPJTP04 | 2871 | 0.0895 | 0.1131 | 0.1297 | 0.0824 | 0.4221 | |
HNYYTP05 | 4263 | 0.0818 | 0.1082 | 0.1223 | 0.084 | 0.4411 | |
HNYLTP06 | 4689 | 0.0976 | 0.1196 | 0.1371 | 0.081 | 0.5556 | |
GXLPTP07 | 5512 | 0.0952 | 0.1312 | 0.1484 | 0.1135 | 0.4684 | |
GXGCTP09 | 2679 | 0.0965 | 0.1041 | 0.1355 | 0.066 | 0.7907 | |
GXXATP10 | 2940 | 0.0724 | 0.0891 | 0.1074 | 0.0628 | 0.8556 | |
ZJLSTP12 | 2355 | 0.0994 | 0.1182 | 0.1341 | 0.0737 | 0.3298 | |
ZJQZTP13 | 3084 | 0.1123 | 0.1105 | 0.1245 | 0.0256 | 0.3962 | |
JXQSTP14 | 3844 | 0.123 | 0.1115 | 0.1243 | 0.0053 | 0.3384 | |
JXXSTP15 | 2552 | 0.0783 | 0.107 | 0.1257 | 0.0922 | 0.3767 | |
JXHCTP16 | 3417 | 0.0778 | 0.1037 | 0.1188 | 0.0866 | 0.3404 | |
JXXGTP17 | 4215 | 0.0919 | 0.096 | 0.1134 | 0.039 | 0.5287 | |
GDNXTP19 | 3515 | 0.0848 | 0.1022 | 0.1154 | 0.0659 | 0.3163 | |
GDHYTP20 | 5221 | 0.1019 | 0.1155 | 0.133 | 0.0638 | 0.2443 | |
GDSGTP22 | 3845 | 0.1078 | 0.0862 | 0.0961 | −0.0208 | 0.4748 | |
YNQJTP24 | 3933 | 0.1144 | 0.1153 | 0.1343 | 0.039 | 0.4327 | |
HBXNTP25 | 2757 | 0.0979 | 0.1057 | 0.1185 | 0.0426 | 0.5005 | |
GZSDTP29 | 4461 | 0.0975 | 0.1147 | 0.1326 | 0.0696 | 0.4221 | |
GZDSTP30 | 9655 | 0.1516 | 0.1121 | 0.1288 | −0.0434 | 0.4646 | |
ZJWYTP32 | 2932 | 0.0885 | 0.106 | 0.1191 | 0.0664 | 0.2539 | |
WZSTP34 | 4820 | 0.125 | 0.1165 | 0.1342 | 0.0208 | 0.4762 | |
HNXNTP36 | 2967 | 0.1034 | 0.0994 | 0.1218 | 0.0332 | 0.4315 |
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Wu, X.-Y.; Li, T.-Z.; Zheng, F.; Chen, J.-B.; Yan, Y.-H.; Huang, J.-X. Population Diversity Analysis Provide Insights into Provenance Identification of Dendrobium catenatum. Genes 2022, 13, 2093. https://doi.org/10.3390/genes13112093
Wu X-Y, Li T-Z, Zheng F, Chen J-B, Yan Y-H, Huang J-X. Population Diversity Analysis Provide Insights into Provenance Identification of Dendrobium catenatum. Genes. 2022; 13(11):2093. https://doi.org/10.3390/genes13112093
Chicago/Turabian StyleWu, Xin-Yi, Ting-Zhang Li, Fang Zheng, Jian-Bing Chen, Yue-Hong Yan, and Jiu-Xiang Huang. 2022. "Population Diversity Analysis Provide Insights into Provenance Identification of Dendrobium catenatum" Genes 13, no. 11: 2093. https://doi.org/10.3390/genes13112093