Phylogeny and Specific Determination of Gloydius halys-intermedius Complex Based on Complete Mitochondrial Genes
Abstract
:1. Introduction
2. Materials and Methods
2.1. Samples and DNA Extraction
2.2. Genome Sequencing, Assembly, and Annotation
2.3. Phylogenetic Tree Construction and Pairwise Distance Estimation
2.4. Molecular Species Delimitation
3. Results
3.1. The Composition of the Mitochondrial Genome
3.2. Phylogenetic Relationships
3.3. Species Delimitation
4. Discussion
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Appendix A
Abbreviations | Full Names |
---|---|
ND2 | NADH dehydrogenase subunit 2 |
COX1 | cytochrome c oxidase subunit I |
COX2 | cytochrome c oxidase subunit II |
ATP8 | ATP synthase F0 subunit 8 |
ATP6 | ATP synthase F0 subunit 6 |
COX3 | cytochrome c oxidase subunit III |
ND3 | NADH dehydrogenase subunit 3 |
ND4L | NADH dehydrogenase subunit 4L |
ND4 | NADH dehydrogenase subunit 4 |
ND5 | NADH dehydrogenase subunit 5 |
ND6 | NADH dehydrogenase subunit 6 |
CYTB | cytochrome b |
ND1 | NADH dehydrogenase subunit 1 |
Appendix B
Appendix B.1
No. | Species | Voucher Number |
---|---|---|
1 | G. caucasicus | B474 |
2 | G. cognatus | IA |
3 | G. halys | KM186844 |
4 | G. intermedius 2 | KM434236 |
5 | G. ussuriensis | KP262412 |
6 | G. intermedius 1 | MW143075 |
7 | G. shedaoensis | Q7 |
8 | G. stejnegeri | S6 |
9 | G. brevicaudus | B6 |
10 | G. himalayanus | MK559438 |
11 | G. changdaoensis | MT731652 |
12 | G. shedaoensis | KT726956 |
13 | O. okinavensis | AB175670-out |
Appendix B.2
1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | 0.005 | 0.005 | 0.004 | 0.009 | 0.005 | 0.005 | 0.004 | 0.008 | 0.008 | 0.005 | 0.005 | 0.009 | |
2 | 0.045 | 0.005 | 0.005 | 0.009 | 0.005 | 0.005 | 0.005 | 0.008 | 0.008 | 0.005 | 0.005 | 0.01 | |
3 | 0.037 | 0.037 | 0.004 | 0.009 | 0.004 | 0.004 | 0.004 | 0.009 | 0.009 | 0.005 | 0.005 | 0.009 | |
4 | 0.036 | 0.04 | 0.026 | 0.009 | 0.003 | 0.003 | 0.004 | 0.009 | 0.008 | 0.005 | 0.003 | 0.009 | |
5 | 0.108 | 0.113 | 0.112 | 0.112 | 0.009 | 0.009 | 0.009 | 0.008 | 0.008 | 0.009 | 0.009 | 0.009 | |
6 | 0.039 | 0.042 | 0.026 | 0.021 | 0.114 | 0.004 | 0.004 | 0.009 | 0.008 | 0.005 | 0.004 | 0.009 | |
7 | 0.035 | 0.044 | 0.03 | 0.015 | 0.114 | 0.026 | 0.005 | 0.009 | 0.008 | 0.005 | 0.003 | 0.009 | |
8 | 0.033 | 0.041 | 0.031 | 0.033 | 0.114 | 0.034 | 0.038 | 0.008 | 0.009 | 0.005 | 0.005 | 0.009 | |
9 | 0.116 | 0.123 | 0.125 | 0.127 | 0.106 | 0.119 | 0.129 | 0.119 | 0.009 | 0.009 | 0.009 | 0.009 | |
10 | 0.114 | 0.118 | 0.125 | 0.121 | 0.114 | 0.122 | 0.117 | 0.119 | 0.132 | 0.008 | 0.008 | 0.008 | |
11 | 0.042 | 0.054 | 0.051 | 0.047 | 0.109 | 0.049 | 0.046 | 0.048 | 0.118 | 0.115 | 0.006 | 0.009 | |
12 | 0.042 | 0.049 | 0.036 | 0.019 | 0.112 | 0.029 | 0.011 | 0.044 | 0.127 | 0.123 | 0.052 | 0.009 | |
13 | 0.137 | 0.137 | 0.139 | 0.14 | 0.128 | 0.137 | 0.137 | 0.139 | 0.147 | 0.12 | 0.129 | 0.14 |
Appendix C
Species | Voucher Number |
---|---|
O. okinavensis * | AB175670-Ovophis okinavensis |
G. shedaoensis | MK064736_G._shedaoensis_CHS329 |
MK064611_G._shedaoensis_CHS090 | |
MK064610_G._shedaoensis_CHS089 | |
KY040587_G._s_shedaoensis_JS1408D2 | |
KT726956_G._shedaoensis_shedaoensis | |
G. intermedius | MK064735_G_intermedius_CHS327 |
MK064733_G_intermedius_CHS324 | |
MK064614_G_intermedius_CHS095 | |
KY040589_G_s_qianshanensis_JS1306Q4 | |
KY040588_G_s_qianshanensis_JS150722 | |
KM434236_G_intermedius | |
G. stejnegeri | MK064732_G_stejnegeri_CHS323 |
MK064731_G_stejnegeri_CHS322 | |
KY040601_G_stejnegeri_JS1508S4 | |
KY040600_G_stejnegeri_JS1409S3 | |
G_stejnegeri_S6 | |
G. ussuriensis | MK064730_G_ussuriensis_CHS318 |
MK064729_G_ussuriensis_CHS316 | |
MK064612_G_ussuriensis_CHS092 | |
KP262412_G_ussuriensis | |
G. brevicaudus | MH220717_G_brevicaudus_ZJ121106 |
MH220697_G_brevicaudus_ZJ100802 | |
MH153664_G_brevicaudus_DWF4 | |
MH153663_G_brevicaudus_DWF3 | |
MH153662_G_brevicaudus_DWF2 | |
MF099695_G_brevicaudus_DWF04 | |
MF099694_G_brevicaudus_DWF03 | |
MF099693_G_brevicaudus_DWF02 | |
KY040616_G_brevicaudus_DL70 | |
KR046009_G_brevicaudus_SR153 | |
KR046007_G_brevicaudus_SR151 | |
KR046006_G_brevicaudus_SR150 | |
KR046005_G_brevicaudus_SR149 | |
G. halys | KY040592_G_halys_JSSD1607H9 |
KY040591_G_halys_JSSD1508X3 | |
KY040590_G_halys_SYNU1301908 | |
KM186844_G_halys | |
G. intermedius | JQ798882_G_intermedius_NIBRRP0000100199 |
JQ798881_G_intermedius_NIBRRP0000100251 | |
MW143075_G_intermedius | |
G. changdaoensi | MT731652_G_changdaoensis |
G. caucasicus | G_caucasicus_B474 |
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Vouchers | Species | Locations |
---|---|---|
AB175670 | Ovophis okinavensis * | Japan, Okinawa Islands |
B474 | G. caucasicus | Azerbaijan, Lankaran Region |
B6 | Gloydius brevicaudus | Liaoning, China |
IA | G. cognatus | Bayan Obo, Inner Mongolia, China |
Q7 | Gloydius shedaoensis | Wafangdian, Liaoning, China |
S6 | Gloydius stejnegeri | Lingshi, Shanxi, China |
KM186844 | Gloydius halys | Inner Mongolia, China |
KM434236 | Gloydius intermedius 2 | Heilongjiang, China |
KP262412 | Gloydius ussuriensis | Heilongjiang, China |
KT726956 | Gloydius shedaoensis | Lvshun, Liaoning, China |
MK559438 | Gloydius himalayanus | Himachal Pradesh, India |
MT731652 | Gloydius changdaoensis | Changdao, Shandong, China |
MW143075 | Gloydius intermedius 1 | Samcheok-si, Gangwon-do, South Korea |
Samples | Species | Length /bp | T% | C% | A% | G% | AT Skew | CG Skew |
---|---|---|---|---|---|---|---|---|
B474 | G. caucasicus | 17,224 | 26.0 | 28.8 | 32.2 | 13.1 | 0.11 | 0.37 |
B6 | Gloydius brevicaudus | 16,655 | 26.1 | 28.5 | 32.2 | 13.2 | 0.10 | 0.37 |
IA | G. cognatus | 17,228 | 25.9 | 28.8 | 32.4 | 12.9 | 0.11 | 0.38 |
Q7 | Gloydius shedaoensis | 17,216 | 25.8 | 28.9 | 32.4 | 12.9 | 0.11 | 0.38 |
S6 | Gloydius stejnegeri | 17,225 | 26.0 | 28.7 | 32.4 | 12.9 | 0.11 | 0.38 |
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Jin, L.; Xia, Z.; Liu, N.; Hou, S.; Lv, C.; Tang, L.; Feng, S.; Shi, J.; Bai, M. Phylogeny and Specific Determination of Gloydius halys-intermedius Complex Based on Complete Mitochondrial Genes. Genes 2025, 16, 276. https://doi.org/10.3390/genes16030276
Jin L, Xia Z, Liu N, Hou S, Lv C, Tang L, Feng S, Shi J, Bai M. Phylogeny and Specific Determination of Gloydius halys-intermedius Complex Based on Complete Mitochondrial Genes. Genes. 2025; 16(3):276. https://doi.org/10.3390/genes16030276
Chicago/Turabian StyleJin, Lijie, Zuyao Xia, Ning Liu, Shengyue Hou, Chuandong Lv, Lianyou Tang, Shuguang Feng, Jingsong Shi, and Ming Bai. 2025. "Phylogeny and Specific Determination of Gloydius halys-intermedius Complex Based on Complete Mitochondrial Genes" Genes 16, no. 3: 276. https://doi.org/10.3390/genes16030276
APA StyleJin, L., Xia, Z., Liu, N., Hou, S., Lv, C., Tang, L., Feng, S., Shi, J., & Bai, M. (2025). Phylogeny and Specific Determination of Gloydius halys-intermedius Complex Based on Complete Mitochondrial Genes. Genes, 16(3), 276. https://doi.org/10.3390/genes16030276