Population Structure and Genetic Diversity of Colletotrichum gloeosporioides on Citrus in China
Abstract
:1. Introduction
2. Materials and Methods
2.1. Collection of Fungal Strains
2.2. DNA Extraction, PCR Amplification, and Sequencing
2.3. Data Analysis
3. Results
3.1. GAPDH Sequence Haplotype Diversity
3.2. Haplotype Network Analysis
3.3. Genetic Differentiation Analysis
3.4. Population Expansion Analysis
3.5. Phylogenetic Relationship Analysis Based on GAPDH Sequences
4. Discussion
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Strain | Site (Code) | Longitude, Latitude | Host (Code) | Genbank Accession of GAPDH | Hyplotype (Hn) | Collection Year |
---|---|---|---|---|---|---|
HY2 | Huangyan, Zhejiang (HY) | 121.17, 28.64 | Citrus sinensis Osbeck (QC) | MT449239 | H5 | 2018 |
HY3 | Huangyan, Zhejiang (HY) | 121.17, 28.64 | Citrus sinensis Osbeck (QC) | MT449240 | H5 | 2018 |
HY4 | Huangyan, Zhejiang (HY) | 121.17, 28.64 | Citrus unchiu Hort. ex Tanaka (WG) | MT449241 | H19 | 2018 |
HY5 | Huangyan, Zhejiang (HY) | 121.17, 28.64 | Citrus unchiu Hort. ex Tanaka (WG) | MT449242 | H17 | 2018 |
HY6 | Huangyan, Zhejiang (HY) | 121.17, 28.64 | Citrus reticulata Blanco cv. Succosa (BDZ) | MT449243 | H5 | 2018 |
HY7 | Huangyan, Zhejiang (HY) | 121.17, 28.64 | Citrus reticulata Blanco cv. Succosa (BDZ) | MT449244 | H5 | 2018 |
HY12 | Huangyan, Zhejiang (HY) | 121.17, 28.64 | Citrus unchiu Hort. ex Tanaka (WG) | MT449249 | H6 | 2018 |
HY14 | Huangyan, Zhejiang (HY) | 121.17, 28.64 | Citrus unchiu Hort. ex Tanaka (WG) | MT449251 | H1 | 2018 |
HY18 | Huangyan, Zhejiang (HY) | 121.17, 28.64 | Citrus reticulata Blanco cv. Succosa (BDZ) | MT449255 | H1 | 2018 |
HY19 | Huangyan, Zhejiang (HY) | 121.17, 28.64 | Citrus reticulata Blanco cv. Succosa (BDZ) | MT449256 | H5 | 2018 |
LH1 | Linhai, Zhejiang (LH) | 121.29, 28.76 | Citrus unchiu Hort. ex Tanaka (WG) | MT449257 | H1 | 2018 |
LH2 | Linhai, Zhejiang (LH) | 121.29, 28.76 | Citrus unchiu Hort. ex Tanaka (WG) | MT449258 | H5 | 2018 |
LH3 | Linhai, Zhejiang (LH) | 121.29, 28.76 | Citrus reticulata Blanco cv. Succosa (BDZ) | MT449259 | H5 | 2018 |
LH4 | Linhai, Zhejiang (LH) | 121.29, 28.76 | Citrus reticulata Blanco cv. Succosa (BDZ) | MT449260 | H5 | 2018 |
LH6 | Linhai, Zhejiang (LH) | 121.29, 28.76 | Citrus reticulata Blanco cv. Succosa (BDZ) | MT449262 | H5 | 2018 |
LH8 | Linhai, Zhejiang (LH) | 121.29, 28.76 | Citrus reticulata Blanco cv. Succosa (BDZ) | MT449264 | H6 | 2018 |
LH9 | Linhai, Zhejiang (LH) | 121.29, 28.76 | Citrus unchiu Hort. ex Tanaka (WG) | MT449265 | H7 | 2018 |
LH10 | Linhai, Zhejiang (LH) | 121.29, 28.76 | Citrus reticulata Blanco cv. Succosa (BDZ) | MT449266 | H5 | 2018 |
LH11 | Linhai, Zhejiang (LH) | 121.29, 28.76 | Citrus reticulata Blanco cv. Succosa (BDZ) | MT449267 | H5 | 2018 |
LH12 | Linhai, Zhejiang (LH) | 121.29, 28.76 | Citrus reticulata Blanco cv. Succosa (BDZ) | MT449268 | H5 | 2018 |
LH13 | Linhai, Zhejiang (LH) | 121.29, 28.76 | Citrus reticulata Blanco cv. Succosa (BDZ) | MT449269 | H5 | 2018 |
LH14 | Linhai, Zhejiang (LH) | 121.29, 28.76 | Citrus unchiu Hort. ex Tanaka (WG) | KC293710 | H5 | 2018 |
JD1 | Jiande, Zhejiang (JD) | 119.56, 29.54 | Citrus unchiu Hort. ex Tanaka (WG) | MT449270 | H5 | 2018 |
JD2 | Jiande, Zhejiang (JD) | 119.56, 29.54 | Citrus unchiu Hort. ex Tanaka (WG) | MT449271 | H5 | 2018 |
JD3 | Jiande, Zhejiang (JD) | 119.56, 29.54 | Citrus unchiu Hort. ex Tanaka (WG) | MT449272 | H6 | 2018 |
JD4 | Jiande, Zhejiang (JD) | 119.56, 29.54 | Citrus unchiu Hort. ex Tanaka (WG) | MT449273 | H5 | 2018 |
JD5 | Jiande, Zhejiang (JD) | 119.56, 29.54 | Citrus unchiu Hort. ex Tanaka (WG) | MT449274 | H5 | 2018 |
JD6 | Jiande, Zhejiang (JD) | 119.56, 29.54 | Citrus unchiu Hort. ex Tanaka (WG) | MT449275 | H5 | 2018 |
JD7 | Jiande, Zhejiang (JD) | 119.56, 29.54 | Citrus unchiu Hort. ex Tanaka (WG) | MT449276 | H5 | 2018 |
JD8 | Jiande, Zhejiang (JD) | 119.56, 29.54 | Citrus unchiu Hort. ex Tanaka (WG) | MT449277 | H11 | 2018 |
GX1 | Mengshan, Guangxi (GX) | 110.53, 24.2 | Mashui tangerine (MSJ) | MT449278 | H5 | 2018 |
GX2 | Mengshan, Guangxi (GX) | 110.53, 24.2 | Mashui tangerine (MSJ) | MT449279 | H5 | 2018 |
GX3 | Mengshan, Guangxi (GX) | 110.53, 24.2 | Mashui tangerine (MSJ) | MT449280 | H5 | 2018 |
GX4 | Mengshan, Guangxi (GX) | 110.53, 24.2 | Mashui tangerine (MSJ) | MT449281 | H5 | 2018 |
GX5 | Mengshan, Guangxi (GX) | 110.53, 24.2 | Mashui tangerine (MSJ) | MT449282 | H5 | 2018 |
GX6 | Mengshan, Guangxi (GX) | 110.53, 24.2 | Mashui tangerine (MSJ) | MT449283 | H5 | 2018 |
GX7 | Mengshan, Guangxi (GX) | 110.53, 24.2 | Mashui tangerine (MSJ) | MT449284 | H1 | 2018 |
GX8 | Mengshan, Guangxi (GX) | 110.53, 24.2 | Mashui tangerine (MSJ) | MT449285 | H5 | 2018 |
GX9 | Mengshan, Guangxi (GX) | 110.53, 24.2 | Mashui tangerine (MSJ) | MT449286 | H1 | 2018 |
SX9 | Chenggu, Shanxi (SX) | 109.03, 34.31 | Citrus unchiu Hort. ex Tanaka (WG) | KC293717 | H9 | 2012 |
SX10 | Chenggu, Shanxi (SX) | 109.03, 34.31 | Citrus unchiu Hort. ex Tanaka (WG) | KC293718 | H2 | 2012 |
SX11 | Chenggu, Shanxi (SX) | 109.03, 34.31 | Citrus unchiu Hort. ex Tanaka (WG) | KC293719 | H5 | 2011 |
SX12 | Chenggu, Shanxi (SX) | 109.03, 34.31 | Citrus unchiu Hort. ex Tanaka (WG) | KC293720 | H3 | 2011 |
QZ1 | Quzhou, Zhejiang (QZ) | 118.88, 28.98 | Citrus unchiu Hort. ex Tanaka (WG) | MT449295 | H10 | 2019 |
QZ2 | Quzhou, Zhejiang (QZ) | 118.88, 28.98 | Citrus unchiu Hort. ex Tanaka (WG) | MT449296 | H11 | 2019 |
QZ3 | Quzhou, Zhejiang (QZ) | 118.88, 28.98 | Citrus unchiu Hort. ex Tanaka (WG) | MT449297 | H11 | 2019 |
QZ4 | Quzhou, Zhejiang (QZ) | 118.88, 28.98 | Citrus unchiu Hort. ex Tanaka (WG) | MT449298 | H15 | 2019 |
QZ5 | Quzhou, Zhejiang (QZ) | 118.88, 28.98 | Citrus unchiu Hort. ex Tanaka (WG) | MT449299 | H11 | 2019 |
QZ6 | Quzhou, Zhejiang (QZ) | 118.88, 28.98 | Citrus unchiu Hort. ex Tanaka (WG) | MT449300 | H14 | 2019 |
QZ7 | Quzhou, Zhejiang (QZ) | 118.88, 28.98 | Citrus unchiu Hort. ex Tanaka (WG) | MT449301 | H15 | 2019 |
QZ11 | Quzhou, Zhejiang (QZ) | 118.88, 28.98 | Citrus paradise Macf (PTY) | MT449305 | H15 | 2019 |
QZ12 | Quzhou, Zhejiang (QZ) | 118.88, 28.98 | Citrus paradise Macf (PTY) | MT449306 | H11 | 2019 |
QZ13 | Quzhou, Zhejiang (QZ) | 118.88, 28.98 | Citrus paradise Macf (PTY) | MT449307 | H18 | 2019 |
QZ14 | Quzhou, Zhejiang (QZ) | 118.88, 28.98 | Citrus paradise Macf (PTY) | MT449308 | H13 | 2019 |
QZ15 | Quzhou, Zhejiang (QZ) | 118.88, 28.98 | Citrus paradise Macf (PTY) | MT449309 | H8 | 2019 |
CA1 | Chun’an, Zhejiang (CA) | 118.56, 29.4 | Citrus unchiu Hort. ex Tanaka (WG) | MT449310 | H11 | 2019 |
CA2 | Chun’an, Zhejiang (CA) | 118.56, 29.4 | Citrus unchiu Hort. ex Tanaka (WG) | MT449311 | H15 | 2019 |
CA3 | Chun’an, Zhejiang (CA) | 118.56, 29.4 | Citrus unchiu Hort. ex Tanaka (WG) | MT449312 | H12 | 2019 |
CA4 | Chun’an, Zhejiang (CA) | 118.56, 29.4 | Citrus unchiu Hort. ex Tanaka (WG) | MT449313 | H16 | 2019 |
CA5 | Chun’an, Zhejiang (CA) | 118.56, 29.4 | Citrus unchiu Hort. ex Tanaka (WG) | MT449314 | H8 | 2019 |
JXGZ1 | Ganzhou, Jiangxi (JXGZ) | 114.9, 25.8 | Citrus sinensis Osbeck (QC) | KC293706 | H4 | 2011 |
JXGZ2 | Ganzhou, Jiangxi (JXGZ) | 114.9, 25.8 | Citrus sinensis Osbeck (QC) | KC293707 | H9 | 2011 |
JXGZ3 | Ganzhou, Jiangxi (JXGZ) | 114.9, 25.8 | Citrus unchiu Hort. ex Tanaka (WG) | KC293708 | H4 | 2011 |
Source | df | SS | MS | Est. Var. | % | Stat | Value | Prob (P) |
---|---|---|---|---|---|---|---|---|
geographic populations | ||||||||
Among Pops | 7 | 6.415 | 0.916 | 0.077 | 19% | PhiPT | 0.190 | 0.001 |
Within Pops | 55 | 17.997 | 0.327 | 0.327 | 81% | |||
Total | 62 | 24.413 | 0.404 | 100% | ||||
host populations | ||||||||
Among Pops | 4 | 3.403 | 0.851 | 0.047 | 12% | PhiPT | 0.115 | 0.002 |
Within Pops | 58 | 21.010 | 0.362 | 0.362 | 88% | |||
Total | 62 | 24.413 | 0.409 | 100% |
Geographical Populations | HY | LH | JD | GX | SX | QZ | CA | JXGZ | Host Populations | QC | WG | BDZ | MSJ | PTY |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
HY | 0.000 | QC | 0.000 | |||||||||||
LH | 0.052 | 0.000 | WG | 0.047 | 0.000 | |||||||||
JD | 0.056 | 0.096 | 0.000 | BDZ | 0.048 | 0.029 | 0.000 | |||||||
GX | 0.039 | 0.052 | 0.028 | 0.000 | MSJ | 0.132 | 0.137 | 0.012 | 0.000 | |||||
SX | 0.005 | 0.051 | 0.046 | 0.065 | 0.000 | PTY | 0.069 | 0.075 | 0.051 | 0.164 | 0.000 | |||
QZ | 0.020 | 0.030 | 0.010 | 0.123 | 0.040 | 0.000 | - | - | - | - | - | - | ||
CA | 0.223 | 0.144 | 0.183 | 0.368 | 0.049 | 0.027 | 0.000 | - | - | - | - | - | - | |
JXGZ | 0.321 | 0.270 | 0.300 | 0.462 | 0.102 | 0.220 | 0.280 | 0.000 | - | - | - | - | - | - |
Hn (Number of Strains) | Geographical Origin | Host Origin | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
HY (n) | LH (n) | JD (n) | GX (n) | SX (n) | QZ (n) | CA (n) | JXGZ (n) | QC (n) | WG (n) | BDZ (n) | MSJ (n) | PTY (n) | |
H1 (2) | H1 (1) | H5 (6) | H1 (2) | H2 (1) | H8 (1) | H8 (1) | H4 (2) | H4 (1) | H1 (2) H2 (1) H3 (1) H4 (1) H5 (9) H6 (2) H7 (1) H8 (1) H9 (1) H10 (1) H11 (5) H12 (1) H14 (1) H15 (3) H16 (1) H17 (1) H19 (1) | H1 (1) | H1 (2) | H8 (1) | |
H5 (5) | H5 (9) | H6 (1) | H5 (7) | H3 (1) | H10 (1) | H11 (1) | H9 (1) | H5 (2) | H5 (10) | H5 (7) | H11 (1) | ||
H6 (1) | H6 (1) | H11 (1) | H5 (1) | H11 (4) | H12 (1) | H9 (1) | H6 (1) | H13 (1) | |||||
H17 (1) | H7 (1) | H9 (1) | H13 (1) | H15 (1) | H15 (1) | ||||||||
H19 (1) | H14 (1) | H16 (1) | H18 (1) | ||||||||||
H15 (3) | |||||||||||||
H18 (1) | |||||||||||||
Total number of strains | 10 | 12 | 8 | 9 | 4 | 12 | 5 | 3 | 4 | 33 | 12 | 9 | 5 |
Haploid diversity (h) | 0.680 | 0.417 | 0.406 | 0.346 | 0.750 | 0.792 | 0.800 | 0.444 | 0.625 | 0.876 | 0.292 | 0.346 | 0.800 |
Unbiased diversity(uh) | 0.756 | 0.455 | 0.464 | 0.389 | 1.000 | 0.864 | 1.000 | 0.667 | 0.833 | 0.903 | 0.318 | 0.389 | 1.000 |
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Liu, B.; Liang, X.; Kong, J.; Jiao, C.; Li, H.; Gai, Y. Population Structure and Genetic Diversity of Colletotrichum gloeosporioides on Citrus in China. Agronomy 2023, 13, 184. https://doi.org/10.3390/agronomy13010184
Liu B, Liang X, Kong J, Jiao C, Li H, Gai Y. Population Structure and Genetic Diversity of Colletotrichum gloeosporioides on Citrus in China. Agronomy. 2023; 13(1):184. https://doi.org/10.3390/agronomy13010184
Chicago/Turabian StyleLiu, Bei, Xingxing Liang, Jinchao Kong, Chen Jiao, Hongye Li, and Yunpeng Gai. 2023. "Population Structure and Genetic Diversity of Colletotrichum gloeosporioides on Citrus in China" Agronomy 13, no. 1: 184. https://doi.org/10.3390/agronomy13010184