Molecular Diversity and Evolutionary Relatedness of Paulownia Witches’-Broom Phytoplasma in Different Geographical Distributions in China
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Plant Material Collection and DNA Preparation
2.2. Selection and Amplification of Housekeeping Genes
2.3. PaWB Phytoplasma Diversity Analysis
2.4. Split Network and Recombination Analysis
2.5. Molecular Typing and Phylogeny of PaWB Phytoplasmas
2.6. Nucleotide Sequence Accession Numbers
3. Results
3.1. Genetic Diversity of 16S rRNA Gene and Different Housekeeping Genes in PaWB Phytoplasma
3.2. Geographical Distribution and Population Genetics Analysis of PaWB Phytoplasma
3.2.1. Genetic Diversity of PaWB Phytoplasma in Different Geographical Populations
3.2.2. Population Genetics and Mismatch Distribution Analysis of PaWB Phytoplasma
3.3. Allelic Sequences Recombination Analysis
3.4. Evolutionary Analysis with goeBURST Algorithm
3.5. Minimum Spanning Tree Analysis
3.6. Phylogenetic Analysis of 16S rRNA Gene Sequences and Concatenated Sequences
3.7. Phylogenetic Analysis of Each Housekeeping Gene in PaWB Phytoplasma
4. Discussion
4.1. PaWB Phytoplasma as a Unique Phylogenetic Branch of Group 16SrI That Is Closely Related to 16SrI-B
4.2. Valuable Methods for PaWB Phytoplasma Traceability and Disease Epidemics Based on MLST Scheme
4.3. Variation in PaWB Phytoplasma Housekeeping Genes Related to Geographical and Environmental Factors
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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Primer Pairs | Primer Sequences (5′-3′) | Amplicon Length (bp) | References | |
---|---|---|---|---|
16S rRNA | P1 | AAGAATTTGATCCTGGCTCAGGATT | 1437–1440 | Dickinson et al., 2013 [34] |
P7 | CGTCCTTCATCGGCTCTT | |||
rp | rp(I)FIA | TTTTCCCCTACACGTACTTA | 1080–1093 | Lee et al., 2003 [35] |
rp(I)RIA | GTTCTTTTTGGCATTAACAT | |||
fusA | YufusAf | GTTGTTGACTACCTTCCTGCTC | 914–926 | Yu et al., 2017 [32] |
YufusAr | TCGCCAATAACATTTCCTAC | |||
secY | AYsecYF1 | CAGCCATTTTAGCAGTTGGTGG | 1215–1258 | Dickinson et al., 2013 [34] |
AYsecYR1 | CAGAAGCTTGAGTGCCTTTACC | |||
tuf | fTuf1 | CACATTGACCACGGTAAAAC | 941–964 | Schneider et al., 1997 [36] |
rTuf1 | CCACCTTCACGAATAGAGAAC | |||
secA | secAfor1 | GARATGAAAACTGGRGAAGG | 713–734 | Hodgetts et al., 2008 [37] |
secArev3 | GTTTTRGCAGTTCCTGTCATNCC | |||
dnaK | YudnaKf | TGCTCTTTCTTATGGCGTTGA | 1135–1164 | Yu et al., 2017 [32] |
YudnaKr | CATTGCGATTCCTTGAGATTC | |||
rpoB | YurpoBf | TTCCCACTACGGCAGATTATG | 1093–1118 | Yu et al., 2017 [32] |
YurpoBr | TGGACGATGCCTCCTTCAC | |||
pyrG | YupyrGf | CCTGGAACAATGAGCCCTTA | 1038–1055 | Yu et al., 2017 [32] |
YupyrGr | TGGCACGAATAAGAACCTAA | |||
gyrB | YugyrBf | TATTCACCCCAAAACAGG | 1248–1279 | Yu et al., 2017 [32] |
YugyrBr | AGTAAAGTTCTTATGTGGGC | |||
ipt | Iptf-BamHI | CGGGATCCATGAAAAAAGTAATCGCTAT | 739–779 | Hu et al., 2013 [38] |
iptr-SalI | ACGCGTCGACATCAGTTTTAAAAAATCGT |
Genes | 16S rRNA | rp | fusA | secY | tuf | secA | dnaK | rpoB | pyrG | gyrB | ipt |
---|---|---|---|---|---|---|---|---|---|---|---|
No. of strains | 122 | 138 | 133 | 134 | 133 | 132 | 130 | 127 | 105 | 86 | 83 |
Fragment length (bp) | 1252 | 956 | 735 | 1138 | 782 | 757 | 979 | 955 | 867 | 1113 | 749 |
cG + C (%) | 47.0 | 34.7 | 37.5 | 31.8 | 37.7 | 34.7 | 33.9 | 33.7 | 33.0 | 32.4 | 30.3 |
Sequence similarity (%) | 99.44 | 99.58 | 99.73 | 99.47 | 99.62 | 99.47 | 99.18 | 99.06 | 99.42 | 99.19 | 99.73 |
No. of variable sites | 10 | 1 | 3 | 9 | 4 | 5 | 11 | 14 | 9 | 10 | 4 |
Percentage of variable sites (%) | 0.80 | 0.10 | 0.41 | 0.79 | 0.51 | 0.66 | 1.12 | 1.47 | 1.04 | 0.90 | 0.53 |
No. of haplotypes | 17 | 2 | 3 | 7 | 5 | 4 | 7 | 11 | 10 | 5 | 5 |
Haplotype diversity | 0.84 | 0.08 | 0.24 | 0.30 | 0.25 | 0.25 | 0.27 | 0.29 | 0.37 | 0.25 | 0.30 |
Nucleotide diversity | 0.00128 | 0.00009 | 0.00063 | 0.00090 | 0.00036 | 0.00094 | 0.00163 | 0.00166 | 0.00120 | 0.00137 | 0.00046 |
Ka/Ks ratio a | 0.35 | 0 | 0.29 | 0.13 | 2.63 | 0.54 | 0.11 | 1.72 | 0.39 | * | 0.14 |
Tajima’s D | −0.342 ns | −0.581 ns | −0.264 ns | −0.900 ns | −1.166 ns | −0.462 ns | −0.526 ns | −1.022 ns | −0.975 ns | −0.610 ns | −1.178 ns |
Fu and Li’s D | −2.269 ns | 0.473 ns | −0.649 ns | −1.838 ns | −2.812 b | −1.182 ns | −0.666 ns | −1.420 ns | −1.711 ns | −0.676 ns | −0.222 ns |
Fu and Li’s F | −1.888 ns | 0.177 ns | −0.619 ns | −1.794 ns | −2.683 b | −1.114 ns | −0.734 ns | −1.520 ns | −1.727 ns | −0.775 ns | 0.618 ns |
phi-test | 0.773 | / | 1.0 | 1.0 | / | 1.0 | 0.042 b | 1.0 | 1.0 | 1.0 | 1.0 |
Populations | No. of Strains | No. of Variable Sites | MLST STs | Diversity of STs | Nucleotide Diversity | Tajima’s D | Fu and Li’s D | Fu and Li’s F |
---|---|---|---|---|---|---|---|---|
Northwest China | 15 | 29 | ST1, ST2, ST3, ST4, ST5, ST6, ST8 | 0.724 | 0.00073 | −2.030 a | −2.604 a | −2.814 b |
Huang-huai-hai Plain | 25 | 11 | ST1, ST4, ST11, ST12, ST14, ST15, ST16, ST17, ST18 | 0.547 | 0.00014 | −2.341 c | −3.775 b | −3.900 b |
Southwest China | 19 | 0 | ST1 | 0 | 0 | / | / | / |
South of the Yangtze River | 46 | 32 | ST1, ST7, ST9, ST10, ST13, ST19, ST20, ST21, ST22 | 0.500 | 0.00153 | 1.089 ns | −0.137 ns | 0.349 ns |
Total | 105 | 42 | 22 | 0.474 | 0.0009 | −0.914 ns | −1.792 ns | −1.724 ns |
Population | Northwest China | Huang-Huai-Hai Plain | Southwest China | South of the Yangtze River |
---|---|---|---|---|
Northwest China | 0 | |||
Huang-huai-hai Plain | 0.01315 | 0 | ||
Southwest China | 0.03968 | 0 | 0 | |
South of the Yangtze River | 0.07562 | 0.20514 | 0.23148 | 0 |
Population | Northwest China | Huang-Huai-Hai Plain | Southwest China | South of the Yangtze River |
---|---|---|---|---|
Northwest China | 0 | |||
Huang-huai-hai Plain | 37.53 | 0 | ||
Southwest China | 12.10 | / | 0 | |
South of the Yangtze River | 6.11 | 1.94 | 1.66 | 0 |
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Kong, D.-Z.; Lin, C.-L.; Yu, S.-S.; Tian, G.-Z.; Ma, H.-B.; Wang, S.-J. Molecular Diversity and Evolutionary Relatedness of Paulownia Witches’-Broom Phytoplasma in Different Geographical Distributions in China. Biology 2022, 11, 1611. https://doi.org/10.3390/biology11111611
Kong D-Z, Lin C-L, Yu S-S, Tian G-Z, Ma H-B, Wang S-J. Molecular Diversity and Evolutionary Relatedness of Paulownia Witches’-Broom Phytoplasma in Different Geographical Distributions in China. Biology. 2022; 11(11):1611. https://doi.org/10.3390/biology11111611
Chicago/Turabian StyleKong, De-Zhi, Cai-Li Lin, Shao-Shuai Yu, Guo-Zhong Tian, Hai-Bin Ma, and Sheng-Jie Wang. 2022. "Molecular Diversity and Evolutionary Relatedness of Paulownia Witches’-Broom Phytoplasma in Different Geographical Distributions in China" Biology 11, no. 11: 1611. https://doi.org/10.3390/biology11111611