Genetic Diversity Analysis of Candidatus Liberibacter Asiaticus Based on Different Types of Prophage

doi:10.16420/j.issn.0513-353x.2023-0187

Acta Horticulturae Sinica ›› 2024, Vol. 51 ›› Issue (4): 727-736.doi: 10.16420/j.issn.0513-353x.2023-0187

• Genetic & Breeding · Germplasm Resources · Molecular Biology • Previous Articles Next Articles

Genetic Diversity Analysis of Candidatus Liberibacter Asiaticus Based on Different Types of Prophage

YOU Ping¹, YANG Jin¹, ZHOU Jun¹^,², HUANG Aijun¹^,², BAO Minli¹^,², YI Long¹^,²^,^*()

¹ School of Life Science，Gannan Normal University，Ganzhou，Jiangxi 341000，China
² National Navel Orange Engineering Research Center，Ganzhou，Jiangxi 341000，China

Received:2023-05-22 Revised:2023-12-25 Online:2024-04-25 Published:2024-04-26
Contact: YI Long

Abstract

Abstract:

To explore the geographical distribution and genetic variability of Candidatus Liberibacter asiaticus（CLas）harboring diverse prophage types in China，300 CLas DNA samples extracted from leaf petioles of CLas infected citrus were collected from six provinces：Guangdong，Guangxi，Hainan，Yunnan，Sichuan and Guizhou. And surveyed for Type 1，Type 2 and Type 3 prophages by specific PCR，then sequenced，and subjected to genetic diversity analysis employing relevant bioinformatics software. The results showed that the presence of eight distinct prophage combinations among the six geographically diverse populations. Notably，the prevalence of CLas strains carrying a single prophage type was dominant，accounting for 53.3% of the samples，with Type 2 prophage being the most prevalent. Analysis of the three prophage gene loci demonstrated a higher content of A + T relative to G + C，indicating an AT preference. Recombination analysis indicated an absence of recombination signals，suggesting the absence of recombination events. The N_m value of gene flow is exceeded 1，indicating frequent gene exchange among different CLas groups. The results of the neutral test，characterized by Tajima’s D，Fu and Li’s D，Fu and Li’s F values，all being less than 0，indicated a historical expansion within the CLas population.

Key words: citrus, Huanglongbing, prophage, genetic diversity

YOU Ping, YANG Jin, ZHOU Jun, HUANG Aijun, BAO Minli, YI Long. Genetic Diversity Analysis of Candidatus Liberibacter Asiaticus Based on Different Types of Prophage[J]. Acta Horticulturae Sinica, 2024, 51(4): 727-736.

Figures/Tables 8

References 30

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省份 Province	采集地点 Collection location	寄主 Host	样本数量 Number of samples
海南 Hainan	澄迈县 Chengmai County	绿橙 Green Orange	11
	琼海市 Qionghai City	柠檬 Lemon	9
	昌江县 Changjiang County	金橘 Kumquat	2
	琼中县 Qiongzhong County	绿橙 Green Orange	12
	海口市 Haikou City	绿橙 Green Orange	16
云南 Yunnan	丽江市 Lijiang City	碰柑 Ponkan	12
	建水县 Jianshui County	脐橙 Navel Orange	17
	德宏州 Dehong Prefecture	茂谷柑 Murcott	3
	鹤庆县 Heqing County	茂谷柑 Murcott	3
	宾川县 Binchuan County	茂谷柑 Murcott	7
	红河市 Honghe City	茂谷柑 Murcott	4
	玉溪市 Yuxi City	沃柑 Orah Mandarin	4
四川 Sichuan	宜宾市 Yibin City	沙糖橘 Shatangju Mandarin	6
	宁南县 Ningnan County	脐橙 Navel Orange	5
	攀枝花市 Panzhihua City	沃柑 Orah Mandarin	30
	雷波县 Leibo County	脐橙 Navel Orange	9
广西 Guangxi	柳州市 Liuzhou City	马水橘 Mashui Orange	5
	河池市 Hechi City	皇帝柑 Huangdi Mandarin	5
	来宾市 Laibin City	沙糖橘 Shatangju Mandarin	5
	南宁市 Nanning City	沙糖橘 Shatangju Mandarin	5
	玉林市 Yulin City	化橘红 Pummelo Peel	5
	桂林市 Guilin City	沙糖橘 Shatangju Mandarin	6
	横县 Heng County	沃柑 Orah Mandarin	5
	梧州市 Wuzhou City	沃柑 Orah Mandarin	7
	贺州市 Hezhou City	沃柑 Orah Mandarin	5
	崇左市 Chongzuo City	沙糖橘 Shatangju Mandarin	2
广东 Guangdong	肇庆市 Zhaoqing City	沙糖橘 Shatangju Mandarin	10
	阳江市 Yangjiang City	沙糖橘 Shatangju Mandarin	11
	博罗县 Boluo County	沙糖橘 Shatangju Mandarin	19
	四会市 Sihui City	沙糖橘 Shatangju Mandarin	10
贵州 Guizhou	罗甸县^* Luodian County	脐橙 Navel Orange	50

省份 Province	采集地点 Collection location	寄主 Host	样本数量 Number of samples
海南 Hainan	澄迈县 Chengmai County	绿橙 Green Orange	11
	琼海市 Qionghai City	柠檬 Lemon	9
	昌江县 Changjiang County	金橘 Kumquat	2
	琼中县 Qiongzhong County	绿橙 Green Orange	12
	海口市 Haikou City	绿橙 Green Orange	16
云南 Yunnan	丽江市 Lijiang City	碰柑 Ponkan	12
	建水县 Jianshui County	脐橙 Navel Orange	17
	德宏州 Dehong Prefecture	茂谷柑 Murcott	3
	鹤庆县 Heqing County	茂谷柑 Murcott	3
	宾川县 Binchuan County	茂谷柑 Murcott	7
	红河市 Honghe City	茂谷柑 Murcott	4
	玉溪市 Yuxi City	沃柑 Orah Mandarin	4
四川 Sichuan	宜宾市 Yibin City	沙糖橘 Shatangju Mandarin	6
	宁南县 Ningnan County	脐橙 Navel Orange	5
	攀枝花市 Panzhihua City	沃柑 Orah Mandarin	30
	雷波县 Leibo County	脐橙 Navel Orange	9
广西 Guangxi	柳州市 Liuzhou City	马水橘 Mashui Orange	5
	河池市 Hechi City	皇帝柑 Huangdi Mandarin	5
	来宾市 Laibin City	沙糖橘 Shatangju Mandarin	5
	南宁市 Nanning City	沙糖橘 Shatangju Mandarin	5
	玉林市 Yulin City	化橘红 Pummelo Peel	5
	桂林市 Guilin City	沙糖橘 Shatangju Mandarin	6
	横县 Heng County	沃柑 Orah Mandarin	5
	梧州市 Wuzhou City	沃柑 Orah Mandarin	7
	贺州市 Hezhou City	沃柑 Orah Mandarin	5
	崇左市 Chongzuo City	沙糖橘 Shatangju Mandarin	2
广东 Guangdong	肇庆市 Zhaoqing City	沙糖橘 Shatangju Mandarin	10
	阳江市 Yangjiang City	沙糖橘 Shatangju Mandarin	11
	博罗县 Boluo County	沙糖橘 Shatangju Mandarin	19
	四会市 Sihui City	沙糖橘 Shatangju Mandarin	10
贵州 Guizhou	罗甸县^* Luodian County	脐橙 Navel Orange	50

原噬菌体类 Prophage type	基因 Gene	引物序列（5′-3′） Primer sequence	退火温度/℃ Annealing temperature	参考文献 Reference
Type 1	SC1_gp035	F：TGGCTCGGGTTCAGGTAAAT；R：AAGGGCGACGCATGTATTTC	60	Zheng et al.,2018a
Type 2	SC2_gp030	F：ACCCTCGCACCATCATGTTA；R：TCGTCTTGATTGGGCAGAGT	60	Zheng et al.,2018a
Type 3	P_JXGC_gp08	F：CTGATCCTTTACCATGCCGC；R：CAGCGAAACCGATCTTGAGG	60	Zheng et al.,2018a

原噬菌体类 Prophage type	基因 Gene	引物序列（5′-3′） Primer sequence	退火温度/℃ Annealing temperature	参考文献 Reference
Type 1	SC1_gp035	F：TGGCTCGGGTTCAGGTAAAT；R：AAGGGCGACGCATGTATTTC	60	Zheng et al.,2018a
Type 2	SC2_gp030	F：ACCCTCGCACCATCATGTTA；R：TCGTCTTGATTGGGCAGAGT	60	Zheng et al.,2018a
Type 3	P_JXGC_gp08	F：CTGATCCTTTACCATGCCGC；R：CAGCGAAACCGATCTTGAGG	60	Zheng et al.,2018a

原噬菌体类型 Prophage type	广东 Guangdong	广西 Guangxi	四川 Sichuan	贵州 Guizhou	云南 Yunnan	海南 Hainan	总数 Total
Type 1	2（4.0%）	1（2.0%）	7（14.0%）	2（4.0%）	21（42.0%）	4（8.0%）	37（12.3%）
Type 2	35（70.0%）	35（70.0%）	2（4.0%）	12（24.0%）	9（18.0%）	24（48.0%）	117（39.0%）
Type 3	2（4.0%）	2（4.0%）	1（2.0%）	0	0	1（2.0%）	6（2.0%）
Type 1 + Type 2	9（18.0%）	0	3（6.0%）	19（38.0%）	6（12.0%）	4（8.0%）	41（13.7%）
Type 1 + Type 3	0	3（6.0%）	24（48.0%）	4（6.0%）	4（8.0%）	5（10.0%）	40（13.3%）
Type 2 + Type 3	0	3（6.0%）	0	0	0	0	3（1.0%）
Type 1 + Type 2 + Type 3	0	0	8（16.0%）	13（26.0%）	0	3（6.0%）	24（8.0%）
NONE	2（4.0%）	6（12.0%）	5（10.0%）	0	10（20.0%）	9（18.0%）	32（10.7%）

Genetic Diversity Analysis of Candidatus Liberibacter Asiaticus Based on Different Types of Prophage

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基因 Gene	地区 Region	变异位点数 Variation sites number	单倍型个数 Haplotype number	H 单倍型多样性 Haplotype diversity	P_i 核苷酸多样性 Nucleotide diversity
SC1_gp035	广东Guangdong	11	7	0.89091	0.00262
	广西Guangxi	0	1	0	0
	海南Hainan	1	2	0.12500	0.00014
	四川Sichuan	27	7	0.41812	0.00198
	贵州Guizhou	0	1	0	0
	云南Yunnan	26	3	0.12688	0.00319
总计Total		38	15	0.27400	0.00155
SC2_gp030	广东Guangdong	0	1	0	0
	广西Guangxi	0	1	0	0
	海南Hainan	0	1	0	0
	四川Sichuan	4	5	0.53846	0.00084
	贵州Guizhou	1	2	0.04545	0.00006
	云南Yunnan	2	3	0.36190	0.00052
总计Total		6	7	0.08500	0.00012
P_JXGC_gp08	广东Guangdong	0	1	0	0
	广西Guangxi	5	3	0.46429	0.00145
	海南Hainan	2	3	0.55556	0.00071
	四川Sichuan	1	2	0.06061	0.00007
	贵州Guizhou	0	1	0	0
	云南Yunnan	0	1	0	0
总计Total		7	6	0.15800	0.00029

基因 Gene	序列条数 Number of sequences	同义突变率（d_S） Synonymous mutation rate	非同义突变率（d_N） non-synonymous mutation rate	d_N/d_S
SC1_gp035	142	1.636 × 10^-3	1.463 × 10^-3	0.894
SC2_gp030	185	0.060 × 10^-3	0.123 × 10^-3	2.050
P_JXGC_gp08	73	0.224 × 10^-3	0.316 × 10^-3	1.411

基因 Gene	遗传分化系数（F_st） Genetic differentiation coefficient	基因流（N_m） Gene flow	中性检验Neutral test
基因 Gene	遗传分化系数（F_st） Genetic differentiation coefficient	基因流（N_m） Gene flow	Fu and Li’s D	Fu and Li’s F	Tajima’s D
SC1_gp035	0.06133	7.65	-1.97423	-2.59921^*	-2.43014^**
SC2_gp030	0.01571	31.14	-4.07222^*	-3.94908^*	-1.88138^*
P_JXGC_gp08	0.02536	19.22	-4.08703^*	-4.06963^*	-2.17028^**

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