全 文 :植物病理学报
ACTA PHYTOPATHOLOGICA SINICA 44(6): 609 ̄619(2014)
Received date: 2013 ̄09 ̄25ꎻ Revised date: 2014 ̄08 ̄24
Foundation item: Public service sectors (agriculture) special project (Grant No. 201003067) from Ministry of Agriculture of the Peoples Repub ̄
lic of Chinaꎻ National Natural Science Fund (Grant No. 31201480) by National Natural Science Foundation of China (NSFC) .
Corresponding author: DENG Xiao ̄lingꎬ professorꎬ specialized in citrus bacterial diseasesꎻ E ̄mail: xldeng@scau.edu.cn
First authors: XU Mei ̄rongꎬ femaleꎬ Ph. D.ꎬ specialized in plant ̄pathogen interactionꎻ E ̄mail: mrxu12345@126.com
ZHENG Zhengꎬ maleꎬ Ph. D. studentꎬ specialized in citrus Huanglongbing microbiologyꎻ E ̄mail: weifeng151210@126.com.
doi:10.13926 / j.cnki.apps.2014.06.007
Intraspecific Genetic Diversity Analysis of
‘Candidatus Liberibacter asiaticus’ by
Short Tandem Repeats and PAGE
XU Mei ̄rong#ꎬ ZHENG Zheng#ꎬ LI Xin ̄yuꎬ HONG Hong ̄xiaꎬ DENG Xiao ̄ling∗
(Guangdong Key Laboratory of Microbial Signals and Disease Controlꎬ College of Resources and Environmentꎬ
South China Agricultural Universityꎬ Guangzhou 510642ꎬ China)
Abstract: The most prevalent uncultured phloem ̄restricted bacterial species associated with citrus huanglong ̄
bing (HLB) disease in the world is ‘Candidatus Libriacter asiaticus’ . To develop a set of short tandem repeat
(STR) markers for ‘Ca. L. asiaticus’ and facilitate studies on its genetic diversity and epidemiology of HLBꎬ
Tandem Repeats Finder software was applied to identify and analyze the STR loci. STR primers were designed
by Primer Premier 5. 0. PopGene and PowerMark were used to analyze polyacrylamide gel electrophoresis
(PAGE) bands of isolates collected from 6 provinces in China. Thirty ̄three of the 36 STR loci could be effec ̄
tively amplified. Twenty polymorphic STR primers were selected and used to differentiate 32 Chinese ‘Ca. L.
asiaticus’ isolates. The Nei’s measure of genetic diversity values for these 20 STRs ranged from 0.06 to 0.81ꎬ
with a mean of 0.38. The shannon’ s diversity indexes were between 0.14 and 1.90ꎬ with a mean of 0.68. In
conclusionꎬ the 20 polymorphic STR loci were used for genetic diversity analysis of ‘Ca. L. asiaticus’ isolates
from different provinces in China. Diversity of ‘Ca. L. asiaticus’ was related to geographic distribution. The
isolates from Guangdong that was considered to be HLB origin were specific. Isolates from Fujianꎬ Guangxi and
Yunnan were suggested to be higher in diversity. Psyllid transmission may play roles in the spread of
‘Ca. L. asiaticus’ between neighbor provinces.
Key words: Huanglongbingꎻ ‘Candidatus Liberibacter asiaticus’ꎻ short tandem repeatsꎻ genetic diversity
基于短串联重复和 PAGE的柑橘黄龙病菌‘Candidatus Liberibacter asiaticus’种间遗传
多样性分析 许美容ꎬ 郑 正ꎬ 李昕昱ꎬ 洪虹霞ꎬ 邓晓玲 (华南农业大学资源环境学院ꎬ广东省微生物信号与
作物病害防控重点实验室ꎬ广州 510642)
摘要:韧皮部杆菌亚洲种(‘Candidatus Libriacter asiaticus’ꎬ‘Ca. L. asiaticus’)是目前流行范围最广、危害最严重的柑橘黄
龙病致病菌ꎮ 本研究利用‘Ca. L. asiaticus’基因组中全套串联重复基因(short tandem repeatꎬ STR)开发了一套系统的方法
用于‘Ca. L. asiaticus’遗传多样性和黄龙病分子流行学研究ꎮ PCR和 PAGE分析筛选到的 36个 STR位点中ꎬ有 33个获得
了有效扩增ꎮ 其中 20对引物对不同来源的 32个样品的扩增产物多态性较好ꎬ最多的可扩增出 9种条带类型ꎮ 采自我国 6
省的 32个‘Ca. L. asiaticus’阳性样品之间的 Shannon’s信息指数为 0.14~ 1.90ꎬ平均为 0.68ꎻNei’s基因多样性指数为 0.06
~ 0.81ꎬ平均为 0.38ꎬ各省的菌株表现出较高的遗传多样性ꎬ特别是来自福建、广西和云南三省的ꎮ 聚类分析发现可能为中
植物病理学报 44卷
国黄龙病发源地的广东省的黄龙病菌株具有一定的遗传特异性ꎻ其余邻省之间存在由木虱传播引起的菌株交流的可能性
可以解释该病害在省际间传播ꎮ 研究表明ꎬ开发的 STR标记结合 PAGE的方法可作为今后菌株遗传多样性和病害分子流
行学分析的高效方法ꎮ
关键词:黄龙病ꎻ ‘Candidatus Liberibacter asiaticus’ꎻ 短串联重复ꎻ 遗传多样性
中图分类号: S436.661.1 文献标识码: A 文章编号: 0412 ̄0914(2014)06 ̄0609 ̄11
Huanglongbing (HLB) (yellow shoot disease)
has been a serious problem in the world’ s citrus in ̄
dustry for hundred years. In the early 19th centuryꎬ
the occurrence of yellowing disease was recorded in
South China [1] . The disease is now widely distribu ̄
ted in most parts of Asiaꎬ African and America where
citrus are grown. HLB ̄affected trees show symptoms
of blotchy mottleꎬ severe chlorosis of foliage or die ̄
backꎬ which causes substantial economic losses.
The pathogen of citrus HLB in Asia and Africa
was first recognized as ‘Candidatus Liberibacter asi ̄
aticus’ (‘Ca. L. asiaticus’) and ‘Ca. L. africanus
[2~4] . A third Liberibacter speciesꎬ ‘Ca. L. america ̄
nus’ was ever reported to be found in São Paulo
State of Brazil [5] . ‘Ca. L. asiaticus’ is also the
most widespread and prevalent species [6] . Guang ̄
dong has long been considered as the origin and
prevalent area for the Asian form of the disease [1ꎬ7] .
The association of “Ca. L. asiaticus” to HLB was
established in 1996[8ꎬ 9] .
The epidemiology characteristics and population
structure of HLB have attracted increasing attention
of researchers. Most of the previous studies focused
on utilizing the conserved genes as genetic markersꎬ
including 16S rRNAꎬ 16S / 23S ribosomal intergenic
regionsꎬ the outer membrane protein ( omp) geneꎬ
ribosomal protein genesꎬ and ψserA ̄trmU ̄tufB ̄
secE ̄nusG ̄rplKAJL ̄rpoB gene cluster[10~21] . In
2009ꎬ the complete genome sequence of ‘Ca. L.
asiaticus’ was obtained through metagenomic ap ̄
proaches[22]ꎬ and thenꎬ bacteriophage ̄type DNA
polymerase region and hypervariable sequence re ̄
gions associated with short tandem repeats were em ̄
ployed for understanding the genetic diversity of this
pathogen[23] . In 2011ꎬ population variation of ‘Ca.
L. asiaticus’ was investigated using a prophage gene
[24] or two hypervariable prophage genes (hyvI and
hyvII) with intragenic tandem repeats [25] .
Distinguishing bacterial isolates using short tan ̄
dem repeats (STR)ꎬ also known as variable number
of tandem repeats (VNTR) is important for epide ̄
miological analysis and understanding the genetic
structure of microbial populations. One genetic
marker containing small tandem repeats (AGACACA)
was first used to distinguish the ‘Ca. L. asiaticus’
populations of Florida (US) from those of Guang ̄
dong ( in China) [23] . In 2011ꎬ Katoh et al.[26] se ̄
lected 4 highly polymorphic loci to differentiate 84
‘Ca. L. asiaticus’ isolates from Japanꎬ and 16 iso ̄
lates from Taiwan or Indonesia. Seven STR markers
were subsequently developed to identify three major
genetic groups of 287 ‘Ca. L. asiaticus’ isolates
from 9 countries[27] .
In this studyꎬ 33 of 78 predicted STR loci were
scanned for their polymorphism through polyacryla ̄
mide gel electrophoresis (PAGE)ꎬ a highly sensitive
technique for the detection of DNA fragment
variations. With the polymorphic lociꎬ genetic diver ̄
sity among ‘Ca. L. asiaticus’ isolates from 6 provi ̄
nces of China was estimated. Genetic groups accord ̄
ing to geographic origins were also identified.
1 Materials and Methods
1.1 Plant material and DNA extraction
Leaf or fruit samples with typical HLB symptoms
were collected on individual plant from provinces of
Fujianꎬ Guangdongꎬ Guangxiꎬ Jiangxiꎬ Yunnanꎬ and
Zhejiang (Table 1). DNA samples were extracted with
HP plant DNA kit (D2485 ̄02ꎬ OMEGA bio ̄tek). Ba ̄
sicallyꎬ 0. 15 g midribs were excised from the leaf
bladeꎬ mixed with extraction bufferꎬ and ground in
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6期 XUMei ̄rong et al:Intraspecific Genetic Diversity Analysis of ‘Candidatus Liberibacter asiaticus’ by Short Tandem Repeats and PAGE
tubes on MP FastPrep ̄24 machine. The final DNA pel ̄
lets were dissolved in TE buffer and checked by elec ̄
trophoresis in 1% (w/ v) agarose gel. HLB ̄associated
Liberibacter ̄free DNA samples of Citrus reticulate
Blanco cv. Shatangju were used as negative controls.
Detection and identification of ‘Ca. L. asiaticus’ was
based on primer pairs OI1/ OI2c [2] .
1.2 STR markers development
Complete genome sequences of two ‘Ca. L.
asiaticus’ strains (CP001677. 5 and CP004005. 1)
were downloaded from GenBank database. A ge ̄
nome ̄wide search was performed to identify all puta ̄
tive STR loci by Tandem Repeats Finder ( version
4.07b) [28] . STR loci were screened by the following
parameters: A) When ‘Percent Matches’ is 100%ꎬ
length of repeated motifs is 4 ~ 10 bpꎻ B) If ‘Per ̄
cent Matches’ are among 90% ̄99%ꎬ the motif size
is bigger than 10 bpꎻ C) Repeat number is more
than 2. Primers were designed to amplify the
screened STR locus according to the search criteria:
length of 15 ~ 25 bpꎬ Tm of 45℃ ~ 65℃ꎬ GC% of
40%~ 65%ꎬ and product size of 100 ~ 500 bp ( for
loci STR 34~ STR 36 with relative larger motif sizeꎬ
product sizes were enlarged accordinglyꎻ STR 28 is
a hypervariable genomic loci. The product size for
the primer designed was 1 742 bp in CP004005.1) .
To test the amplification efficiency and
specificity of the designed primersꎬ two DNA
samples from HLB ̄infected and HLB ̄free Citrus
reticulate Blanco cv. Shatangju trees were used as
PCR templates. Twenty ̄five μL mixtures were used
for conventional PCR. To screen the polymorphic
STR primersꎬ thirty ̄two DNA samples were
obtained from HLB ̄infected plants in 6 provinces of
China. Primers presented polymorphisms were
named as key primers.
1.3 PCR based genotyping
PCR was performed in 15 μL reaction mixture
volumes containing 1 × reaction buffer ( LOT #
L0425Cꎬ TIANGEN BIOTECH CO.ꎬ LTD)ꎬ 1. 5
μL of 0.2 mM dNTPs (LOT#L0625Cꎬ TIANGEN
BIOTECH CO.ꎬ LTD)ꎬ 1 pmol of primer pairsꎬ
about 5 ng diluted DNA samplesꎬ 0.15 U Taq DNA
polymerase (LOT#L0328Cꎬ TIANGEN BIOTECH
CO.ꎬ LTD) . Conventional PCR was performed in a
PTC ̄100 or PTC ̄200 Thermal Cycler ( MJ Re ̄
search) with an initial 5 min denaturation at 95°Cꎬ
followed by 34 cycles of each (95°Cꎬ 30sꎻ 56°Cꎬ
30sꎻ 72°Cꎬ 30s)ꎬ then extended at 72°C for 7 min.
Exactly 0. 8 μL PCR products mixed with loading
buffer were separated on 6% (w / v) polyacrylamide
gels for 6 h with 110 V voltage ( For STR34 ~
STR36ꎬ electrophoresis time was set as 8 h) . Silver
staining was used to visualize polymorphic alleles.
The stained gel was photographed by a color digital
camera (Nikonꎬ DX SWM ED A spherical) and
DNA bands were recorded. Agarose gel electropho ̄
resis was used to resolve amplicons from STR28ꎬ as
they were too large (800 ̄2 200 bp) for PAGE.
1.4 Genotype differentiations and genetic di ̄
versity analyses
Genotypes were identified based on combination
of allelic data amplified from all polymorphic primers.
A data set read according to the band number and
band size were built and used for the analysis of
genetic diversityꎬ linkage disequilibrium and genetic
structure. Software Popgene 1. 32 (http: / / www.
ualberta.ca / ~ fyeh / index.html) was used to analyze
percentage of polymorphic bands ( PPB)ꎬ Nei ’ s
genetic diversity ( H )ꎬ and shannon ’ s diversity
indexes(I) at each locus as well as across all loci for
all isolates. Phylogenetic trees were constructed by
usingthe PowerMark V3.0 software (http: / / statgen.
ncsu.edu / powermarker / index.html) .
2 Results
2.1 Isolates were screened from different ge ̄
ographic areas
Forty ̄five of 50 leaf samples were tested to be
‘Ca. L. asiaticus’ positive. Thirty ̄two of these were
used in the following diversity analysis. The 32 iso ̄
lates of 8 different varieties were collected from 6
different provinces (Table 1) .
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植物病理学报 44卷
Table 1 Isolates of “Candidatus Liberibacter asiaticus” used in the study
Isolate Codea Location Variety Sampling position Symptom Sampling date
JX ̄1 Xunwu Tangerine Leaf Vein corkingꎬ slight yellowing 2012.06.19
JX ̄2 Xunwu Tangerine Leaf Vein corkingꎬ yellowing 2012.06.19
JX ̄3 Xunwu Navel orange Leaf Blotchy mottle 2012.06.19
JX ̄4 Xinfeng Navel orange Leaf Blotchy mottle 2012.06.19
JX ̄5 Xinfeng Navel orange Leaf Blotchy mottle 2012.06.19
GX ̄1 Guilin Pummelo Leaf ‘Green island’ 2012.10.15
GX ̄2 Guilin Pummelo Leaf ‘Green island’ 2012.10.15
GX ̄3 Guilin Pummelo Leaf Blotchy mottle 2012.10.15
GX ̄4 Guilin Pummelo Leaf Vein corkingꎬ mottling 2012.10.15
GX ̄5 Guilin Navel orange Leaf Blotchy mottle 2012.12.30
ZJ ̄1 Wenzhou Mandarin Leaf Blotchy mottle 2012.11.16
ZJ ̄2 Wenzhou Mandarin Leaf Blotchy mottle 2012.11.16
FJ ̄1 Shanghang Pummelo Leaf Blotchy mottle 2012.10.03
FJ ̄2 Shanghang Pummelo Leaf Zinc ̄pattern ̄deficiency 2012.10.03
FJ ̄3 Yongchun Pummelo Leaf Yellowing 2012.02.21
FJ ̄4 Yongchun Pummelo Leaf Blotchy mottle 2012.03.23
FJ ̄5 Sanming Pummelo Leaf Blotchy mottle 2012.10.29
FJ ̄6 Sanming Pummelo Leaf Blotchy mottle 2012.10.29
YN ̄1 Binchuan Orange Leaf Slight blotchy mottle 2012.04.15
YN ̄2 Binchuan Orange Fruit Greening 2012.04.15
YN ̄3 Jianshui Orange Leaf Zinc ̄pattern ̄deficiency 2012.09.25
YN ̄4 Jianshui Orange Leaf Mottlingꎬ zinc ̄pattern ̄deficiency 2012.09.25
YN ̄5 Jianshui Orange Leaf Mottlingꎬ yellowing 2012.09.25
YN ̄6 Jianshui Orange Leaf Blotchy mottle 2012.10.15
YN ̄7 Jianshui Mandarin Leaf Blotchy mottle 2012.10.15
YN ̄8 Jianshui Pummelo Leaf Blotchy mottle 2012.10.15
GD ̄1 Yunfu Tangerine Leaf Mottlingꎬ zinc ̄pattern ̄deficiency 2013.01.29
GD ̄2 Yunfu Tangerine Leaf Zinc ̄pattern ̄deficiency 2013.01.29
GD ̄3 Deqing Tangerine Leaf Blotchy mottle 2013.03.10
GD ̄4 Deqing Tangerine Leaf ‘Green island’ꎬ Zinc ̄pattern ̄deficiency 2013.03.10
GD ̄5 Deqing Mandarin Leaf Blotchy mottle 2013.03.10
GD ̄6 Deqing Mandarin Leaf Blotchy mottle 2013.03.10
aYN: Yunnan provinceꎻ FJ: Fujian provinceꎻ JX: Jiangxi provinceꎻ GX: Guangxi provinceꎻ ZJ: Zhejiang provinceꎻ GD:
Guangdong province.
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6期 XUMei ̄rong et al:Intraspecific Genetic Diversity Analysis of ‘Candidatus Liberibacter asiaticus’ by Short Tandem Repeats and PAGE
2.2 Polymorphic primers were selected for
diversity analysis
A total of 78 STR motifs were predicted from
two ‘Ca. L. asiaticus’ genomes. Of the 78 STR mo ̄
tifsꎬ 36 were screened for polymorphisms by the
methods mentioned above (Fig. 1ꎬ Table 2) . Three
of the designed primers ( STR9ꎬ STR11ꎬ and
STR26) had no target amplicons of the expected size
( Fig. 1 ) . Four primer pairs ( STR8ꎬ STR10ꎬ
STR20ꎬ and STR32) produced multiple amplicons
in addition to the expected amplicons. The product
sizes were among 150 ~ 300 bp except for STR28ꎬ
STR34ꎬ STR35ꎬ and STR36. PAGE method cannot
be used to separate STR28 amplicons because the
size is about 2 kb.
For the 33 available primersꎬ 14ꎬ 3ꎬ and 3 pairs
produced 1ꎬ 2ꎬ and 3 bandsꎬ respectively. Interesting ̄
lyꎬ 8ꎬ 3ꎬ 2ꎬ and 1 pairs of primers amplified products
with 1~2ꎬ 1~3ꎬ 1~4ꎬ and 1~5 bandsꎬ respectively.
Twenty of the 33 available primer pairs (60. 61%)
were polymorphic among the 32 samplesꎬ as repre ̄
sentatively shown in Fig. 2. The polymorphic primers
were named as key primers (Table 2) .
Fig. 1 Conventional PCR results of 36 primer pairs on ‘Candidatus liberibacter
asiaticus’ by agarose gel electrophoresis
M: DS2000 DNA markerꎻ ‘+’: Midrib DNA extracted from ‘Candidatus libribacter asiaticus’ infected Citrus
reticulate Blanco cv. Shatangjuꎻ ‘  ̄‘: Midrib DNA extracted from healthy leaves of Citrus reticulate Blanco cv. Shatangju.
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植物病理学报 44卷
Fig. 2 DNA polymorphisms resolved by polyacrylamide gel electrophoresis among 32
‘Candidatus Liberibacter asiaticus’ isolates amplified by selected short tandem repeat primers
Isolates were from Jiangxi (1~5)ꎬ Guangxi (6~10)ꎬ
Zhejiang (11~12)ꎬ Fujian (13~18)ꎬ Yunnan (19~26)ꎬ and Guangdong (27~32) provinces.
2.3 Genotype and genetic diversity of the 32
isolates
Among the 32 isolatesꎬ 2 ~ 9 genotypes were i ̄
dentified for each key primer. Table 3 shows the
Shannon’ s diversity indexes and Nei’ s genetic di ̄
versity ( H ) of all polymorphic markers in the
screened ‘Ca. L. asiaticus’ population. The Shan ̄
non’ s diversity indexes ranged from 0.14 to 1.90ꎬ
with a mean of 0. 68. While the H indexes of the
population were among 0.06 and 0.81ꎬ with a mean
of 0.38. The genetic distance and genetic similarity
were calculated with the isolates from 6 regions. The
genetic similarity among different geographic groups
was 0.48~0.97ꎬ with a mean of 0.76. Overall geno ̄
type genetic similarity were the highest in Jiangxi
province ( 0. 81 ~ 0. 97)ꎬ followed by Guangdong
province (0.81~0.95) . The genetic similarities were
relatively lower in other 3 provincesꎬ with Guangxi
of 0.70 ~ 0.97ꎬ Fujian of 0.62 ~ 0.97 and Yunnan of
0.64~0.90. No data was available for Zhejiang provi ̄
nce because of the small population size. The overall
genotype data indicated that the genetic diversity exis ̄
ted among the isolates of different provinces and
within one province. Isolates from Fujianꎬ Guangxiꎬ
and Yunnan were suggested to be higher in diversity.
2.4 Genetic structure of isolates from
different regions
A clustering analysis made by PowerMark V3.0
identified five major groups of ‘Ca. L. asiaticus’
( Fig . 3 ) . Isolates from Guangdong were clustered
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6期 XUMei ̄rong et al:Intraspecific Genetic Diversity Analysis of ‘Candidatus Liberibacter asiaticus’ by Short Tandem Repeats and PAGE
Table 2 Characteristics of short tandem repeat primer sequences used to identify
‘Candidatus Liberibacter asiaticus’
Primer Forward primer / 5 ̄ 3 Reverse primer / 5 ̄ 3
Expect
size / bp
Repeat unit
size / bp
Primer type
Las ̄STR1 TCGCTTGAAAGTTATTATTGGG GCATAAGAATAGAAGAACCTA 181 4 Key primer
Las ̄STR2 TTTCCAAGTCATTTCCG CACCGACCAATACAACG 219 4 Ordinary primer
Las ̄STR3 ATTCATGGGAAGCGTAA ATGCTCAGAACACTGCA 253 4 Key primer
Las ̄STR4 TTTTGGGAAGAGTTGC TCTTTCGTTATTTCTGGTA 205 4 Key primer
Las ̄STR5 ACAGGGACGGTGAAACA TGCCTTGACGCAATCTA 176 4 Key primer
Las ̄STR6 GATATGGGTATGCTCG TAGTGTTTCTTGTGCTG 236 4 Ordinary primer
Las ̄STR7 CGCCTATAAATCCCTT CTGTTGCACCCGACT 140 5 Key primer
Las ̄STR8 AAGGGATTCTTACTATGTG TCGTGCTGCTTTGTT 226 6 Key primer
Las ̄STR9 ACGATTTACAAGTTCA ATTATTGGGAGGGAA 249 6 Unusable primer
Las ̄STR10 TGTACGTTCGGAGAAG GGTCTGTATCTGGTGC 250 6 Ordinary primer
Las ̄STR11 GTTTCACAGTCCAAAAT AACGCACAGATAAGC 252 6 Unusable primer
Las ̄STR12 GTTGCTTCGTTTATCC GCATTCTGTGCCTCTT 239 7 Key primer
Las ̄STR13 GTAGGAGTCCCCGAAAT GCCTGTACGAGGTTTGA 246 7 Key primer
Las ̄STR14 TTTTGGAGGAACTAACG TCACATGAATATGAACCC 235 7 Key primer
Las ̄STR15 TGGGAGATTCGTGATGT ATAGCCGTTGGAGGTAG 287 7 Ordinary primer
Las ̄STR16 GTACTATGTTTAGCCTGTA CTTCTAATCAATAGACCC 228 8 Ordinary primer
Las ̄STR17 AGGGGTGTTTCTGTC ATAAAATCAATGTGGC 155 10 Ordinary primer
Las ̄STR18 CAGATGCCGACCTTC GTGAGCTGTAGTCCCTAT 234 10 Key primer
Las ̄STR19 CCATAGGTTGGGAATC TGCCGAATAAGTCGTTT 247 11 Ordinary primer
Las ̄STR20 CCGTCCTGATGTGGT TTGATCTTAATCGGTCTC 224 13 Ordinary primer
Las ̄STR21 AATAAGTATTAAAAGGTCGG GCTAAGGAGGGTACAGAG 195 13 Ordinary primer
Las ̄STR22 GTAAATGATCCACCAC CAAAACCAAGATAGACT 186 15 Ordinary primer
Las ̄STR23 ATGGCAGACGGTGAAATT TATCCTCAAGGCAAACAA 253 16 Ordinary primer
Las ̄STR24 TGCGTCAGTTTCTCGTTT CGTTCCAGGTGTTCATTC 280 18 Ordinary primer
Las ̄STR25 TCAGTTCGTCCTTGC TCATACCTATTCACCGT 252 21 Ordinary primer
Las ̄STR26 GGCAAGCCATACAAA AAGAAAGCGTAAGCAA 178 21 Unusable primer
Las ̄STR27 TGCCACCGAATAGAA TACATCGTGTAATAGATGAA 223 21 Key primer
Las ̄STR28 CATCCTTGTCGTCATAGAA GGAAGTAAATCAGGTAGCC 1742 24ꎬ 48ꎬ 96 Key primer
Las ̄STR29 TCCAAGCTGTTATCCA GCGAAATCAGTATGCC 191 27 Key primer
Las ̄STR30 TTTCCTTTGGTTTCTTCT CACCACCACAAACATTAG 171 33 Key primer
Las ̄STR31 ATGAGTCGGGACGGAAGG CGGGCTAACGCACAA 192 39 Key primer
Las ̄STR32 TGATAACAAGCACCTCT CTAATCTGAACCCAAAC 229 57 Key primer
Las ̄STR33 TTTGTCCTGTATTCGTA ACTCCCCTCTTATCAA 200 63 Key primer
Las ̄STR34 ACATAAACCCAAACTAGC GGCATTGTTCTTGACCGT 329 86 Key primer
Las ̄STR35 GAGACGGACACTCAACA GCAAGGGATTTATGCT 429 147 Key primer
Las ̄STR36 AGATATTCCCAAAGCACG ATTTGGTTTGTCCGAAGG 661 252 Key primer
Key primer: Primers that produce polymorphismꎻ Ordinary primer: Primers that amplify the same product among all isolates in
the experimentꎻ Unusable primer: Primers without target amplicons.
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植物病理学报 44卷
Table 3 Genetic diversity of 32 isolates ana ̄
lyzed using polymorphic short tan ̄
dem repeat primers
Primer
Sample
size
Nei’s genetic
diversity (H)
Shannon’s
diversity index ( I)
Las ̄STR1 29 0.38 0.65
Las ̄STR3 30 0.55 1.05
Las ̄STR4 28 0.29 0.47
Las ̄STR5 30 0.32 0.50
Las ̄STR7 32 0.12 0.23
Las ̄STR8 32 0.43 0.62
Las ̄STR12 29 0.68 1.34
Las ̄STR13 32 0.81 1.90
Las ̄STR14 25 0.44 0.78
Las ̄STR18 32 0.55 1.04
Las ̄STR22 28 0.19 0.34
Las ̄STR27 25 0.21 0.37
Las ̄STR29 32 0.06 0.14
Las ̄STR30 21 0.09 0.19
Las ̄STR31 24 0.75 1.49
Las ̄STR32 32 0.12 0.23
Las ̄STR33 32 0.45 0.64
Las ̄STR34 32 0.12 0.23
Las ̄STR35 30 0.50 0.69
Las ̄STR36 31 0.50 0.69
Mean 30 0.24 0.43
Sample size: The number of isolates with amplification bands
used for analysis.
into a distinct group (Group IV) . Three groups con ̄
tain isolates mainly from neighbor provinces: Group
I ( from Fujian and Jiangxi )ꎬ Group III ( from
Guangxi and Yunnan)ꎬ and Group V ( from Jiangxi
and Zhejiang) . Isolates from 3 provinces were clus ̄
tered into Group II. Most isolates in this group were
collected from diseased pummel trees. The analysis
based on the genotypes assessed the genetic structure
of ‘ Ca. L. asiaticus ’ . The results showed that
grouping of ‘Ca. L. asiaticus’ was related to geo ̄
graphic origins and citrus varieties. Psyllid transmis ̄
sion was suggested to explain the similar ‘Ca. L.
asiaticus’ genotype between neighbor provinces.
3 Discussion
Three speciesꎬ ‘Ca. L. asiaticus’ꎬ ‘ Ca. L.
americanus’ and ‘Ca. L. africanus’ were responsi ̄
ble for HLB disease. Most studies focused on the in ̄
terspecific diversity of ‘Ca. L. spp.’ꎬ or intraspeci ̄
fic diversity of ‘ Ca. L. asiaticus’ from different
countries [10ꎬ 12ꎬ 17ꎬ 21ꎬ 23] . Few literatures reported the
genetic diversity of this bacteria within one country
or province [13] . Limited strains or STR sites were
involved in most references. For exampleꎬ 16S
rDNA and 16S / 23S intergenic region sequences
could distinguish only interspecific isolates or ‘Ca.
L. asiaticus ’ isolates from different countries
[10ꎬ 15ꎬ 29] . The omp genes of ‘Ca. L. asiaticus’ with ̄
in one country were usually highly homogeneous[20] .
Similar to our studyꎬ Islam et al. [27] used seven
polymorphic microsatellite markers to analyze 287
isolatesꎬ but mainly concluded that ‘Ca. L. asiatic ̄
us’ isolate diversity existed worldwide. China has a
long citrus cultivation history and citrus HLB history.
‘Ca. L. asiaticus’ is widely distributed in 11 of the
18 citrus growing provinces or municipalities. There ̄
foreꎬ investigation of the genetic diversity of ‘Ca.
L. asiaticus’ in different geographical regions of
China is important for us to understand the occur ̄
rence and epidemiology of HLB. The results of this
study demonstrated the feasibility of STR ̄PAGE in
genetic diversity analysis in China.
Several efforts have been made to reveal genetic
diversity of ‘Ca. L. asiaticus’ . Of themꎬ Katoh et
al. [26] evaluated more than 4 loci with relatively lar ̄
ger size of amplicons. Moreoverꎬ sequencing proce ̄
dures are usually used to achieve high resolution tan ̄
dem repeat difference. Comparativelyꎬ the PCR ̄
PAGE method in this study is effectiveꎬ simpleꎬ and
economical. Howeverꎬ it still has disadvantages.
Some DNA bands ( for exampleꎬ STR12) are too
faint to readꎬ leading to difficulty in genotype deter
mination. Primers are restricted due to the involve ̄
ment of short sequences. The amplicons larger than
500 bp are difficult to be distinguished.
616
6期 XUMei ̄rong et al:Intraspecific Genetic Diversity Analysis of ‘Candidatus Liberibacter asiaticus’ by Short Tandem Repeats and PAGE
Fig. 3 Individual assignments of ‘Candidatus Liberibacter asiaticus’ isolates obtained
from six different provinces in China by short tandem repeats diversity
YN: Isolates from Yunnan provinceꎻ FJ: Isolates from Fujian Provinceꎻ JX: Isolates from Jiangxi provinceꎻ
GX: Isolates from Guangxi provinceꎻ ZJ: Isolates from Zhejiang provinceꎻ GD: Isolates from Guangdong province.
It is expected that ‘ Ca. L. asiaticus ’ was
spread from one location to another in China. Iso ̄
lates from 6 provinces could be clustered into 5 sub ̄
groups. Isolates of group Ⅰꎬ Ⅲꎬ or Ⅴ were from
neighbor provincesꎬ suggesting the overlapping
movement of “Ca. L. asiaticus” . Besidesꎬ variations
of STR loci are probably associated with bacterial
environmental adaptation. This may explain the
presence of different STR groups in different
geographical locations. Our observation seems
provide a robust framework for understanding the
pathogenicity difference and molecular epidemiology
of HLB.
HLB was first observed and studied in Guang ̄
dong[1ꎬ 7ꎬ 30]ꎬ one of the major citrus ̄producing
provinces in Chinaꎬ and then spread from south to
north in Guangdong and now present in all 12 pre ̄
fecture cities [31] . In our recent study [32]ꎬ “Ca. L.
asiaticus” population in Guangdong was confirmed
to be significantly different from that of other seven
provinces. Consistentlyꎬ all Guangdong isolates were
in one cluster in this study. But it should be noted
that sample size from each province in this study is
relatively small. The robustness of this STR ̄PAGE
technique may provide a sensitive tool to further in ̄
vestigate the “Ca. L. asiaticus” population variation
716
植物病理学报 44卷
in Guangdong with more samples collecting from
different regions and citrus cultivars.
Acknowledgements
We acknowledge Dr. Jianchi Chen from United
States Department of Agricultureꎬ Agricultural Re ̄
search Serviceꎬ for editorial assistance. We would
like to thank Dr. Jianlong Xu ( Institute of Crop Sci ̄
enceꎬ Chinese Academy of Agricultural Sciences)
for data analysis assistance. This work is supported
by Ministry of Agriculture of the People’ s Republic
of China (201003067) and National Natural Science
Fund ( 31201480 ) by National Natural Science
Foundation of China (NSFC) .
References
[1] Reinking O A. Diseases of economic plants in southern
China [ J] . Philippine Agriculturistꎬ 1919ꎬ 8: 109 -
134.
[2] Jagoueix Sꎬ Bove J Mꎬ Garnier M. The phloem ̄limi ̄
ted bacterium of greening disease of citrus is a member
of the α subdivision of the Proteobacteria [J] . Interna ̄
tional Journal of Systematic Bacteriologyꎬ 1994ꎬ 44:
379-386.
[3] Murray Rꎬ Schleifer K. Taxonomic notes: a proposal
for recording the properties of putative taxa of pro ̄
caryotes [ J ] . International Journal of Systematicꎬ
1994ꎬ 44: 174-176.
[4] Garnier Mꎬ Jagoueix-Eveillard Sꎬ Cronje P Rꎬ et al.
Genomic characterization of a liberibacter present in an
ornamental rutaceous treeꎬ Calodendrum capenseꎬ in
the Western Cape Province of South Africa. Proposal
of ‘Candidatus Liberibacter africanus subsp. capensis’
[ J ] . International Journal of Systematic and
Evolutionary Microbiologyꎬ 2000ꎬ 50: 2119-2125.
[5] Texeira D Cꎬ Ayres Jꎬ Kitajima Eꎬ et al. First report
of a Huanglongbing ̄like disease of citrus in Sao Paulo
Stateꎬ Brazil and association of a new Liberibacter spe ̄
ciesꎬ ‘Candidatus Liberibacter americanus’ꎬ with the
disease [J] . Plant Diseaseꎬ 2005ꎬ 89: 107-107.
[6] Gottwald T R. Current epidemiological understanding
of citrus Huanglongbing [J] . Annual Review of Phyto ̄
pathologyꎬ 2010ꎬ 48: 119-139.
[7] Lin K H. Observations on yellow shoot of citrus. Etio ̄
logical studies of yellow shoot of citrus ( in Chinese)
[J] . Acta Phytopathologica Sinica (植物病理学报)ꎬ
1956ꎬ 2: 1-42.
[8] Deng X Lꎬ Tang W W. The studies on detection of
citrus Huanglongbing pathogen by polymerase chain
reaction ( in Chinese) [ J] . Journal of South China
Agricultural University (华南农业大学学报)ꎬ 1996ꎬ
17(3): 119-120.
[9] Tian Y Nꎬ Ke Sꎬ Ke C. Detection and quantitation of
citrus Huanglongbing pathogen by polymerase chain re ̄
action ( in Chinese) [J] . Acta Phytopathologica Sinica
(植物病理学报)ꎬ 1996ꎬ 26(3): 243-250.
[10] Adkar-Purushothama C Rꎬ Quaglino Fꎬ Casati Pꎬ et
al. Genetic diversity among ‘Candidatus Liberibacter
asiaticus’ isolates based on single nucleotide polymor ̄
phisms in 16S rRNA and ribosomal protein genes [J] .
Annals of Microbiologyꎬ 2009ꎬ 59: 681-688.
[11] Hu W Zꎬ Wang X Fꎬ Zhou Yꎬ et al. Diversity of the
omp gene in Candidatus Liberibacter asiaticus in China
[J] . Journal of Plant Pathologyꎬ 2011ꎬ 93: 211-214.
[12] Bastianel Cꎬ Garnier ̄Semancik Mꎬ Renaudin Jꎬ et al.
Diversity of ‘ Candidatus Liberibacter asiaticusꎬ’
based on the omp gene sequence [J] . Applied and En ̄
vironmental Microbiologyꎬ 2005ꎬ 71: 6473-6478.
[13] Furuya Nꎬ Matsukura Kꎬ Tomimura Kꎬ et al. Se ̄
quence homogeneity of the ψserA ̄trmU ̄tufB ̄secE ̄
nusG ̄rplKAJL ̄rpoB gene cluster and the flanking re ̄
gions of ‘Candidatus Liberibacter asiaticus’ isolates a ̄
round Okinawa main island in Japan [ J] . Journal of
General Plant Pathologyꎬ 2010ꎬ 76: 122-131.
[14] Ghosh Dꎬ Bhose Sꎬ Mukherjee Kꎬ et al. Sequence and
evolutionary analysis of ribosomal DNA from
Huanglongbing (HLB) isolates of Western India [ J] .
Phytoparasiticaꎬ 2013: 1-11.
[15] Jagoueix Sꎬ Bove J Mꎬ Garnier M. Comparison of the
16S / 23S ribosomal intergenic regions of ‘Candidatus
Liberobacter asiaticum’ and ‘Candidatus Liberobacter
africanumꎬ’ the two species associated with citrus
huanglongbing ( greening) disease [ J] . International
Journal of Systemic Bacteriologyꎬ 1997ꎬ 47: 224-227.
816
6期 XUMei ̄rong et al:Intraspecific Genetic Diversity Analysis of ‘Candidatus Liberibacter asiaticus’ by Short Tandem Repeats and PAGE
[16] Tomimura Kꎬ Miyata S ̄iꎬ Furuya Nꎬ et al. Evaluation
of genetic diversity among ‘ Candidatus Liberibacter
asiaticus’ isolates collected in Southeast Asia [ J] .
Phytopathologyꎬ 2009ꎬ 99: 1062-1069.
[17] Subandiyah Sꎬ Iwanami Tꎬ Tsuyumu Sꎬ et al. Com ̄
parison of 16S rDNA and 16S / 23S intergenic region
sequences among citrus greening organisms in Asia
[J] . Plant Diseaseꎬ 2000ꎬ 84: 15-18.
[18] Shan Z Jꎬ Feng Zꎬ Zhou Gꎬ et al. Cloning and se ̄
quence analysis of 16S rDNA of citrus Huanglongbing
agents collected from five provinces in south China ( in
Chinese) [J] . Journal of South China Agricultural Uni ̄
versity (华南农业大学学报)ꎬ 2008ꎬ 29(2): 25-29.
[19] Kong W Wꎬ Deng X Lꎬ Liang Z Hꎬ et al. Cloning and
sequencing of the citrus Huanglongbing pathogen DNA
( in Chinese) [ J] . Acta Phytopathologica Sinica (植
物病理学报)ꎬ 2000ꎬ 30(1): 71-75.
[20] Wang Z Zꎬ Zhou B Bꎬ Tian S Cꎬ et al. Genetic diver ̄
sity of Candidatus Liberibacter asiaticus isolates from
different geographical regions in China ( in Chinese)
[J] . Acta Phytopathologica Sinica (植物病理学报)ꎬ
2009ꎻ 39 (6): 593-599.
[21] Teixeira Dꎬ Eveillard Sꎬ Sirand ̄Pugnet P et al. The
tufB ̄secE ̄nusG ̄rplKAJL ̄rpoB gene cluster of the
liberibacters: sequence comparisonsꎬ phylogeny and
speciation [J] . International Journal of Systematic and
Evolutionary Microbiologyꎬ 2008ꎬ 58: 1414-1421.
[22] Duan Y Pꎬ Zhou L Jꎬ Hall D Gꎬ et al. Complete ge ̄
nome sequence of citrus Huanglongbing bacteriumꎬ
‘Candidatus Liberibacter asiaticus’ obtained through
metagenomics [ J] . Molecular Plant ̄Microbe Interac ̄
tionsꎬ 2009ꎬ 22: 1011-1020.
[23] Chen J Cꎬ Deng X Lꎬ Sun Xꎬ et al. Guangdong and
Florida populations of ‘Candidatus Liberibacter asiatic ̄
us’ distinguished by a genomic locus with short tandem
repeats [J] . Phytopathologyꎬ 2010ꎬ 100(6): 567-572.
[24] Liu Rꎬ Zhang Pꎬ Pu X Lꎬ et al. Analysis of a
prophage gene frequency revealed population variation
of ‘Candidatus Liberibacter asiaticus’ from two citrus ̄
growing provinces in China [J] . Plant Diseaseꎬ 2011ꎬ
95: 431-435.
[25] Zhou L Jꎬ Powell C Aꎬ Hoffman M Tꎬ et al. Diversity
and plasticity of the intracellular plant pathogen and in ̄
sect symbiont ‘Candidatus Liberibacter asiaticus’ as
revealed by hypervariable prophage genes with intra ̄
genic tandem repeats [ J] . Applied and Environmental
Microbiology 2011ꎬ 77: 6663-6673.
[26] Katoh Hꎬ Subandiyah Sꎬ Tomimura Kꎬ et al. Differen ̄
tiation of ‘Candidatus liberibacter asiaticus’ isolates
by variable ̄number tandem ̄repeat analysis [ J] . Ap ̄
plied and Environmental Microbiologyꎬ 2011ꎬ 77:
1910-1917.
[27] Islam M ̄Sꎬ Glynn J Mꎬ Bai Yꎬ et al. Multilocus
microsatellite analysis of ‘ Candidatus Liberibacter
asiaticus ’ associated with citrus Huanglongbing
worldwide [J] . BMC Microbiologyꎬ 2012ꎬ 12: 39.
[28] Benson G. Tandem repeats finder: a program to ana ̄
lyze DNA sequences [ J ] Nucleic Acids Research
1999ꎬ 27(2): 573-580.
[29] Ding Fꎬ Deng X Xꎬ Hong Nꎬ et al. Phylogenetic analy ̄
sis of the citrus Huanglongbing (HLB) bacterium based
on the sequences of 16S rDNA and 16S / 23S rDNA in ̄
tergenic regions among isolates in China [J] . European
Journal of Plant Pathologyꎬ 2009ꎬ 124: 495-503.
[30] Chen Q P. 1943. A report of a study on yellow shoot
disease of citrus in Chaoshan [ J] . New Agriculture
Quarterly Bulletinꎬ 3: 142-177.
[31] Deng X Lꎬ Gao Y Dꎬ Chen J Cꎬ et al. Curent situation
of ‘Candidatus Liberibacter asiaticus’ in Guangdongꎬ
Chinaꎬ where citrus Huanglongbing was first described
[J] . Journal of Integrative Agricultureꎬ 2012ꎬ 11(3):
424-429.
[32] Ma W Qꎬ Liang M Dꎬ Guan Lꎬ et al. Ecology and
epidemiology population structures of ‘ Candidatus
Liberibacter asiaticus’ in southern China [J] . Phytopa ̄
thologyꎬ 2014ꎬ 104(2): 158-162.
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