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Biosaintifika
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http://journal.unnes.ac.id/nju/index.php/biosaintifika
DOI: 10.15294/biosaintifika.v8i2.5448
How to Cite
Kurniawaty, N., Hidayat, P. & Rauf, A. (2016). Characterization of Three Species
of Thrips on Banyan, Nutmeg, and Marine Seruni Plants Based on COI Gene. Bio-
saintifika: Journal of Biology & Biology Education, 8(2), 185-192.
Correspondence Author: p-ISSN 2085-191X
Jl. Raya Darmaga, Bogor, Jawa Barat, Indonesia e-ISSN 2338-7610
E-mail: niakurniawaty255@gmail.com
Nia Kurniawaty et al. / Biosaintifika 8 (2) (2016) 185-192
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pins. Place a drop of hoyers solution on the object Biosystem,US). The PCR contained Go Tag Green
glass with a diameter of 13 mm and place a thrips Master Mix 12.5 μL, 9.5 μL ddH2O, forward pri-
into this drop, ventral side uppermost, and gen- mer 1μL, reverse primer 1μL, and DNA temp-
tly lower a slide onto the drop. Invert the slide as late 1 μL. A portion of mtCOI was amplified
soon as the solution has spread sufficiently. Place using the universal primers LCO1490(3’-GGT-
immediately into an oven at 35-40°C. Then leave CAACAAATCATAAAGATATTGG-5’) and
for a few hours before attempting to study. When HCO2198(5’TAAACTTCAGGGTG
the mountant was dried, ring with nail varnish ACCAAAAAATCA-3’) (Folmer et
and labelled appropriately. Identification of trips al.,1994). Thermocycling was 5 minutes at 94oC,
conducted directly under a stereo microscope an then with 35 cycles of 1 minute at 94oC, 35
OLYMPUS CX21FSI with Dino-eye camera seconds at 52oC, 1 minute 30 seconds 72oC and 7
AM4232. Identification used key identification minutes at 72oC. Visualization of DNA fragment
of Mound and Kibby (1998), Sartiami & Mound as the result of electrophoresis amplification used
(2013) & Subagyo (2014). agarose gel 1% in Tris-borate (TBE) buffer 0.5X
with voltage of 50 volt for 50 minutes. PCR prod-
Molecular Characterization uct were electrophoresis in 2% agarose gels. Gels
DNA Extraction were stained ethidium bromide for 15 minutes,
Total genomic DNA was extracted from visualized and photographed under UV light.
single thrips using the slightly modified proto-
col by Goodwin et al. (1994). Briefly, individual Data Analysis
thrips imago were placed in eppendorf tube 1.5 Direct sequenced at Genetica Science.
mL, then it was added the CTAB bufer extrac- Sequence were trimmed to aligned manually in
tion 100 μL (CTAB 2%, NaCl 1.4 M, Tris-HCI BioEdit ver.7.0.9. then analyzed by using BLAST
100 mM, EDTA 20 mM, and PVP 1% [-40ºC]), programme. Nucleotide matrix formation was
1 μL of protainase K. Plastic grinders were used conducted with Clustal x (1.83) software, whi-
to crush the insect, an the tube were incubated at le the phylogenetic tree from morfological data
65 oC for 3 minutes. The tube was added CI 100 constructed by NTSys21, and sequence data
μL with 24:1 ratio. It were vortexed for 3 minu- constructed by Molecular Evolutionary Genetic
tes, and were centrifuged at 10 000 rpm for 15 Analisis (MEGA 6) software with UPGMA met-
minutes. The supernatant that had been formed hode and bootstrap for 1000 replicates
was taken of 60 μL, and moved into new tube.
Then, added sodium acetate 3 M (pH 5.2) 6 μL RESULT AND DISCUSSION
and 44 μL isopropyl. The homogenate was store
-20oC for 24 hours. After the preparation, the tube Based on the results of this research, the
were centrifuged at 10.000 rpm for 10 minutes thrips found in banyan, nutmeg, and marine seru-
and the supernatant were disposed. The pellets ni plants were the members of the Phlaeothripi-
was washed by using 100 μL of 80% ethanol and dae family. The morphological identification
was centrifuged at 8000 rpm for 5 minutes. Final showed that the three samples belong to different
step, the supernatant was disposed and the pellets species. They were Gynaikothrips uzeli (Zimmer-
was dried for less than 1 hour and then resuspent man), Haplothrips ganglbaueri (Schmutz), and Pseu-
using TE buffer 20 μL for subsequent PCR amp- dophilothrips ichini (Table 1).
lification. G. uzeli sample had morphological char-
acteristics such as: an antenna consisting of 8
DNA Amplification segments, shape of the end of its stylet is curve
The Polymerase Chain Reaction (PCR) and narrow, cheeks without setae, the pronotum
was used to amplified 710 bp of COI gene. All usually with less than 5 paors of well-developed
PCRs were performed in 25μL reaction with setae, forewings without venation with paralel
Perkin Elmer 480 Thermocycler (Applied sides, tergites with only 2 pairs of wing-retaining
Table 1. Host plants and thrips species of the Phlaeothripidae found in research location.
Location
Species Host Plants Coordinate
(Village/ Subdistrict/ Regency)
G. uzeli Banyan Cisantana/ Cigugur/ Kuningan 102°26’42.21’’E;6°56’37.71”S
H. ganglbaueri Marine Seruni Sukajadi/ Tamansari/ Bogor 106°43’38.47’’E;6°38’16.29’’S
P. ichini Nutmeg Ciapus/ Ciomas/ Bogor 106°44’21.88’’E;6°37’32.48’’S
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setae. H. ganglbaueri had antenna consisting 8 seg- more COI gene sequence possible identify unkno-
ments, forewings constricted medially, matano- wn specimens by comparing their COI sequence
tum with weakly reticulates sculpture, antennal and has been used for identification purposes in
segment IV with 4 sense cone. P. ichini has usually projects known as species barcoding. Basically,
with 5 pairs of well-developed setae and sculpture biodiversity and polymorphism can be seen from
usually more or less striate or in distinc. forewings DNA sequences of certain fragments of an orga-
without venation with paralel sides, tergites with nism genome (Suryanto, 2001).
only 2 pairs of wing-retaining setae. Sequence analysis is a technique consid-
ered as the best technique to see biodiversity in
Amplification and Alignment COI gene a group of organism. Basically, biodiversity and
The diagnostic PCR succesfull distinguis- polymorphism can be seen from DNA sequenc-
hed the three COI of thrips. Specimens with COI es of certain fragments of an organism genome
gene produced a single PCR product of ± 710 bp (Suryanto, 2001). The characteristics of DNA nu-
(Figure 1). The second band from G. uzeli (banyan cleotide of COI gene G. uzeli was 704 pb, but with
tree), third band from H. ganglbaueri (marine seru- the content of the lowest A base (Adenine) and
ni/Widelia biflora) and fourth band from P. ichini T base (Thymine) of 70,60% followed by P. ichini
(nutmeg tree). This study succeed to identified 702 pb sequences with AT 73.03% composition.
thrips species by using COI gene. Based on the re- The height of AT composition was a special char-
sults there were three thrips sequences in which acteristic of nucleotide array of mtCOI gene on
each sample had different lenght in nucleotide insects. A and T base have weak hydrogen bonds
array. It was happened bacause the three samp- so that easy to changed (Liu & Beckenbench,
les from different taxonomy level in genus. As 1992). Base on the results of nucelotide array of
described Karimi et al. (2010) based on COI gene BLAST of G. uzeli in Indonesia has similarity
sequences, also successfully distinguished some value of similarity of 95% with the same species
of thrips species of four different genus. Further- from China, H. ganglbaueri found has 92% with H.
Figure 2. Results of DNA visualization of COI gene fragment of three thrips species by using univer-
sal primer (M) Marker 1 kb (Thermo Scientific, US), (1) Positive control (G. uzeli), (2) G. uzeli, (3) H.
ganglbaueri, and (4) P. ichini.
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Table 2. DNA BLAST of COI gene on three thrips species by using BLAST-N programme
Max Total Query cover Ident
Description Origin E value Accession
Score Score (%) (%)
G. uzeli China 950 950 91 0.0 93 JN181200
H. ganglbaueri Australia 830 830 87 0.0 92 EF468730
P. ichini Canada 628 628 90 0.0 84 KJ087886
ganglbaueri from Australia, P. ichini has 84% with within insect species was recieved with genetic
P. ichini from Canada. It is so since the three sam- distance value 0.05-0.23 or homology value 73-
ples took place in different taxonomy level (Table 95%. It can be seen from Caligula japonica (Lepi-
2). Karimi et al. (2010) suggest that based on COI doptera: Saturniidae) (Li et al., 2009), Diadegma
gene sequences, it had successfully distinguished (Hymenoptera: Ichneumonidae) (Wagener et al,
some of thrips species of four different genus. 2006), and mosquitos (Cywinska et al., 2006).
Base on the results of nucelotide array of Ubaidillah & Sutrisno (2009), the presence of
BLAST of G. uzeli from Indonesia, it had the the differences of nucleotide sequence array oc-
similarity percentage of 93% with the same spe- cur due to the mutation. It can cause the change
cies from China. H. ganglbaueri found in marine of nucleotide base which then change encoded
seruni (Widelia biflora) showed the similarity per- amino acid (Hawkes et al., 2004). Our analyses
centage of 92% with H. ganglbaueri species from clearly indicate that genetic differentiation hap-
Australia. Then, samples of P. ichini nutmeg tree pen because geographic isolation and genetic
indicated the similarity percentage of 84% with P. drift. According to Templeton (1998) genetic
ichini from Canada (Table 2). variation is distributed spatially within a species
The results of DNA sequences alignment geographical range. Resricted gene flow and his-
of COI gene of the three samples (Table 3) showed torical events can be interwined, and cladistical
that the three species were taxonomically sepa- analyses can constructed their temporal juxta po-
rated. It can be seen from the nucleotide array of sition, thereby yielding great insight into both the
mtCOI gene that had been successfully aligned in evolutionary history an population structure of
which there were differences in some points of the species.
nucleotide base sequences of each genus. The Phylogenetics tree based on COI gene (Fig-
number of converse nucleotide of the three spe- ure 3) showed that there were two main groups of
cies was 622 pb and the nucleotide variation was thrips, P. ichini and G. uzeli. Claodgram construc-
27.8% or 173 pb. That was the variation of the ar- tion was based on the DNA sequences of mtCOI
ray of each sample. When there was variation of gene demonstrating the separated classification
array occured in a nucleotide alignment with the with bootsrap value between in-group sequences
old ones, it would show the mutation, including (G. uzeli, H. ganglbaueri, P. ichini) and out-group se-
insertion, deletion, or rearrangement of genetic quence (Ceratothripoides brunneus). The first group
materials (Dharmayanti, 2011; Hoy, 2003). was P. ichini with H. ganglbaueri as sister-grup with
the bootstrap value of 84%. The second group
Genetic Distance and Phylogenetic Tree Based was G. uzeli, from Indonesia classifying with G.
on Gene Sequence uzeli from China with the bootsrap value of 100%.
Based on the mtCOI gene sequences of This study investigated the utility of COI
three species, it can be analyzed genetic distance for identifying thrips species. As demonstrated
and phylogenetic construction. High value of in this work, there is a relationship between phy-
genetic distance indicates that they are closely logeny and origin evolution of thrips species. We
related. G. uzeli has genetic disctance value 6.2% interpret our analyses of congruence phylogenet-
with the same species from China. H. ganglbaueri ics tree as suggesting that the different data sets
8.9% with the same species from Australia, while provide complementary information that is not
P. ichini 15.8% with P. ichini species from Canada contradictory. Crespi et al. (1998) result showed
(Table 4). adult morphology data was not significant from
G. uzeli and H. ganglbaueri species showed sequences of COI gene so that can support the
hight similarity levels with haplotype in GenBank results of morphological identification of thrips
as showed low genetic distance value. It was quite species classification from Tubulifera (Phlaeo-
different from P. ichini in which the similarity lev- thripidae). Karimi et al. (2010) also used COI
els with haplotype in GenBank was low. Howev- gene to identified some of thrips species, the re-
er, according to Li et al. (2009), genetic distance sult showed there was closely relations of evolu-
189
Table 3 Variation of DNA nucleotide array of COI gene of thrips
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Nia Kurniawaty et al. / Biosaintifika 8 (2) (2016) 185-192
Table 4. Genetic distance of DNA sequences of COI gene on three thrips species
Species Origin Accession 1 2 3 4 5 6
G. uzeli Indonesia - ID
G. uzeli China JN181200 0.062 ID
H. ganglbaueri Indonesia - 0.239 0.182 ID
H. ganglbaueri Australia EF468730 0.247 0.205 0.089 ID
P. ichini Indonesia - 0.355 0.292 0.266 0.303 ID
P. ichini Canada KJ087886 0.210 0.155 0.140 0.175 0.158 ID
100 H.ganglbaueri
57 H.ganglbaueri_Aus_EF468730
84
P.ichini_Knd_KJ087886
P.ichini
G.uzeli
100 G.uzeli_Chn_JN81200
Ceratothripoides_brunneus
Figure 3. Thrips cladogram based on DNA sequnce nuclotide fragment of COI gene by using UPGMA
method
tion of each thrips species. The phylogeny con- results of morphological identification of thrips
struction with out-group showed that there was a species classification from Phlaeothripidae.
clear separation among the species. Sequence of
COI gene considered as a very great genetic mark- CONCLUSION
er in encoding DNA. The data of DNA sequence
array of COI gene is also the completing data of Gynaikothrips uzeli (Zimmerman), Hap-
biological and morphological data. The phyloge- lothrips ganglbaueri (Schmutz), and Pseudophi-
netic tree formed in here was based on the results lothrips ichini was found in weeping fig (Ficus ben-
of a research by Karimi et al. (2010) that used jamina), nutmeg (Myristica fragrans), and marine
DNA of mtCOI gene to identify some of thrips seruni (Wedelia biflora) plants. The characteristics
species in which there was familiarity relations of of mtCOI of G. uzeli, H. ganglbaueri, and P. ichini
evolution of each thrips species. The cladogram were 704, 686, and 702 bp dominated by Adeni-
construction with out-group showed that there ne and Thymine base with nucleotide variation
was a clear separation among three species. value of 27.8%. Sequences data of mtCOI DNA
Molecular identification by using COI gene can be used for thrips identification.
had successfully identified the three thrips spe-
cies because the gene were conserve (Herbert et ACKNOWLEDGMENT
al., 2003). Karimi et al. (2010) added that DNA
of COI gene is considered as a very great genetic This research was well supported by
marker in encoding DNA. The data of DNA se- BPOTN research grant programme number 319/
quence array of COI gene is also the completing IT3.41.2/L2/SPK/2014.
data of biological data and morphological char-
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