DNA
Barcoding and Phylogenetic Analysis of the Species in the Genus Alpinia
1Institute of
Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet,
Cau Giay, Hanoi, Vietnam
2VNTEST
Institute for Quality Testing and Inspection, Nguyen Xien, Thanh Xuan, Hanoi,
Vietnam
3Vietnam
National Museum of Nature, Vietnam Academy of Science and Technology, 18 Hoang
Quoc Viet, Cau Giay, Hanoi, Vietnam
4Institute of
Ecology and Biological Resources, Vietnam Academy of Science and Technology, 18
Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
5Graduate
University of Science and Technology, Vietnam Academy of Science and
Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
†Co-first
authors and contributed equally to this work
*For correspondence: hienlethu@igr.ac.vn
Received 11 August 2022; Accepted 17 November 2022;
Published 27 February 2023
Abstract
Alpinia Roxb.
is the largest and most taxonomically complex genus of the flowering plant
family Zingiberaceae. Internal transcribed spacer (ITS) region of ribosomal DNA
has been used to resolve the phylogenetic relationships in Zingiberaceae family
and its genera including Alpinia, Globba, and Amomum. In this
study, the ITS region was used as additional molecular
data for species classification in the genus Alpinia. Genomic DNAs from leaf samples of 23 Alpinia species and 11 taxa collected in Vietnam were isolated and
used as templates for PCR amplifications of the ITS region. Phylogenetic
trees were constructed via both
Neighbor Joining and Maximum Likelihood methods using 36 reference Alpinia sequences along with 30
sequences obtained in this study. Results demonstrated that DNA barcoding using
the ITS region is a reliable tool for supporting the identification of Alpinia species. Morphological
characteristics and ITS sequences help to better understand the phylogenetic
relationship of the species in the genus Alpinia
distributed throughout Vietnam. © 2023 Friends Science Publishers
Keywords: Alpinia; DNA barcode; ITS; Phylogenetic
relationship; Species Identification
Introduction
Alpinia Roxb. is the largest and most taxonomically complex
genus of the flowering plant family Zingiberaceae. This genus has approximately
250 species distributed among areas of tropical and subtropical climates,
including Asia, Australia, and the Pacific Islands (Smith 1990; Larsen 1998; Vu
et al. 2019). Most Alpinia species are commonly grown for their flowers (e.g., A. purpurata), while others have economic
potential and are used as spices (e.g., A. galanga) and medicines (e.g.,
A. bracteata) (Wu 2000; Kress et al. 2005; Uma and
Muthukumar 2014). According to Smith’s
classification, the genus Alpinia consists
of two subgenera, Alpinia, and Dieramalpinia. In Vietnam, most of the Alpinia species belongs to the subgenus Alpinia which was divided into four
groups, Dydimanthus, Alpinia, Guillania, and Allughas (Smith
1990). Recently, several species have
been recorded for Vietnam’s flora such as A.
rugosa in Thua Thien-Hue province, A.
graminifolia in Quang Ninh and Bac Giang provinces, and A. coriandriodora in Bac Kan province (Le
et al. 2017; Nghiem et al. 2018; Vu et al.
2019). By early 2019, 36 species of Alpinia
have been recorded to be found throughout the country (Vu et al. 2019). Sixteen species are traditionally used as medicines
by the Vietnamese people to treat common illnesses, such as stomachache,
indigestion, cholera, dysentery, diarrhea, vomiting, excessive urination at
night, and natural ejaculation. Various parts of the plant (rhizome, tuber,
leaves, flowers, seed, and fruit) are used to remedy these symptoms, with the
rhizome being the most commonly used part (Nguyen et al. 2014; Nghiem et
al. 2018).
Over the last two decades,
DNA barcoding has been rapidly developed as an useful tool for species
classification, biodiversity investigation and conservation, molecular
phylogeny and evolutionary studies (Kang et
al. 2017). The method is based on the principle of comparing short and
universal DNA sequences from standard regions of the genome that have
efficiently high evolution rates, allowing it to be appropriate for classifying
members of a specific genus (Hebert et al.
2003). The advantage of this molecular approach is that the starting material
can be as small as a sample of a plant tissue, and the identification process
is fast and reproducible (Hartvig et al.
2015). DNA barcodes utilized for plant taxonomic classification belong to the
internal transcribed spacer (ITS) region in the nuclear genome and psbA-trnH,
matK, rbcL, trnL-trnF in the chloroplast genome (Kress et al. 2005; Kress and Erickson 2007; CBOL
Plant Working Group et al. 2009; Panaligan et al. 2021).
Among
these DNA barcodes, ITS is the most widely used marker in plant phylogenetic
studies because of its high resolution of inter- and intraspecific
discrimination (Cheng et al. 2016; Keskin et al. 2017). Previous studies indicated
that ITS possessed greater discriminatory ability when compared to other
markers from chloroplast genomes (Hollingsworth et al. 2011; Huang et al.
2015). However, the main drawbacks of using this region as a core universal DNA
barcode for plant classification are results of the incomplete concerted
evolution of multiple copies, different alleles from paternal and maternal
parents, DNA contamination of different species, amplification and sequencing
success rate, and other technical problems (China Plant BOL Group et al. 2011; Hollingsworth et al. 2011). This region belongs to
ribosomal DNA in the nuclear genome (Kang et
al. 2017) and is comprised of the ITS1 intergenic spacer, 5.8S rDNA, and the ITS2 intergenic
spacer, whose size ranges from 400 to 1000 bp in total (Álvarez and Wendel 2003).
Among these three partial sequences,
5.8S is the most conserved region while other two spacers possess high
discriminatory ability with an abundance of variable sites (Hollingsworth et al. 2011). ITS helped resolve the phylogenetic
relationships in Zingiberaceae family and its genera including Alpinia, Globba, and Amomum (Vinitha et al. 2014). Using ITS and trnL-F
sequences, the phylogeny of tribe Zingibereae was studied (Ngamriabsakul et al. 2003). ITS along with trnK-matK
were used for investigating the phylogeny, evolution, and classification of the
Globba genus (Williams et al. 2004). The molecular
phylogenetic analysis based on multiple accessions of ITS and matK regions of Alpinia, Amomum, Elettaria, Elettariopsis, Geocharis,
Geostachys, and Hornstedtia genera revealed
that Alpinia genus consists six
clades (Boer et al. 2018). Within the genus Alpinia,
Kress et al. (2005) reported the most
extensive phylogenetic analysis based on molecular characteristics using ITS
and matK regions. This study combined
the morphology (Smith 1990) and molecular based analyses to build a six-clade
classification system for the genus Alpinia
(Kress et al. 2005). ITS1 was also
used as molecular evidence in Qiao’s analysis to differentiate an Amomum species from Alpinia (Qiao et al. 2009).
Tan et al. (2020) demonstrated the
high species identification of Alpinia
species collected in Peninsular Malaysia using the ITS2 region. The efficacy of 4 barcoding loci including ycf1b, rbcL, ITS and ITS2
were evaluated on 13 species belonging to 4 genera of Zingiberaceae (Saha et al.
2020).
In Vietnam, there are still
difficulties in species identification among the genus Alpinia due to similarities in morphological characteristics and
the lack of DNA barcode studies. Thus, in the present study, the ITS region was
used as additional molecular data for species classification in the genus Alpinia. Our aim is to obtain a better
understanding of phylogenetic relationship of the Alpinia species distributed throughout Vietnam. These molecular
data provide supportive information for identification
of sampled species and the phylogeny data are useful
for further investigation on the divergence and branching of species and
selected clades within the genus Alpinia
and family Zingiberaceae.
Materials and Methods
Materials
Forty-four leaf samples from
23 species Alpinia and 11 taxa were
collected from different regions throughout Vietnam from 2010 to 2018 and
stored on silica-gel within 24 hours of collection till further use (Table 1
and Fig. 1). All specimens were morphologically identified by Nguyen Quoc Binh
and Nguyen Phuong Hanh using comparative morphological method (Nguyen et al. 2017) and deposited at the
Vietnam National Museum of Nature (VNMN). All laboratory work and bioinformatics
analysis were performed at the Institute of Genome
Research, Vietnam Academy of Science and Technology.
Methods
Total DNA extraction, and amplification of ITS region: Twenty milligrams of each of the lyophilized leaf specimens were used for
total genomic DNA extraction using GeneJET Plant Genomic DNA Purification Kit
(Thermo Fisher Scientific, USA), according to the protocol supplied by the manufacturer.
The ITS region was amplified from the genomic DNA using DreamTaq DNA
polymerase (Thermo Fisher Scientific, USA). The forward and reverse primers
used to amplify the ITS sequence in this study were ITS-F (5’-ACG AAT TCA TGG
TCC GGT GAA GTG TTC G-3’) and ITS-R (5’-TAG AAT TCC CCG GTT CGC TCG CCG TTA
C-3’) (Sun et al. 1994). PCR was
performed on a Mastercycler Pro (Eppendorf, Germany) under the following
conditions: an initial denaturation step at 94°C for 5 min, followed by 40
cycles of denaturation at 94°C for 2 min, primer annealing at 54°C for 30 s,
extension at 72°C for 50 s Table 1: Alpinia samples used in this study
No. |
Sample ID |
Morphology identification |
Collected location |
Collection time |
1 |
PD1 |
A. aff. Calcarata |
Phong Dien, Thua Thien-Hue |
12 October 2016 |
2 |
SH83 |
A. aff. Coriandriodora |
Na Ri, Bac Kan |
07 April 2016 |
3 |
SH84 |
A. aff. Coriandriodora |
Na Ri, Bac Kan |
11 April 2016 |
4 |
2179 |
A. aff. Coriandriodora |
Trang Dinh, Lang Son |
07 April 2015 |
5 |
2197 |
A. aff. Coriandriodora |
Kim Hy, Bac Kan |
13 March 2013 |
6 |
SH87* |
A. blepharocalyx |
Tam Dao National Park, Tam Dao, Vinh Phuc |
14 April 2016 |
7 |
SH650 |
A. blepharocalyx |
Forest Inventory and Planning Institute, Thanh Tri, Ha
Noi |
20 April 2018 |
8 |
1093* |
A. bleviligulata |
Bach Ma National Park, Phu Loc, Thua Thien-Hue |
29 August 2010 |
9 |
SH89 |
A. calcicola |
Tam Dao National Park, Tam Dao, Vinh Phuc |
15 April 2016 |
10 |
SH91 |
A. conchigera |
Bach Ma National Park, Phu Loc, Thua Thien-Hue |
15 May 2016 |
11 |
2190* |
A. galanga |
Binh Gia, Lang Son |
03 May 2016 |
12 |
SH669 |
A. galanga |
Mai Chau, Hoa Binh |
27 June 2018 |
13 |
SH06* |
A. globosa |
Tam Dao National Park, Tam Dao, Vinh Phuc |
08 October 2014 |
14 |
SH94* |
A. gramineum |
Son Dong, Bac Giang |
29 May 2016 |
15 |
2189 |
A. kwangsiensis |
Loc Binh, Lang Son |
03 May 2016 |
16 |
SH649 |
A. latilabris |
Forest Inventory and Planning Institute, Thanh Tri,
Hanoi |
20 April 2018 |
17 |
SH90 |
A. maclurei |
Xuan Son National Park, Tan Son, Phu Tho |
07 May 2016 |
18 |
SH93 |
A. maclurei |
Xuan Son National Park, Tan Son, Phu Tho |
22 May 2016 |
19 |
SH163 |
A. menghaiensis |
Tam Dao, Vinh Phuc |
12 April 2017 |
20 |
2186* |
A. oblongifolia |
Tam Dao National Park, Tam Dao, Vinh Phuc |
09 October 2014 |
21 |
2182* |
A. oxymitra |
Phu Quoc, Kien Giang |
19 May 2015 |
22 |
SH185 |
A. oxymitra |
Phu Quoc, Kien Giang |
19 May 2016 |
23 |
SH661 |
A. oxymitra |
Phu Quoc, Kien Giang |
05 June 2018 |
24 |
SH156 |
A. pinnanensis |
Tam Dao National Park, Tam Dao, Vinh Phuc |
05 November 2016 |
25 |
SH85* |
A. polyantha |
Son Dong, Bac Giang |
28 April 2016 |
26 |
SH88 |
A. pumila |
Tam Dao National Park, Tam Dao, Vinh Phuc |
15 April 2016 |
27 |
SH125 |
A. purpurata |
Krong Bong, Dak Lak |
08 July 2016 |
28 |
2188 |
A. strobiliformis |
Loc Binh, Lang Son |
03 May 2016 |
29 |
2194* |
A. zerumbet |
Tan Son, Phu Tho |
18 May 2016 |
30 |
SH101 |
A. "kontumensis" |
Dak Glei, Kon Tum |
01 July 2016 |
31 |
SH176 |
A. "kontumensis" |
Dak Glei, Kon Tum |
19 July 2017 |
32 |
SH86 |
A. "tamdaoensis" |
Tam Dao National Park, Tam Dao, Vinh Phuc |
14 April 2016 |
33 |
2183* |
A. "tamdaoensis" |
Tam Dao, Vinh Phuc |
10 January 2015 |
34 |
SH167* |
A. spp. 1 |
Tam Dao, Vinh Phuc |
08 July 2017 |
35 |
SH97* |
A. spp. 2 |
Dak Glei, Kon Tum |
01 July 2016 |
36 |
SH155* |
A. spp. 3 |
Tam Dao National Park, Tam Dao, Vinh Phuc |
04 November 2016 |
37 |
2180* |
A. spp. 5 |
Trang Dinh, Lang Son |
22 April 2015 |
38 |
SH651 |
A. spp. 6 |
Forest Inventory and Planning Institute, Thanh Tri,
Hanoi |
20 April 2018 |
39 |
SH652 |
A. spp. 7 |
Forest Inventory and Planning Institute, Thanh Tri,
Hanoi |
20 April 2018 |
40 |
SH653 |
A. spp. 8 |
Bidoup Nui Ba National Park, Lac Duong, Lam Dong |
23 April 2018 |
41 |
SH479 |
A.
spp. 9 |
Cu Jut, Dak Nong |
15 October 2017 |
42 |
SH486 |
A. spp. 10 |
Cu Jut, Dak Nong |
15 October 2017 |
43 |
SH532 |
A. spp. 11 |
Dak Song, Dak Nong |
18 October 2017 |
44 |
SH538 |
A. spp. 12 |
Dak Song, Dak Nong |
18 October 2017 |
*Samples
failed in amplification and sequencing were marked in dark and light grey,
respectively
and final extension at
72°C for 10 min. For each reaction, the PCR mixture consisted of 2.0 µL 10X DreamTaq buffer, 1.0 µL each 10 µM primer, 0.5 µL 2.5 mM dNTPs, 0.15 µL of 5 U/µL DreamTaq DNA
polymerase, 18.85 µL milliQ, and 1.0 µL template DNA for a total volume of 20
µL. PCR products were detected by
0.8% agarose gel electrophoresis and purified using GeneJET PCR Purification
kit (Thermo Fisher Scientific, USA).
Sequencing and alignment of ITS region: Sanger sequencing of ITS region was performed on an ABI
3500 Genetic Analyzer system using BigDye Terminator v. 3.1 Cycle Sequencing
Kit (Thermo Fisher Scientific, USA). Raw sequencing results were compared and
aligned using the program BioEdit 7.0.5. Sequences obtained in this study were
submitted to GenBank with accession number from MN545627-MN545656. BLAST (Basic
Local Alignment Search Tools) searches for evaluating the species
identification ability were performed using reference sequences on GenBank.
Fig. 1: Different types of Alpinia genus collected in Vietnam
(a) A. aff. calcarata; (b) A.
aff. coriandriodora; (c) A.
blepharocalyx; (d) A. bleviligulata; (e) A.
calcicola; (f) A. conchigera; (g) A.
galanga; (h) A. gramineum; (i) A.
kwangsiensis; (j) A. latilabris; (k) A.
maclurei; (l) A. menghaiensis; (m) A.
oblongifolia; (n) A. oxymitra; (o) A.
pinnanensis; (p) A. polyantha; (q) A.
pumila; (r) A. purpurata; (s) A.
strobiliformis; (t) A. zerumbet;
(u) A. "kontumensis";
(v) A. "tamdaoensis";
(w) Alpinia spp. 2; (x) Alpinia spp. 7
Table 2: Success rate of PCR amplification and sequencing of ITS region in
sample set
|
Number
of success samples |
Success
rate (%) |
Genomic
DNA extraction |
44 |
100 |
PCR
amplification |
37 |
84 |
Sequencing
|
30 |
81 |
Phylogenetic analysis and species classification: The
matrix for phylogenetic analysis consisted of ITS sequences obtained in this
study and reference sequences, and the global alignment was performed using
MAFFT version 7.407 (Katoh et al.
2002) with local re-alignment using MUSCLE version 3.8.1551 (Edgar 2004). Phylogenetic
tree of the aligned ITS sequence sets was separately reconstructed by Neighbor
Joining (NJ) and Maximum Likelihood (ML) methods with Kimura 2-parameter model
of 1000 replicates using MEGA.X (Kumar et
al. 2018) with 1000 replicates. Phylogenetic variation was estimated with
bootstrap values (%), which indicated confidence interval between phylogenetic
lineages of the studied samples on the tree. Information of the ITS fragments
of studied samples, including accession numbers of referred taxa as showed in
Fig. 3a, b. Outgroup selection for phylogenetic analysis was
ITS sequence from A. longipetiolatum.
BLAST searches results were used as an
initial classification to localize each sample into sister species groups.
Comparison between NJ and ML phylogenetic trees was performed based on nodes
with bootstrap value greater than 50. Ambiguous branches and nodes were excluded
from the analysis. Results from both phylogenetic tree construction methods and
BLAST searches were then compared to morphology based classification. Results
from the comparison were used to evaluate the discriminating ability of ITS
regions in certain groups of Alpinia species.
Results
Total DNA extraction and amplification of ITS region
Genomic DNAs were isolated
from 44 leaf samples of species Alpinia
and had sufficient quality for further uses. After the extraction step, genomic
DNA was used as template for PCR amplification of the ITS region. The
length of the amplicons obtained with universal primers for ITS amplification
was approximately 850 bp, as expected (Fig. 2). The success rate of PCR
amplification was 84% due to failures in the amplification of 7 DNA samples
(Table 2).
Sequencing and alignment of ITS region
Total 37 PCR products were
purified and sequenced using Sanger-based sequencing system. Among those
samples, 30 sequences were obtained, which contributed to 81% of the success
rate for sequencing the ITS region. Most of the samples that were failed to
amplify and sequence were collected during the period from 2010 to 2016. The
above proportions showed difficulties in amplification and sequencing of ITS
region for prolonged storage samples despite optimizing effort.
Fig. 2: Electrophoresis of PCR products of 800 bp
amplified between ITS-F and ITS-R primers and gDNA of representative samples
from 44 samples of Alpinia species. SH85-PD1:
ID of the samples with detailed in Table 1; M: Hyper ladder 1kb (Bioline, UK)
Table 3: Species identification of Alpinia species using ITS region
No. |
Sample ID |
GenBank accession number |
Morphological classification |
Molecular based
classification |
1 |
PD1 |
MN545627 |
A. aff.
calcarata |
A. calcarata/ A. galanga |
2 |
SH83 |
MN545628 |
A. aff. coriandriodora |
A. coriandriodora |
3 |
SH84 |
MN545629 |
A. aff.
coriandriodora |
A. coriandriodora |
4 |
2179 |
MN545630 |
A. aff.
coriandriodora |
A. tonkinensis |
5 |
2197 |
MN545631 |
A. aff.
coriandriodora |
A. coriandriodora |
6 |
SH650 |
MN545632 |
A. blepharocalyx |
Generated a separated branch |
7 |
SH89 |
MN545633 |
A. calcicola |
A. tonkinensis |
8 |
SH91 |
MN545634 |
A. conchigera |
A. calcarata/ A. galanga |
9 |
SH669 |
MN545635 |
A. galanga |
A. galanga |
10 |
2189 |
MN545636 |
A. kwangsiensis |
A. kwangsiensis |
11 |
SH649 |
MN545637 |
A. latilabris |
Generated a separated branch |
12 |
SH90 |
MN545638 |
A. maclurei |
A. maclurei |
13 |
SH93 |
MN545639 |
A. maclurei |
A. maclurei |
14 |
SH163 |
MN545640 |
A. menghaiensis |
A. kwangsiensis |
15 |
SH185 |
MN545641 |
A. oxymitra |
A. oxymitra |
16 |
SH661 |
MN545642 |
A. oxymitra |
A. oxymitra |
17 |
SH156 |
MN545643 |
A. pinnanensis |
A. pinnanesis |
18 |
SH88 |
MN545644 |
A. pumila |
A. pumila |
19 |
SH125 |
MN545645 |
A. purpurata |
A. purpurata |
20 |
2188 |
MN545646 |
A. strobiliformis |
A. strobiliformis var. glabra |
21 |
SH101 |
MN545647 |
A. "kontumensis" |
Generated a separated branch |
22 |
SH176 |
MN545648 |
A. "kontumensis" |
A. nutans |
23 |
SH86 |
MN545649 |
A. "tamdaoensis" |
A. chinensis/ A. japonica/ A. pumila |
24 |
SH651 |
MN545650 |
A. spp. 6 |
Generated a separated branch |
25 |
SH652 |
MN545651 |
A. spp. 7 |
Generated a separated branch |
26 |
SH653 |
MN545652 |
A. spp. 8 |
A. nutans |
27 |
SH479 |
MN545653 |
A. spp. 9 |
Generated a separated branch |
28 |
SH486 |
MN545654 |
A. spp. 10 |
Generated a separated branch |
29 |
SH532 |
MN545655 |
A. spp. 11 |
A. conchigera |
30 |
SH538 |
MN545656 |
A. spp. 12 |
Generated a separated branch |
Raw sequences obtained from
the sequencing step were proceeded to a rough editing process. Ambiguous nucleotides
and background noises in obtained sequences were removed to enhance the
accuracy of the analysis. Afterwards, sequences from 30 samples were searched
and compared to reference sequences in GenBank using web-based BLAST server.
Results in identity reference were used to evaluate the species identification
ability and to find the relationship of species within the genus Alpinia.
Sequence alignment was performed using both global and local approaches to
reduce overall error rate caused by a wide range of sequence variations. A
total of 36 reference sequences of species in the genus Alpinia from GenBank, along with 30 sequences in this study, were
included in the alignment (Suppl. material 1). The alignment matrix had a total
length of 593 bp, covering partial sequence of ITS1, 5.8S, and ITS2 regions.
Phylogenetic analysis
Based on the nucleotide
matrix, phylogenetic trees were constructed using both Neighbor Joining (Fig.
3a) and Maximum Likelihood methods (Fig. 3b) with 1000 replications. Amomum longipetiolatum, a species of
closely related genus of Alpinia was
used as an outgroup sequence. Bootstrap values were estimated in both methods.
Only bootstrap values greater than 50 were displayed in the phylogenetic tree
for better observation and comprehension (Fig. 3). Therefore, only branches
with reliable support were useful for species discrimination process. Table 3 summarized
the species classification of 30 samples from the
|
|
Fig. 3: Phylogenetic trees of Alpinia species constructed using Neighbor Joining (a) and Maximum Likelihood (b) methods
genus Alpinia in Vietnam. In general, there were 14 samples including
PD1, SH83, SH84, 2197, SH669, 2189, SH90, SH93, SH185, SH661, SH156, SH88,
SH125, and 2188 belonged to 10 species had identities between morphological and
phylogenetic specification. Four out of 30 samples were classified as different
species from morphological discrimination including samples 2179, SH89, SH91,
and SH163. PD1 was the only sample that showed incongruence between the two
phylogenetic trees. Remaining 12 samples were either generated separated branches
or considered belonged to distinct taxa that have sequences currently not available.
Besides, there were incongruences in molecular based species identification
between samples in the same species such as A. aff. coriandriodora
and A. “kontumensis”. These conflicts were results of distinct
geographical characteristics of collected locations, differences in collection
time, and lack of reference sequences for Alpinia species in Vietnam on
GenBank.
Discussion
The low amplification and sequencing
success rates of the ITS region were observed in several
previous studies due to divergent paralogous copies within individuals and
fungal contamination in a certain group of plants (Hollingsworth et al. 2011; Vinitha et al. 2014). In this study, the success
rates of more than 80% for PCR amplification and sequencing of interested
samples are similar to the previous study of China Plant BOL Group et al. (2011).
The alignment matrix of 66
ITS sequences consisted of a multitude of differences in nucleotide sequences
among both samples used in this study and reference sequences. The conserved
regions observed in the matrix were from the 5.8S, while most of the variations
were distributed in ITS1 and ITS2. These regions had a potential in species
classification due to their high resolutions of inter- and intraspecific
relationship (Cheng et al. 2016).
However, in the genus Alpinia,
ambiguous nucleotides in ITS1 and ITS2 of GenBank reference sequences generated
difficulties in alignment and species identification. Therefore, a combination
of sequence alignment and BLAST searches were necessary to enhance the accuracy
of species identification.
The
phylogenetic tree of the ITS region showed the relationship between Vietnamese Alpinia species used in this study and Alpinia species available in GenBank.
According to the phylogenetic analysis, SH91 (A. conchigera), PD1 (A.
aff. calcarata), and SH532 (A. spp. 11) were sisters to the group of
A. calcarata and A. galanga.
This relationship between A. conchigera,
A. calcarata and A. galanga was
supported by fruit wall anatomy study of Liao & Wu (Liao and Wu 1996) and
molecular based classification of Kress et
al. (Kress et al. 2005). This
species group belongs to the subsection Alpinia,
Catimbium (section Alpinia), and Strobidia (section Allughas)
according to Smith (Smith 1990) and Clade II (Galanga clade) in Kress’s classification system (Kress et al. 2005). The only sample belongs to
Clade V (Eubractea clade) in this
study was SH125 (A. purpurata,
section Guillainia) along with A. elegans (section Kolowratia) and A. vittata (section Dieramalpinia). Other
species used in the present study belong to Clade IV (Zerumbet clade). Among these samples, SH101 (A. “kontumensis”), SH649 (A. latilabris, subsection Catimbium, section Alpinia), SH650 (A.
blepharocalyx, subsection Catimbium,
section Alpinia), SH651 (A. spp. 6), SH652 (A. spp. 7), SH479 (A. spp. 9), SH486 (A. spp.
10), and SH 538 (A. spp. 12)
generated a separated branch, indicating that these samples were distinct from
all the Alpinia species sequences in
GenBank. These species also formed a distinct group in Kress’s study (Kress et al. 2005). SH176 (A. “kontumensis”) and SH653 (A. spp. 8), which were not identified by morphological characteristics
and were closely related to A. nutans
from section Dieramalpinia (bootstrap
value equal 82). The sample SH163 (A.
menghaiensis, subsection Catimbium,
section Alpinia) and SH479 were
closely related to A. kwangsiensis (subsection Catimbium, section Alpinia). The sample 2179 (A.
aff. coriandriodora, subsection Alpinia, section Alpinia) and SH89 (A.
calcicola, subsection Catimbium,
section Alpinia) were placed in the
same branch with A. tonkinensis
(subsection Alpinia, section Alpinia) with strong support (bootstrap
values equal 95 and 94 in NJ and ML trees, respectively). Another sample SH86 (A.
“tamdaoensis”), was closely related to A.
chinensis (subsection Alpinia,
section Alpinia), A. japonica (subsection Alpinia,
section Alpinia), and A. pumila (section Didymanthus).
Species identification
results of 14 samples were similar to those concluded by morphological
classification. However, in several complex groups of Alpinia genus, there were conflicts between species classification
based on morphology and molecular marker. SH91 (A. conchigera) was not in the same grouped with A. conchigera species (AF478712.1).
References sequence for other ambiguous sample, SH163 (A. menghaiensis) was currently unavailable. Therefore, except for
the sample 2179 which showed clear difference between morphological and
molecular based identification, other conflict samples had insufficient amount
of reference ITS sequences, which might lead to unreliable discriminating
results. Previous studies have indicated the effectiveness of ITS region in resolving
phylogenetic relationships at different taxonomic levels (Vinitha et al. 2014; Boer et al.
2018). The conflicts may occur
due to the lack of reference sequences, and high variation of ITS sequence.
The main results in this
present study were supported by the phylogenetic research and molecular based
classification of Kress et al. (2005).
According to Kress’s classification system, Alpinia
species in Vietnam belong mainly to Clade IV. The BLAST searches and phylogenetic
analysis showed the high species identification ability of the region ITS as
molecular marker.
Conclusion
This study clearly indicated
that DNA barcoding using ITS region is a reliable method for supporting species
classification in the genus Alpinia.
ITS can be applied to rapid identification of these medicinal and ornamental plants, along with their
products.
Acknowledgements
This work was supported by Vietnam
Academy of Science
Author Contributions
Le Thi Thu Hien and Nguyen Quoc Binh initiated this
study. Nguyen Quoc Binh and Nguyen Phuong Hanh collected and identified plant
materials. Nguyen Nhat Linh, Le Thi Thu Ha, Pham Le Bich Hang, and Luu Han Ly
performed the experiments. Nguyen Nhat Linh, Le Quang Trung, Nguyen Hai Ha, and
Le Thi Thu Hien performed data analysis and drafted the manuscript. All authors
have read, commented and approved the final manuscript.
Conflicts of
Interest
The authors declare no conflicts of interest.
Data
Availability
DNA barcoding sequences used in this study were available on GenBank
(https://www.ncbi.nlm.nih.gov/nucleotide) and their accession numbers were
provided in Suppl. material 1.
Ethics
Approval
Ethical approval is not applicable in this study.
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