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Fazekas Et Al 2012 - DNA Barcoding Methods For Land Plants
Fazekas Et Al 2012 - DNA Barcoding Methods For Land Plants
Abstract
DNA barcoding in the land plants presents a number of challenges compared to DNA barcoding in many
animal clades. The CO1 animal DNA barcode is not effective for plants. Plant species hybridize frequently,
and there are many cases of recent speciation via mechanisms, such as polyploidy and breeding system
transitions. Additionally, there are many life-history trait combinations, which combine to reduce the like-
lihood of a small number of markers effectively tracking plant species boundaries. Recent results, however,
from the two chosen core plant DNA barcode regions rbcL and matK plus two supplementary regions
trnH–psbA and internal transcribed spacer (ITS) (or ITS2) have demonstrated reasonable levels of species
discrimination in both floristic and taxonomically focused studies. We describe sampling techniques, extrac-
tion protocols, and PCR methods for each of these two core and two supplementary plant DNA barcode
regions, with extensive notes supporting their implementation for both low- and high-throughput facilities.
Key words: DNA barcoding, Plant field collecting, Plant DNA extraction, PCR amplification, Cycle
sequencing, rbcL, matK, trnH–psbA, Internal transcribed spacer
1. Introduction
W. John Kress and David L. Erickson (eds.), DNA Barcodes: Methods and Protocols, Methods in Molecular Biology, vol. 858,
DOI 10.1007/978-1-61779-591-6_11, © Springer Science+Business Media, LLC 2012
223
224 A.J. Fazekas et al.
useful DNA barcode (5). This has led to the search for an equivalent
DNA barcode for land plants. The primary focus of this search has
been the plastid genome, with many authors recognizing that mul-
tiple regions are required (5–12). Selecting a standard plant DNA
barcode has been difficult, as all of the various candidate loci have
different strengths and weaknesses, with no clear-cut front runners.
In a community-authored paper, the combination of portions
of the plastid regions rbcL and matK was suggested as the core
DNA barcode for land plants (13) and subsequently provisionally
adopted by the Consortium for the Barcode of Life. In addition to
this core DNA barcode, other loci are often required to increase
the levels of species resolution. At the 2009 International Barcode
of Life Conference in Mexico City, it was recommended that the
community continue to gather data from additional DNA barcod-
ing loci to establish whether other loci should be formally incorpo-
rated into the plant DNA barcode. The two most widely used
supplementary loci are the plastid intergenic spacer trnH–psbA (one
of the leading contenders for the core plant DNA barcode) and the
nuclear ribosomal internal transcribed spacers (ITS). The nuclear
ribosomal ITS regions had previously been discounted as a stan-
dard DNA barcode due to concerns over paralogy and the presence
of putative pseudogenes which lead to sequencing difficulties in
many plant groups (e.g., refs. 14–18). However, the increased
resolution of ITS over plastid DNA barcodes in many studies
(e.g., ref. 19) suggests that it should continue to be explored as
part of the plant DNA barcode, and some authors have noted that
just using a subset of the ribosomal cassette (ITS2) can lead to
greater amplification and sequencing success compared to the entire
ITS region (20). We, therefore, include methods for all four of
these regions [rbcL, matK, trnH–psbA, and ITS (including ITS2)]
to provide the maximum utility to users of plant DNA barcoding.
Details of other loci that have been used in plant DNA barcoding
studies can be found elsewhere (e.g., refs. 5, 11, 13, 21).
It should be noted that levels of species discrimination in plants
with standard DNA barcoding loci are in general lower than those
obtained by CO1 in many animal groups (22). This is in part due
to the lower rate of nucleotide substitution in the plastid genome,
but also due to other reasons, including hybridization, polyploidy,
speciation via breeding system transitions, species defined on very
narrow taxon concepts, large ancestral population sizes, and low
levels of intraspecific gene flow for plastid markers (23, 24). These
issues are not evenly distributed among all plant groups; therefore,
it is expected that resolution at the species level will be reasonably
good in some groups and quite poor in others. In floristic contexts
where geographical limitation usually restricts the number of
closely related species, rates of species discrimination are expected
to be greater (e.g., refs. 25, 26).
Methods are invariably open to improvement from a variety of
sources, and there are often many ways to achieve the same result.
11 DNA Barcoding Methods for Land Plants 225
For example, the reader may have a different way of drying plant
samples or prefer to do PCR in larger reaction volumes. Where
multiple methods are commonly in use, we attempt to provide
details for each. The notes provided in the last section illuminate
some of the principles that the methods we have provided aim to
achieve. Some of the methods provided have been optimized to
be cost-efficient, and are those currently in use at the Canadian
Centre for DNA Barcoding (http://www.ccdb.ca/pa/ge/
research/protocols).
2. Materials
2.1. Field Collecting 1. Field press with blotting paper and spacers for voucher
preparation.
2. Jewelry tags for labeling.
3. Silica gel (with 10–30% indicating silica beads).
4. Waterproof markers or pens.
5. Container(s) for silica drying of tissue, e.g., 20-ml scintillation
vials, sealable plastic whirl-packs, zip-lock bags, or coin enve-
lopes/tea bags that can be placed in a sealable container.
2.3. Tissue 1. Grinding beads: for example, stainless steel 440C 3.17 mm
Subsampling for DNA beads.
Extraction 2. Small forceps.
3. Latex or nitrile disposable gloves.
4. Ethanol: 100%.
5. ELIMINase®, DNA AWAY®, or a similar product.
6. Alcohol burner.
7. For single tube-based extractions: 2-ml screw-cap tubes with
O-ring seals that are strong enough to withstand the homog-
enization process without breaking.
8. For plate-based extractions: Racked sterile mini tube strips
with cap strips (e.g., PROgene® Mini Tube System 1.1 ml 8
Strip Pre-sterilized Mini Tube and sterile cap strips).
2.4. DNA Extraction: 1. Equipment for tissue grinding: for example, FastPrep® or
Single Sample-Based TissueLyser with tube adaptor.
Extraction: 2. Microcentrifuge with a rotor for 2-ml tubes.
Commercial Kits
3. Vortex.
226 A.J. Fazekas et al.
4. Ethanol: 100%.
5. Heating block/incubator capable of heating to 70°C.
6. Pipettes and pipette tips.
7. 1.5- or 2-ml microcentrifuge tubes.
8. Individual tube-based DNA extraction kit.
9. Latex or nitrile disposable gloves.
10. ELIMINase®, DNA AWAY®, or a similar product.
2.6. DNA Extraction: 1. Equipment for tissue grinding (e.g., TissueLyser with plate
Plate-Based Extraction adaptor).
(96 Samples): 2. Centrifuge with a deep-well swinging bucket rotor capable of
Commercial Kits achieving 5,600–6,000 × g force.
3. Ethanol: 100%.
4. Incubator capable of heating to 70°C.
5. Pipettes and pipette tips.
6. Latex or nitrile disposable gloves.
7. ELIMINase®, DNA AWAY®, or a similar product.
11 DNA Barcoding Methods for Land Plants 227
8. 96-well microplate.
9. Reagent reservoirs (100 ml).
10. Plate-based DNA extraction kit.
Table 1
General PCR mix for rbc L, ITS, ITS2, and trn H–psb A
A.J. Fazekas et al.
3. Methods
3.1. Field Collecting 1. Prior to going to the field, dispense the silica gel into scintilla-
tion vials (~2/3–3/4 full), plastic bags (~15 ml of silica), or a
1-L container (~15% full) for coin envelopes or tea bags.
2. Harvest the plant: whole plant if small, or a branch with leaves
from woody shrubs or trees.
3. Place the voucher in the field press such that identifying
features (flowers, fruits, both sides of leaves) can be easily
inspected when dried.
4. Identify the voucher with a unique collecting number, either
with a jewelry tag attached to the voucher or by writing on the
paper the sample is pressed in.
11 DNA Barcoding Methods for Land Plants 231
5. Take a small amount of leaf tissue (3–10 cm2; see Notes 1–6),
and place in either: the scintillation vial containing silica gel,
the plastic bag containing silica gel, or a coin envelope/tea
bag, which is placed in the 1-L container with silica gel.
6. Label the container or coin envelope with the same collection
number as the voucher.
3.2. Sample Storage 1. Store the tissue samples in a dry location or retain in silica until
ready to subsample for DNA extraction (see Note 7).
3.3. Tissue 1. Clean the bench working area with ELIMINase®, DNA
Subsampling: For DNA AWAY®, or a similar product.
Extraction Using 2. With clean gloves and forceps, add one clean grinding bead to
Single Tubes each tube and recap tubes.
3. Sterilize the forceps by dipping them in alcohol and flaming
them.
4. Open a container with the sample, break off a piece of leaf or
find a piece of the right size (see Notes 8–13), and insert it into
a tube.
5. Label the tube with the collection number.
6. Clean the forceps by dipping them in alcohol and flaming, and
then repeat step 4 for the remaining samples.
7. Change gloves often (or any time, you feel that they may have
become contaminated).
3.5. Tissue Disruption 1. Homogenize the plant material with the grinding bead using a
FastPrep®, TissueLyser, or a similar instrument: for the
TissueLyser, apply 28 Hz for 30 s, then rotate the adaptors,
and repeat once (or a maximum of two more times if necessary
to obtain good disruption) (see Note 14).
2. Briefly centrifuge the tubes or the plate of strip tubes after
homogenization to limit the amount of material stuck to the
cap (see Note 15).
3.7. DNA Extraction: 1. Carefully remove the screw caps from each tube and discard
For Non-kit, Single the caps. Powderized plant tissue will be adhered to the cap
Sample-Based and will easily dislodge if the caps are not handled carefully
Methods (Adapted (see Note 15).
from Ref. 26) 2. Dispense 200 μl of CTAB lysis buffer to each tube and recap
the tubes with new caps.
3. Gently invert each tube in order to mix the powderized plant
material with the lysis buffer, and briefly centrifuge the tubes
for 1,000 × g force for 1 min to collect the sample to the
bottom.
4. Incubate the samples for 1 h at 65°C with occasional mixing
by inversion.
11 DNA Barcoding Methods for Land Plants 233
3.8. DNA Extraction: 1. Remove one set of strip tubes to a separate holder for cap
For Non-kit, Plate- removal and addition of CTAB lysis buffer.
Based Methods 2. Carefully remove the strip of caps using each individual cap tab
(Adapted from Ref. 26) to pull the cap off the tube, and discard the strip caps.
Powderized plant tissue will be adhered to the cap and will eas-
ily dislodge if the caps are not handled carefully (see Note 15).
3. Dispense 200–350 μl of CTAB lysis buffer to each tube
(depending on the amount of sample) and recap the tubes with
a new strip cap.
234 A.J. Fazekas et al.
26. Remove the glass fiber plate and retain it at −20°C as a backup
until the extraction is determined to be successful, after which
it can be discarded.
27. Cover the DNA plate with aluminum sealing film and store at
4°C for short-term storage or at −20°C (preferably at −80°C)
for long-term storage.
3.9. PCR: PCR Mixture 1. Prepare and label a 1.5-ml microcentrifuge tube for the PCR
cocktail of 100 reactions (Table 1). This number of reactions is
recommended when using a 96-well plate to accommodate
pipetting error.
2. Defrost all components of the cocktail at room temperature,
except the polymerase which has to be kept at −20°C at all
times prior to use.
3. Prepare the PCR cocktail adding the components in order
listed in Tables 1–3 (see Notes 18–21). See also Table 4 for the
standard primers for amplification of rbcL, matK, ITS, ITS2,
and trnH–psbA.
4. Vortex the mix and centrifuge at 1,000 × g force briefly.
5. Dispense 10.5 μl of the PCR cocktail in each well using the
same tip [replace tip occasionally (every 16 wells) to reduce
pipetting error].
6. Add 2 μl of the sample DNA (30–50 ng/μl) to each well.
Leave one or two wells blank as a negative control. Use a fresh
tip for each DNA sample.
7. Seal the plate tightly with aluminum foil (using a roller to seal)
or thermo-seal cover (apply heat to seal) (see Note 22).
8. Centrifuge the plate at 1,000 × g force for 1 min (see Note 23).
9. Place the plate into the thermo-cycling block, close it, and
apply the appropriate PCR program.
3.10. PCR Thermal 1. rbcL, trnH–psbA (see Notes 24 and 25): 94°C for 4 min;
Cycling Programs 35 cycles of 94°C for 30 s, 55°C for 30 s, 72°C for 1 min; final
extension 72°C for 10 min.
2. trnH–psbA for ferns and allies, and bryophytes (see Note 25):
94°C for 4 min; 2 cycles of 94°C for 45 s, 50°C for 45 s, 72°C
for 1 min; 35 cycles of 94°C for 45 s, 45°C for 45 s, 72°C for
1 min; final extension 72°C for 10 min.
3. trnH–psbA using Phusion polymerase (see Note 26, Table 3):
98°C for 45 s; 35 cycles of 98°C for 10 s, 64°C for 30 s, 72°C
for 40 s; final extension 72°C for 10 min.
4. matK first round (matK-KIM1R/matK-KIM3F) (see Note
27): 94°C for 1 min; 35 cycles of 94°C for 30 s, 52°C for 20 s,
72°C for 50 s; final extension 72°C for 5 min.
236
Table 2
PCR mix for mat K
A.J. Fazekas et al.
1.5 mM MgCl2)b
Fourth dNTPs 10 mM 0.056 mM 0.056 5.6
Fifth Forward primer 10 μM 0.1 μM 0.1 10
Sixth Reverse primer 10 μM 0.1 μM 0.1 10
Seventh Polymerase 2 U/μl 0.025 U/μl 0.125 12.5
Total volume of PCR mix 9 900
Last DNA (30–50 ng/μl) 1
Total volume of reaction 10
a
Recommended amount to mix for a 96-well plate
b
Note that in limited trials HF buffer does not appear to be compatible with trehalose
DNA Barcoding Methods for Land Plants
237
238
Table 4
Primers commonly used for DNA barcoding in plants
3.11. PCR Product 1. Open the package with precast agarose gel (see Note 30),
Determination: remove the plastic comb, and place the gel on the mother
Electrophoresis E-base.
with Precast E-gels 2. Set the mother E-base at “EG” program and a runtime of
4 min.
3. Load 14 μl of molecular-grade water into each well of the
96-well precast agarose gel.
4. Load 3–4 μl of each PCR product into the corresponding
E-gel well.
5. Slide E-gel into electrode connections of mother E-base and
start electrophoresis. A green light indicates the beginning of
run. A red light and beeping indicate the end of run. Stop the
current by pressing pwr/prg button.
6. Remove E-gel from base and capture a digital image with the
imaging documentation system.
3.12. PCR Product There is a large selection of gel combs and trays on the market
Determination: designed to accommodate different numbers of samples. Please
Electrophoresis with refer to the manufacturer’s notes for the recommended volume of
Routine Agarose Gels agarose to be used.
1. Select the appropriate gel tray and combs for the number of
samples to be run (leaving an appropriate number of wells free
for size standards). Seal the ends of the tray with masking tape
or use a gel-forming cassette.
2. Weigh out the agarose and place in a glass conical flask. To
check PCR success, a 1% agarose gel is used; 1% agarose
gel = 1 g of agarose per 100 ml of 1× TBE buffer.
3. Add the appropriate volume of 1× TBE buffer to the agarose
and gently swirl.
4. Heat the solution in a microwave on maximum heat setting for
approx. 30 s, remove flask from the microwave, and gently
swirl to mix. Continue to heat, mixing occasionally. Carefully
240 A.J. Fazekas et al.
6. Add 2 μl of diluted PCR product to each well (use fresh tip for
each PCR product).
7. Place aluminum foil or heat-seal cover over the top of the
96-well plate. Apply heat for heat-seal cover, and use roller to
close the plate tightly (see Note 22).
8. Spin the plate using centrifuge at 1,000 × g force for 1 min (see
Note 23).
9. Place the plate into the thermocycler block and apply the pro-
gram (see Note 32): 96°C for 2 min; 30 cycles of 96°C for
30 s, 55°C for 15 s, 60°C for 4 min; hold at 4°C.
10. After cycle sequencing reaction is complete, keep the plate in a
dark box at 4°C to avoid degradation of BigDye™.
3.14. Cycle 1. Measure dry Sephadex G-50 (Sigma-Aldrich, Cat. No. G5080-
Sequencing Cleanup 500 g) with the MultiScreen Column Loader (Millipore, Cat.
and Processing for an No. MACL09645) into the Acroprep 96 Filter plate with 0.45 μm
ABI 3730xl Capillary GHP membrane (PALL, Cat. No. PN5030). This loader adds
Sequencer the specific amount of Sephadex required (see Note 33).
2. Hydrate each well with 300 μl of molecular-grade water using
a pipette.
3. Let the Sephadex hydrate overnight at 4°C or for 3–4 h at
room temperature before use.
4. Assemble the Sephadex plate onto the collection plate and
secure with two rubber bands.
5. Centrifuge at 750 × g force for 3 min to drain the water from
wells. Discard water from the collection plate (when centrifug-
ing two plates, make sure that both sets have equal weight
which can be achieved by using additional rubber bands). The
collection plate can be reused without autoclaving.
6. Add the entire volume of the sequencing reaction to the centre
of the Sephadex columns using a pipette.
7. Add 25 μl of 0.1 mM EDTA to each well of the Sephadex
plate.
8. Elute clean sequencing reaction by attaching a 96-well plate to
the bottom of Sephadex plate and secure with rubber bands.
9. To balance two plates, attach additional rubber bands as
needed.
10. Centrifuge at 750 × g force for 3 min. Remove Sephadex
plate.
11. Cover the top of the collection plate with a septum.
12. Place 96-well plate into black plate bases and attach white plate
retainer.
11 DNA Barcoding Methods for Land Plants 243
3.15. Sequence Editing Careful and consistent editing of the raw sequence data is a critical
component of generating a high-quality dataset. There are a num-
ber of software programs (e.g., Sequencher, CodonCode Aligner,
etc.) that allow the import of raw trace files and include a variety of
editing features. Since each sequence editing program is different,
we cannot include a software-specific detailed editing procedure.
We present instead the chain of events involved in going from the
output of the sequencer to a useable sequence.
1. Retrieve electropherogram trace files from sequencer.
2. Import trace files into a sequence editing software package.
3. Generate sequence-quality scores for individual trace files.
4. Trim primer sequences from the sequences.
5. Trim sequences from both ends based upon minimum quality
threshold (e.g., mean QV > 20 and no more than 2 bp QV < 20
in any 20-bp window).
6. Assemble forward and reverse sequence traces for each indi-
vidual sample to create a sequence contig.
7. Manually edit individual sequences: pay particular attention to
bases with low-quality scores or ambiguous calls (see Notes
34–37).
8. Acquire sequence-quality statistics for individual forward and
reverse sequences (e.g., length of read, proportion of bases
with QV > 20).
9. Generate consensus sequence.
10. Acquire consensus sequence quality statistics (e.g., length of
consensus, percentage of bidirectional coverage, proportion of
bases with QV > 20 for unidirectional and bidirectional por-
tions of the consensus).
11. Export consensus sequence for downstream analysis.
4. Notes
21. PCR cleanup is both expensive and time consuming, but can
be avoided through use of the low concentrations of primers
and dNTPs in the PCR mix and the subsequent dilution of the
PCR product prior to cycle sequencing reaction. This protocol
provides a high success rate for PCR and sequences for regions
that are amplified by universal, highly conserved primers (plas-
tid rbcL, trnH–psbA, and nuclear ribosomal ITS2). In contrast,
the matK DNA barcoding region needs distinct conditions for
successful PCR amplification. For matK, the concentration of the
primers, dNTPs, and Taq polymerase cannot be significantly
reduced. Based on experiments optimizing the PCR condi-
tions for matK, we recommend a protocol with diluted DNA
(0.3–0.5 ng/μl) and a smaller PCR reaction volume (7.5 μl).
These conditions have yielded a higher rate of PCR success and
increased sequence quality over the general PCR mix.
22. The volumes of the PCR and cycle sequencing reactions rec-
ommended here are very small. Thus, it is very important to
follow the instructions in Subheadings 3.9 and 3.14 carefully.
The foil or thermal-seal cover should be placed evenly and
tightly over the PCR plate without wrinkles or holes to prevent
evaporation during PCR cycling.
23. Centrifuging is required to collect the PCR components at the
bottom of the well and eliminate any air bubbles that might
have been trapped. It also aids in mixing the PCR components
with the DNA sample, or cycle sequencing mix with PCR
product.
24. Although rbcL is present in the vast majority of land plants,
there are some groups, such as holoparasites, that no longer
have a functioning copy of this gene. As a result, the primers
most commonly used typically do not work in these groups.
25. The primers most widely used for PCR amplification of the
plastid trnH–psbA intergenic spacer for DNA barcoding are
those recommended by Kress et al. (7) or Kress and Erickson
(10) (Table 4). They are, respectively, trnH2 (originally from
ref. 28) and psbAF (originally from ref. 29) or trnH(GUG)
and psbA (originally from ref. 30). In bryophytes, this region
is often short (<200 bp) and an alternative primer, psbA501f
(31) located further back in the psbA gene can be used to
obtain additional characters in combination with the primer
trnH2.
26. The trnH–psbA region often contains homopolymer runs that
are known to reduce sequence quality after the run. Fazekas
et al. (32) have shown that the use of alternative polymerases,
such as Phusion (Finnzymes) or Herculase II Fusion (Agilent),
can improve quality for runs of up to 13–14 bases.
248 A.J. Fazekas et al.
27. The matK gene region is more difficult to amplify and sequence
than rbcL for a number of reasons. First, it is approximately
300 bp longer than rbcL, and thus more sensitive to DNA
degradation. Second, the presence of mononucleotide repeats
in some groups dramatically affects the quality of the sequence
reaction, resulting in a contig that is primarily supported by
two unidirectional sequences with only a small amount of over-
lap. Finally, matK requires different primer combinations for
different taxonomic groups. Therefore, it is important to esti-
mate the taxonomic composition of the plate prior to amplifi-
cation. If the plate contains angiosperms from different genera,
families, and even orders, the combination of matK-KIM1R/
matK-KIM3F is the optimal first choice. This primer combina-
tion was recommended as the first choice by the CBOL Plant
Working Group (13), and has been confirmed in thousands of
PCRs from floristic projects in biodiversity hot spots. Those
samples, which failed in the first round, are collected into a
new plate, and subjected to a second round of PCR using the
primers matK390f/matK1326r (failure tracking). Usually, the
combination of these two sets of matK primers yields around
80% successful sequences in floristic projects focusing on angio-
sperms. However, if the project is represented by one specific
group like a genus or family that does not work well with any
of these primer combinations, it is best to search for appropri-
ate primers for this group. A selection of order-specific primers
has been published by Dunning and Savolainen (33). Two
alternate primer pairs for gymnosperms (NY552F/NY1150R
and matKpkF4/matKpkR1) are given in Table 4. Routine
amplification of this region is difficult in non-seed plants and
the development of primers for ferns/fern allies and bryo-
phytes is currently underway.
28. ITS and ITS2 offer higher levels of species discrimination in
some groups. However, one risk with ITS is that of fungal
contamination. Even the cleanest leaf sample will likely have
fungal hyphae associated with it, and in some groups this can
be a serious source of contamination. For the entire ITS region,
the use of the angiosperm-specific primers AB101 and AB102
can reduce this problem for flowering plants.
29. In situations where PCR is unsuccessful or patchy in its success,
some optimization of PCR conditions can improve success. An
often-successful first approach is to dilute the DNA ten times.
DNA is often not limiting in PCR, but the extraction process
occasionally does not remove all PCR inhibitors sufficiently.
A dilution often reduces inhibitors to the point, where PCR
can succeed. Other steps to improve success are as follows: (a)
for faint or absent PCR products: a decrease in primer-annealing
temperatures, an increase in primer concentration, an increase
11 DNA Barcoding Methods for Land Plants 249
Acknowledgments
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