Jimenez Etal - 2013 - COI and ITS Asplanchna
Jimenez Etal - 2013 - COI and ITS Asplanchna
Jimenez Etal - 2013 - COI and ITS Asplanchna
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Journal of Environmental Biology ISSN: 0254- 8704
CODEN: JEBIDP
Abstract
We evaluated different strains of the rotifer Asplanchna brightwellii collected from central Mexico
using morphology, morphometry and molecular tools (CO1 and ITS). Three distinct clonal populations
from each of the 3 regions (Mexico City, State of Mexico and State of Guerrero) were established under
Publication Info
laboratory conditions. For a given waterbody, morphometric comparisons within the populations of
A. brightwellii showed almost stable measurements of trophi and with no statistically significant
Paper received:
differences among them (p>0.05). However, asplanchnid body length and width as well as the cyst
30 August 2012 diametervaried significantly depending on the waterbody from which A. brightwellii was collected.
The smallest adults (about 700 µm) were from Valerio Trujano lake (Guerrero State) samples while the
Revised received: largest were from Xochimilco lake. Similar tendencies were reflected in the diameter of resting eggs.
09 January 2013 In addition, morphologically the cysts of A. brightwellii from the three waterbodies showed slightly
different pattern. The number of globular structures on the surface of cysts was smaller for Valerio
Accepted: Trujano strain, while these were larger and less numerous for both Xochimilco and Zumpango strains.
01 February 2013 The ITS region tree displayed two groups Xochimilco and Valerio Trujano Zumpango, this analysis did
not reflect the morphological grouping; on the contrary the CO1 gene tree separated the populations
according to morphological clusters and location (Xochimilco, Valerio Trujano and Zumpango lakes).
When the tree was built using the combination of both ITS and CO1 sequences, the phylogenetic
relationships observed on CO1 gene were consistent; but showed differences with the relationships
observed on ITS region tree (only two groups).
Key words
CO1, Fingerprinting, ITS, Resting eggs, Rotifers, Trophi
© Triveni Enterprises, Lucknow (India ) Journal of Environmental Biology, Vol. 34, 1039-1046, November 2013
foot and Asplanchna planktonic without foot (Walsh et al., from molecular data and that derived from morphological
2005). Within the genus Asplanchna there are nine species analysis. The molecular analysis includes scrutiny of large
which are distributed from temperate to tropical regions and small subunits of ribosomal RNA genes (rRNA),
(Segers, 2007). The general body shape of Asplanchna is mitochondrial DNA, mainly the cytochrome oxidase c
not very useful for identification. Therefore trophi is largely subunit 1 gene (CO1) and sequence analysis of the internal
used for distinguishing different species. However, currently transcribed spacer (ITS) regions of the rRNA genes (Cooke
there are still many problems related to taxonomy of trophi and Duncan, 1997).
in the genus Asplanchna, because the differences among
the closely related species (e.g., A. brightwellii and A. The CO1 gene has been chosen as DNA barcoding
sieboldii) are difficult to describe (Altindag et al., 2009; of eukaryotes. It codifies for a mitochondrial protein, which
Chang et al., 2010). In addition, within a given species of is important in the electron transport chain, and therefore
Asplanchna the morphological variations in trophi of field- has a central role in the metabolism of eukaryotic aerobic
collected specimens are large and can lead to mistakes in organisms. In addition, mitochondrial genes have high
identifying the species.For example, the trophi size of A. evolutionary rates than nuclear genes (Strüder-Kypke and
sieboldii can vary from 130-170 µm and the tooth on the Lynn,2010). However,CO1 gene has limited use for
inner margin of rami also varies considerably (José de Paggi, identifying certain taxonomic groups, such as fungi, with
low amounts of variation in the genes and also by the
2002). In addition, A. sieboldii develops different morphs
variable structure of the mitochondrial genomes. Therefore,
depending on the availability of food in the environment
ITS has been established as a barcode for fungi and thought
(Chang et al., 2010). If the available prey items are large
be a more suitable DNA barcoding for plants (Chen et al.,
(such as cladocerans or copepods) then the large
2010).
campanulate forms appear in the population;when the food
availability is in short, to avoid cannibalism, some individuals The aim of this work was to understand whether
in the population develop lateral humps (Wallace et al., intra- and inter-populational variability of A. brightwellii
2006). Morphometric analysis of clonal cultures of a given from geographically isolated waterbodies in three States of
species of Asplanchna is helpful to quantify the range of Central Mexico indicate the possible existence of cryptic
variation in the morphology of trophi. This approach too diversity. For this, data of trophi measurements, structure
has limitations because establishing clonal cultures of of resting eggs and CO1 gene analysis were used. We also
widely separated geographic strains is both expensive and analyzed the ITS sequence as a complementary to barcode
regulatory national laws often prevent introduction of foreign and thus we compared the results of ITS with the CO1 gene
taxa. The establishment of cultures of clones of species classification.
obtained from within a nation is thus helpful for
morphometric analysis of different stages in the life history. Materials and Methods
However, this alone is not sufficient for species that show
Live zooplankton samples from different zones
cryptic diversity. Therefore, it is necessary to employ other
(pelagic and littoral or near shore) of the three freshwater
biological tools such as molecular analysis (Schröder and
bodies viz., Xochimilco Nativitas, (Mexico City), Zumpango
Walsh, 2010).
(State of Mexico), Valerio Trujano (Guerrero State) were
Temperature is one the important natural variables separately collected using a plankton net of 50 µm mesh
affecting the morphology, distribution and density of rotifers size (Table 1). All the chosen waterbodies are within the
(Wallace and Snell, 2010).Factors other than temperature national territorial limits of Mexico, and differ by a distance
too have considerable influence on the morphological traits of about 500 km. Live samples were brought to the laboratory
of rotifers. In addition to the well-known phenomenon of and observed using a Nikon stereomicroscope SMZ645.
cyclomorphosis that occurs in various rotifer genera Selected physico-chemical variables of water were also
including Asplanchna, factors such as topographical, measured from the site at the time of sampling. From the live
hydrological and altitude offer opportunities for the zooplankton samples, we isolated between 10 and 20
development of isolated populations (Wallace et al., 2006). individuals of Asplanchna spp., and transferred them
This aspect has not been well studied for many rotifer genera individually into100 ml glass beakers containing 50 ml of
except for Brachionus (Ortells et al., 2006). Genetic traits of moderately hardwater, the EPA medium. The EPA medium
isolated populations are also dependent on physical barriers was daily prepared by dissolving 1.14 mM NaHCO3, 0.44
(Hoffmann and Rieseberg, 2008). mM CaSO4, 0.50 mM MgSO4 and 54 mM KCl in 1 l of distilled
water (Weber, 1993). In order to feed Asplanchna, we
Recently molecular analysis has been considered as separately cultured three brachionid rotifers, viz. Brachionus
a valuable tool for phylogenetic studies where it has been havanaensis, B. rubens and Plationus patulus using the
demonstrated the congruence between taxonomy derived single celled green alga Chlorella vulgaris as the diet. C.
polymerase (Invitrogen) using specific primers for a large spine on the inner margin of the ramus.Information
mitochondrial CO1 gene HCO2198: 5´TAA ACT TCA GGG on the morphometry of A. brightwellii obtained from
TGA CCA AAA AAT CA 3´ : 5´TGA TTT TTT GGT CAC different waterbodies showed significant differences in the
CCT GAA GTT TA 3´and for nuclear ITS region (ITS4: body size and the trophi size (Table 2).For a given waterbody,
TCCTCCGCTATTGATATGC, ITS5: GGAAGTAAAAG comparisons within the three populations of A. brightwellii
TCGTAACAAGG). For the PCR amplification we used the showed almost stable measurements of trophi and with no
following program: 1 cycle for 2 min at 94 °C, 30 cycles for 30 statistically significant differences among them (p>0.05, one
sec at 94 °C, 30 sec at 57° C annealing temperature of ITS way ANOVA, Table 3). However, asplanchnid body length
region, 1 min at 72°C; and 1 cycle for 5 min at 72°C; for CO1 and width varied significantly depending on the waterbody
amplification were 40 cycles with a annealing temperature from which A. brightwellii was collected. In addition,
of 45º C. The PCR products were verified by electrophoresis populations of A. brightwellii from Valerio Trujano and
in 1% agarose gel electrophoresis, purified by gel band Xochimilco, but not those of Zumpango, showed differences
purification kit (GE Healthcare) and cloning in pDrive in the cyst diameter (Fig. 2). Compared to inter-populational
(Qiagen) or pCR 2.1 TOPO (Invitrogen) vectors following differences, those of intra-strain are far greater. The smallest
the manufacturer’s instructions. The vectors were adults (about 700 µm) were from Valerio Trujano lake
sequenced in the DNA Sequencing Laboratory of our (Guerrero State) samples while the largest were from
university (UBIPRO, FES Iztacala), using the automated Xochimilco lake.The body size of A. brightwellii from
sequencer 3100 Genetic Analyzer (Aplied Biosystems). The Zumpango showed intermediate values. Similar tendencies
vectors were sequenced in both directions with the universal were reflected in trophi size and the diameter of resting
primers T7, SP6, M13 Reverse or M13 Forward. A total of eggs (Table 4).
650 and 789 bp was used for phylogenetic analysis with
CO1 gene and ITS region. Morphologically the cysts of A. brightwellii from
the three different waterbodies showed slightly different
The phylogenetic estimations among Asplanchna pattern (Fig. 2). The number of globular structures on the
brightwellii were done using PAUP 4.0b10 for 32.bit surface of cysts was smaller for Valeriano Trujillo strain,
Microsoft Windows (Sinauer Associates, Sunderland, USA), while these were larger and less numerous for both
and a heuristic search was carried out with 100 random Xochimilco and Zumpango lakes.
stepwise addition replicates. There was a maximum of 1000
trees for each replicate. Successive approximations were CO1 and ITS phylogenetic analysis : To determine if the
performed on data sets weighted a posteriori based on the CO1 and ITS sequence reflect the morphological and
rescaled consistency index derived from trees obtained from morphometric differences observed in the three clones of
A. brightwellii;we amplified these markers and obtained a
unweighted parsimony analyses. A total of 1000 replicates
650 bp of the CO1 gene and a 789 bp of ITS region. A total
bootstrap was done, and a consensus tree was obtained
of 13 sequences was aligned by CLUSTAL W program and
using the majority rule. The branches with less than 50%
obtained an ITS and CO1 gene tree by a heuristic search
bootstrap support were collapsed in the consensus tree.
based on maximum parsimony with a bootstrap of 1000
The multiple alignments were done using the ClustalX
iterations, resulting in the final consensus tree (and the
Program with default settings (Thompson et al., 1997).
branches were collapsed using majority-rule). The ITS
Results and Discussion region tree displayed two groups Xochimilco and Valerio
Trujano-Zumpango (Fig. 3a); this analysis did not reflect
Morphology and Morphometry : Selected data on the the morphological grouping; on the contrary, the CO1 gene
physico-chemical variables showed that altitude and tree separated the organisms according to morphological
temperature varied, while the other two parameters were clusters and location (Xochimilco, Valerio Trujano (Guerrero)
nearly similar (Table 1). The trophi of A. brightwellii is and Zumpango lakes) (Fig. 3b). In the CO1 gene sequence
different from other congeneric species and can be easily one hundred ten sites were variable and fifty five were
distinguished, for example from A. sieboldii that possesses parsimony informative sites, whereas for the ITS sequence,
Table 1 : Sample collection sites, mean temperature, pH, K and the number of individuals used for morphometry
Table 2 : Results of one way-ANOVA performed on the body Table 3 : Results of one way-ANOVA performed on the body
size, width, lengths of rami, bulla, spine on the inner margin of size, width, lengths of rami, bulla, spine on the inner margin of
rami and cyst diameter of A. brightwellii obtained from three rami and cyst diameter of three cultured populations of A.
freshwater bodies (Xochimilco lake, Zumpango lake and Valerio brightwellii obtained from Xochimilco lake, Zumpango lake or
Trujano lake) Valerio Trujano lake
Fig. 2 : Morphology of cysts of cultured A. brightwellii. X = Xochimilco (Mexico City), VT: Valerio Trujano ( State of Guerrero); Z:
Zumpango (State of Mexico)
(Cyclopoidea) feed on Asplanchna (Brandl, 2005). Although et al., 2010). Therefore, ITS is thought to be alternative
we encountered cyclopoids in our plankton collections, approach for evaluating such species. The variability in
these were not quantified. genes of any species of Asplanchna is not well established.
However, it is largely believed that Asplanchna with shortest
Information about food resources of A. brightwellii generation time among all rotifer species (Dumont and Sarma,
from the chosen waterbodies is also scanty. We found 1995) is considered to one factor that could contribute to
Brachionus havanaensis, Keratella cochlearis and high amount of variation in genes. In addition, members of
Polyarthra vulgaris in relatively higher abundances (50 Asplanchna reproduce rapidly and build up populations
ind. l-1) in the zooplankton samples. Both Brachionus and that quickly crash with the production of cysts (Wallace
Keratella are preferred prey items for Asplanchna while and Snell,2010). The genetic recombination due to sexual
Polyarthra generally escapes predation (Chang et al., 2010). reproduction together with variable food and feeding habits
contribute to variations in the morphology of trophi and
The differences in the morphological traits are also
cysts.
reflected in the molecular analysis adapted in this work.
Both ITS and CO1 indicated results depending on the power From the maximum parsimony trees, it is evident that
of resolution of the techniques. It is generally assumed that populations of A. brightwellii from Valerio Trujano and
CO1 is a less powerful tool to evidence the genetic Zumpango were closely related than the either to
divergence among populations of the same species (Chen Xochimilco. The phylogenetic significance of this remains
Table 4 : Morphometric data on the body size, trophi size and cyst diameter of A. brightwellii cultured under laboratory conditions. For
each site, the measurements (µm) were based on three clones
A. brightwellii Xochimilco
A. brightwellii Xochimilco 100
100
A. brightwellii Xochimilco
A. brightwellii Xochimilco
Asplanchna sieboldii
Asplanchna sieboldii
Fig. 3 : Maximum parsimony trees of ITS region (A) and CO1 gene (B) resulting from analysis of the ITS region and CO1 gene sequences of
A. brightwellii species. The source of clone is indicated after the species name. Asplanchna sieboldii and Asplanchna sp. were used as outgroup.
Bootstrap values for 1000 replicates are shown above branches.
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