Download 1 Introduction and literature Review Productivity of

Introduction and literature Review
Productivity of plant communities results from interactions of shoots and roots
with the environment (Grubb, 1985; Tilman, 1988). One of the more important and
least understood biotic zones of interaction is the soil immediately surrounding the
roots and influenced by them: the rhizosphere (Fogel and Hunt 1983). The great
majority of organisms in the rhizosphere belong to the microorganisms and these
include representatives of all the major groups like bacteria, actinomycetes, fungi,
protozoa and microalgae. In addition, micro fauna, such as nematodes and mites, are
found at significantly elevated concentrations in the rhizosphere as compared to rootfree soil (Bazin et al., 1990).
Microorganisms and processes in the rhizosphere profoundly influence plant
growth through their effects on uptake, storage, and cycling of nutrients of a plant,
suppression of pathogens, fertility and organic component metamorphosis and
development etc that influence the of soil architecture. Large, stable and active soil
microbial community is an underpinning for sustaining the productivity of soils under
sustainable and organic farming systems these will developed by with different
strategies such as crop rotation and application of organic amendments that
significantly increase organic matter of soil and it improves quality and soil biology
(Bending et al., 2002 and 2004; Buyer et al., 2010). Protecting the functional
biodiversity of rhizosphere and its organisms through proper management practices
are very essential in maintaining an ecosystem health and resiliency (Coleman et al.,
1984). Young soils (containing sandy primary minerals and allophane in the clay
fraction) are composed of many tubular mesopores (from 3 to 30 μm diameter) and
macro pores (from 30 to 300 μm diameter) that allow high hydraulic conductivity at
saturation (Cabidoche et al., 2009).
Phytonematodes are a very successful group of organisms that can destroy
arable crops upto 10% of all (Gommers et al, 1992). A figure that is comparable with
the destructive effects of insects. Despite the tremendous pest status and importance
of nematodes. A majority of them are free living and occur in every conceivable
environment. It has been claimed that if all the matter was destroyed except
nematodes, you would still be able to see the world in outline. Increased attention has
been focused on their study as their importance has been more and more widely
recognized.
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In 1920 ‘Nematology’, as a special subject was conceptually initiated by
Cobb. It is a science that includes the study of organisms among invertebrates called
the “nemas” or thread like worms popularly known as eel worms, round worms,
thread worms etc. Cobb (1920) coined the word ‘nematology’ for this field of study
knowledge of nematodes parasites in animals and humans probably dates back to the
origin of man. As far back as 1533-1550 B.C. the guinea worm and Ascaris
lumbricoides were reported in ancient Egyptian history.
The nematodes which inhabit the soil, especially in the rhizospheres of plants
play a vital role in their growth and production (Masters et al., 1993; Van der Putten
et al. 2001). We are usually unaware of the presence of these little denizens of the
earth because of their microscopic size and their protected position within the soil.
They rarely leave a crop free of their attack, be it in the kitchen garden, field or
orchards (Bonkowski and Roy 2005).
Nematodes are the most abundant primitive multicellular animals on earth.
Numerically, nematodes are dominating organisms on earth and they are between 80
to 90% of all multicellular animals on earth may be nematodes (Jairajpuri and Ahmad,
1992; Bloemers et al., 1997). Nematodes occupied in different environments such as
soil, sea or fresh water, as free-living, parasitic or predacious animals. Their food
includes algae, bacteria, fungi, plants and other free living nematode species, as well
as almost all invertebrates like insects and spiders, vertebrates including fishes,
amphibians, reptiles, aves and mammals. The majority of nematodes are found within
the top 10 cm of the soil, although some species may be living is deeper layers
(Yeates et al., 1984). Because, nematodes are so abundant and relatively easy to
sample they have been much used as bio indicators of soil conditions and nature
(Ferris et al., 2001; Yeates, 2003; Viketoft, 2007). Soil nematodes have widely
differing nutritional need and feeding behaviors and therefore occupy different trophic
levels in soil and its food webs (Yeats et al., 1993). They can be grouped according to
the type of food they consume and the morphology of their mouthparts. The most
common groups are plant-parasitic, fungivorous, bacterivorous, omnivorous and
predatory nematodes (Yeates et al., 1993).
In 1594, William Shakespeare gave us our first record of plant-parasitic
nematodes. The first ever authentic scientific record of a plant-parasitic nematode was
made by Barber (1901) with the identification of root-knot nematodes from tea
plantation, however, nematology can be considered to be only around 40-years-old in
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India. The organized research on Plant-parasitic nematodes by full time researchers
started towards the end of the fifties and early sixties. During the past quarter of a
century, a number of important nematode pests have been discovered. The organized
research on phytonematology was initiated in 1958 with the identification of Molya
disease of wheat and barley in the state of Rajasthan. It is identified as the “Vinegar
eels” which were found in practically all vinegar, was the first information on free
living nematodes, given by Borellius (1656). These studied were succeeded by
observations of “Anguina triciti” infesting cereals, by Linnaeus, Steinbeck and
Scopels. The name “Father of nematology”, was conferred on Bostian and the science
of “Nematology”, as distinct and separate branch from Helminthology, was first
established by Cobb, (1913).
Plant-parasitic nematodes, due to difficulties in isolating and identifying them,
remained a little known group till the past three decades (Poinar, 1983). They were
then recognized as one of the fore most problems confronting agriculture and this
study of nematodes which was designated as phyto or agro-nematology. Also new
advances in technology have occurred and the role of nematodes in disease complexes
and virus transmission has been elucidated.
Members of phytonematodes group have a stylet in their mouth and use it to
penetrate the plant cells wall to absorb their contents. In addition to their direct effect
on plant health, nematodes play different roles in disease complexes i.e (1) vectors
(e.g. Several viruses), (2) wounding agents, (3) host structural and functional
modifiers, (4) host resistance breakers, and (5) rhizosphere environmental modifiers
as they cause increased root exudation, thereby affecting microbial communities and
activity in the rhizosphere (Bardgett et al., 1999; Brussard et al., 2001; Desaeger et al.,
2004). Different species of these nematodes effects plants in various ways.
Nematodes that feed on the epidermis or root cortex such as Paratylenchus,
Helicotylenchus usually have less effect on plant productivity and energetics than
vascular parasites e.g. Heterodera, Meloidogyne species (Bernhard, 1992). Basing on
plant age and the species one come across change in nematode species and its rate of
infection particularly seedlings more prone to damage by nematodes more because
their tissues are highly susceptible to attack by nematode parasites as they are more
favorable for nematode development (Ruehle, 1973). Plant parasitic nematodes are
notorious pest in agricultural crops. These nematodes are taxonomically and tropically
diverse in both terrestrial and aquatic habitats. They play an important role in
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terrestrial ecosystems through microbial grazing, root parasitism and affecting carbon
and other nutrient cycles and their flow in soils (Yeats, 2003). Finally it helps in the
development of healthy and productive soil which provides essential nutrients for
plant growth. At the same time, it supports the diverse and active soil community that
balances the total structure and function of an ecosystem (Insam, 2001; Friedel et al.,
2001; Mader et al., 2002). Soil microorganism’s especially some nematodes free
living nematodes play important role in mineralization and break down of organic
compounds in soil (Traunspurger et al., 1997; Ajah et al 2006). These nematode
communities also reflect the difference between disturbed and undisturbed
environments (Yeast and King 1997, Masse et al., 2002; Liang et al 2003). Natural
fallow improve the physicochemical parameters of soil that favour plant growth, its
productivity (Brussard et al 2001). Cultivation of more crops per year, short duration
of high yielding varieties, maximum use of fertilizer, increased frequency of
irrigation, crop rotation, seasonal changes, soil moisture and temperature affects the
nematode population structure (Rossner 1972; Yeates 1982; Norton and Niblack
1991).
In India plant-parasitic nematode species like Meliodogyne sp., Pratylenchus
sp., Anguine tritici, have been reported to be widely distributed and causing
considerable damage (Prasad et al, 1987). Further survey on a large scale alone can
provide sufficient information for taking up intensive investigations on host-parasite
relationship and other allied aspects which would enable us to work out quantum of
damage and ensuing loss of our national economy studies have also revealed that
nematodes not only feed on plant tissues as ecto and endo parasites but also
collaborates with other pathogens such as fungi, bacteria, insects and viruses forming
disease complexes by which they cause severe damage of unlimited proportions.
These host-parasitic relationships and developments of nematode community are
predictable, under the pressure of the change in vegetation (Mass et al., 1997 and
2004), which affects the all living organisms.
Root-knot nematodes Meloidogyne sp. are plant-parasitic nematodes. Around
2000 plants are susceptible and Meloidogyne sp. cause approximately 5% of crop loss
at global level (Hussey and Janssen, 2002). Root-knot nematodes infection starts
when infective second-stage juveniles (J2) hatch from eggs in the soil. Later, they
penetrate plant roots behind the root cap and migrate intercellularly from cortical
tissue to the vascular cylinder and then become sedentary. Then they inject secretions
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into five to seven undifferentiated procambial cells in the vascular cylinder near the
head of the J2 to become multi-nucleate (Hussey and Grundler, 1998) and to form
very specialized feeding cells called “Giant cells” on which the juveniles (J2) and
later the females spherical feed (Sijmons et al., 1994). Furthermore, plant cell size
increases dramatically and walls are remodeled by formation of ingrowths and the
cytoplasm becomes dense with an increase in cell organelles (Baum et al., 1996). The
root-knot nematodes complete their life cycle. With nourishment from the giant-cells
after thus the females lay eggs into a gelatinous matrix outside the root surfaces.
The infection of the root systems by plant parasitic nematodes of the genus
Meloidogyne sp is easily recognized by a gall. These ‘galls’, descend from the
development of the giant cells and the females inside the roots. Root-knot nematode
damage results in poor growth reduced resistance to other stresses and finally decline
in quality and yield of the crop and (e.g. drought, other diseases). A high level of rootknot nematode damage can lead to total crop loss. Nematode damaged roots do not
utilize water and fertilizers effectively, and finally leading to additional economic
losses. Infection of young plants by phytonematodes may be lethal, while infection of
mature plants causes decreased yield. The most common species is Meloidogyne
incognita (Kofoid and White) Chitwood, which causes considerable economic losses
in many crops (Lamberti, 1997). Meloidogyne sp. can be managed by cultural
practices, employment of resistant cultivars and nematicides, one of the primary
means of control for root-knot nematodes. Multiplication of nematodes can also be
regulated by soil microorganisms such as bacteria, nematophagous, and mycorrhizal
fungi (Sikora, 1992b; Duponnois et al., 1994 and 1997).
Generally the nematode community found in high density at rooted 0-20cm
soil layer. Some families of nematodes prefer still deeper. Soil layers like
Trichodoridae and Longidoridae, because these families are sensitive for dehydration,
light and other environmental factors (Wyss 1970; Rossner 1972; Boag et al 1987;
Weischer and Almeida 1995; Ploeg, 1998). The soil nematode community structure is
generally used as a bioindicator of an ecosystem (Bongers, 1990). These soil
nematodes affects plant growth and vigour (Frecman and Caswell, 1985; Coleman,
2008). The role of the nematodes community in the ecosystems is essential
knowledge for managing plant nematode populations, clarifying the role of nematodes
in dispersing algae, fungi, bacteria, phages and virus, decreasing energy inputs to
farming, disposing of organic wastes and dealing with nematode tolerance to
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nematicides and keys to understanding of the distribution and diversity of nematode in
ecosystems, as well as their population dynamics and their influence in food sources.
Many nematodes are cosmopolitan in distribution while others appear to be restricted
to specific climate zones. Many genera of parasitic nematodes such as Meloidogyne
sp, Paratylenchus sp, Heterodera sp, etc are evidently distributed throughout the
world’s many varied climatic and topographic areas.
Molecular Techniques for the Identification of Nematodes:
Biodiversity can be expressed as species diversity, genetic diversity and
functional ecosystem. Accurate identification of nematode species is an essential first
step in understanding their biology, ecology and taxonomy in the case of plantparasitic nematode management in agroecosystem.
In terrestrial systems, nematode diversity appears to be under reported
(Lawton et al. 1998), for example, only about 200 species of soil nematodes being
described from the British Isles (Boag and Yeates, 1998). The maximum number of
nematode taxa described from a single soil site is 228 from a prairie in Kansas, USA
(Orr and Dickerson 1966; Boag and Yeates 1998). Given that many nematode species
have yet to be formally described morphologically (Platt, 1994), a robust and
transferable system of identification, applicable to all individuals and taxa is very
much needed.
Nematodes are remarkably consistent in their anatomy (Bird et al., 1991), and
their identification is essentially based on morphological characters. Recently direct
examination of genetic material has, been used as it represents the most powerful
method for nematode recognition (Giorgi et al, 2002). Although phytoparasitic
nematodes have evolved specific structures for their survival as parasites, these
adaptations are essentially built around a basic framework of nematode anatomy
(Riddle et al, 1997). The nematode Caenorhabditis elegans, is the best organism as it
is highly understood and characterised multicellular organism in a phylogenetic and
evolutionary context, together with plant-parasitic nematodes (Riddle et al., 1997).
Morphological and morphometric characters have been used to discriminate
between nematode taxa traditionally, both for diagnostic purposes and to clarify the
evolutionary relationships between them (Maggenti, 1991). These diagnostic methods
can be time consuming, requiring a lot of skill and expertise (Subbotin et al., 2000). In
addition, many taxa can be diagnosed only from adult male or female specific
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structure, or from population measures of relative morphological characters. In such
cases, larvae, individuals of the “wrong” sex or individual specimens may not be
identifiable. For many studies, identifications are only made at the generic level and
not to be a named species even today (Mai and Mullin, 1996; Floyd et al., 2002).
There is currently much interest in the use of DNA sequences as markers for
taxonomic identification and biodiversity surveys, an approach also known as DNA
barcoding (Hebert et al., 2003). In recent times the nucleotide sequences of fragments
of rRNA genes have been identified in various species of plant parasitic nematodes
and it has become a new field for both identification and taxonomic approaches in
phytonematology (Giorgi et al., 2002). The Internal Transcribed Spacer Region (ITS),
is located between the repeating array of nuclear 18S and 28S ribosomal DNA genes,
it is a versatile genetic marker. The level of variation in this region makes it suitable
for detecting genetic variation among genera, species and within species (Devran et
al., 2002).
The nucleotide base sequence is the primary source of biological variation. A
wide range of molecular tools are now available for the analysis of this genetic
variation and many of which can be used to be adapted for taxonomic and diagnostic
purposes in nematology (Powers and Fleming, 1998). Molecular methods for diversity
assessment have already aided in the understanding of other groups of organisms that
are difficult or impossible to study by any other means (Floyd et al., 2002). The
techniques that use universal primers to target microbial genes have significant
advantages, e.g., convenience, high-throughput, and considerable savings in time
(Puitika et al., 2007); it is a quicker and more efficient way of studying nematode
diversity than traditional taxonomic methods, which depend on morphological criteria
(Floyd et al., 2002). Also, knowledge of genetic diversity in the case of plant-parasitic
nematodes is very essential to develop effective resistance plant breeding programs of
the host plant (Hahn et al., 1994; Roberts, 2002).
Among eukaryotes, including organisms as diverse as protozoa, plants,
vertebrates, and fungi, ITS data have been used in constructing phylogenetic trees,
determining taxonomic identity estimating genetic population structures and
evaluating population- level evolutionary processes. The structure of the rDNA
cistron contributes to its wide applicability. The rDNA cistron is divided into different
domains that evolve at different rates: Hence, this ITS region is used to address
diagnostic and evolutionary problems at various levels of divergence of species. The
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rDNA is a component of the middle repetitive family of the nuclear DNA genome.
The presence of multiple copies of these genes in the nuclear genome facilitates PCR
amplification from even single juvenile and adult nematodes. The ITS, intergenic
spacer (IGS) and rDNA genes of nuclear genome display a concerted evolution.
Copies of these genes from a single individual tend to be similar to one another, At
the same time, they are distinct from those of other species (Elder and Turner, 1995).
The application of the ITS helped to identification various nematodes has been
used by various nematologists (Ferris et al., 1993, 1994, 1995;Campbell et al., 1995;
Cherry et al., 1997; Chilton et al., 1995; Epe et al., 1996; Fallas et al., 1996; Gasser
and Hoste, 1995; Hoste et al., 1995; Ibrahim et al., 1994, 1997;Joyce et al., 1994;
Kaplan, 1994; Nasmith et al., 1996; Orui, 1996; Reid, 1994; Stevenson et al., 1995;
Szalanski et al., 1997; Thiery and Mugniery, 1996; Vrain et al., 1992; Vrain and
McNamara, 1994; Wendt et al., 1995; Zijlstra et al., 1995, 1997). Earlier researchers
worked on nematodes identification based on ITS sequences, DNA based approaches
have been successful used for the molecular diagnostics of Rotylenchulus sp (Vovlas
et al., 2008; Atighi et al., 2011; Cantalapiedra-Navarrete et al., 2012).
The rDNA gene family is a multi-gene family. In eukaryotes, the 5' to 3'
organization of the gene family are: an external transcribed spacer (ETS), the gene
18S, an internal transcribed spacer (ITS 1), the 5.8S gene, ITS 2, 28S gene and
intergenic spacer (Hillis and Davis, 1986) (Fig. No. 1) ITS, located between the
repeating array of nuclear 18S and 28S ribosomal DNA genes, is a versatile genetic
marker. The 18S small subunit ribosomal gene is employed for barcoding of
nematode and any other organism (Floyd et al., 2002 and 2005).
Fig. 1.1: Diagram of the ribosomal DNA gene family in animals (from Hillis and
Davis 1986). The regions coding for the 18S, 5.8S and 28S subunits of rRNA are
shown by bars; NTS = non-transcribed spacer, ETS = external transcribed spacer, ITS
= internal transcribed spacer regions.
The polymerase chain reaction (PCR) can be used to isolate and amplify a
selected gene from a mixed sample of DNA. It provides a highly sensitive method for
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DNA amplification and identification (Powers and Harris, 1993). It is very useful as it
is rapid means for determining species identity from any nematode stage or even its
eggs (Szalanski et al., 1997; Shurtleff et al., 2000). Amplification product of the ITS
region can be obtained when genomic DNA is amplified with "universal" PCR primer
sets, suggests any species, population, or ecological community of nematodes or other
organisms can be studied using a molecular approach based on the rDNA ITS region
and it is achieved by the universal amplification method that amplify ITS from
individual nematodes (Vrain and McNamara, 1994). Only few sequences available in
the primary nucleotide databases span of the entire rDNA array, In several cases,
phylogenetic relationships within different species of plant-parasitic nematodes was
studied and understood even if only fragments of ribosomal genes were available
(Banna et al., 1997, Subbotin et al., 2001).
Variation in DNA sequence of the ITS regions of the ribosomal DNA cistron
are generally used to identify many nematode taxa (Power et al., 1997). This variation
is detected by amplifying the ITS regions using conserved PCR primers which were
located in the flanking 18S, 5.8S and 28S genes. Nematode species can be easily
distinguished on the basis of the size of the amplified PCR product or by cleaving the
PCR products with sequence specific restriction enzymes. Generating diagnostic
PCR-restriction fragment length polymorphism (PCR-RFLP) profiles (Powers et al.,
1997). The use of PCR to quantify the amounts of plant pathogen DNA is commonly
used in the diagnostics of plant pathogens (Robb and Nazar, 1996). Quantitative PCR
can be achieved by adding a known amount of internal standard template DNA to the
PCR reaction mixture. This template is competitively co-amplified with the target
DNA and the relative amounts of target and internal standard PCR product generated
can be used to determine the concentration of the unknown DNA (Fleming et
al.,1998).
Floyd et al. (2005) designed a set of oligonucleotide primers, which will
specifically amplify nematode 18S genes. The alignment was examined for regions
conserved among all so as to provide sufficient information to resolve individuals into
distinct taxa, nematodes this facility is not present in fungi, and which would generate
a fragment of at least 500 bp in length. Many researchers are making attempts to
integrate morphological and molecular analyses of nematodes. It is an approach which
helps in of characterizing free living, entomopathogenic and plant-parasitic nematodes
(Evans, 1995; Thomas, 1997). In the last two decades, most molecular studies were
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conducted on nematodes for identification of root-knot nematodes and cyst nematodes
(Powers and Harris, 1993; Szalanski et al., 1997; Cherry et al., 1997; CastagnoneSereno et al., 1999; Subbotin et al., 2000; Zijlstra et al., 2000; Grenier et al., 2001;
Elbadri et al., 2002; Devran et al., 2002; Chen et al., 2003; Kerkoud et al., 2007;
Vovlas et al., 2007).
A standardized taxonomic bio marker is useful when populations contain a
large number of juvenile stages, dimorphic sexes, or unfamiliar nematodes. PCRRFLP profiles of ITS from individual nematodes helps to assess nematode diversity in
ecological studies and useful for species comparison and identification.
Phylogenetic in biology is the study of evolutionary relatedness among various
taxa of different organisms. Now a days it is studied through molecular sequencing
data and morphological data matrices. The term phylogenetics is of greek origin from
the terms phyle/phylon meaning “tribe, race”, and genetikos meaning “relative to
birth” (Liddell et al.,1968). Phylogenetic is a branch of life science that deals with the
study of evolutionary realations among various species or populations of organisms.
(Biology online. Retrieved 2013-02-15).
The basic principles of phylogeny are based on similarity of ancestry origin
and leads evolutionary divergence. In classical phylogenetic analysis, emphasis has
been give to the morphological features of the species (Baum et al., 1995). Many
numerical taxonomists did it for many years (Sneath et al., 1973). Such studies are
now extended to molecular level and it is leading to the emergence of molecular
phylogeny (Suarez-Diaz et al., 2008). This method relies on the amount of
information that can be obtained from DNA, RNA, Proteins and immunoglobulin
(Edwards et al. 1964).
Construction of phylogenetic tree:
Phylogenetic trees are constructed using computational bioinformatic
phylogenetic methods. The distance matrix methods such as neighbor-joining method
require multiple sequence alignments to calculate genetic distance (Swofford et al.,
1996). Other methods include maximum parsimony and probabilistic interference
techniques provide information about maximum likelihood. The most popular and
commonly used methods of bio informatics used for construction of phylogenetic
trees are classified into two types: 1. Phenetic methods 2. Cladistic methods
(Folinsbee et al., 2007).
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1. Phenetic methods:
The phenetic methods are distance-based methods that measure the pairwise
differences among sequences under study and calculate a distance matrix. This matrix
is later used to construct the phylogenetic trees (Felsenstein et al.,1993). These
phenetic methods are based on the relative numbers of similarities and differences
among organisms in a branching hierarchy tree called a “Phenogram”. Phenogram is a
branching diagram that links entities by estimating overall similarity. Here, in which
the entities are parallel to each other. In the phenogram, taxa with the shorter
distances are classified more closely than those that are far. Distance methods are
relied more on the relationships among data sets than evolutionary pathway
(Felsenstein et al., 2004). Distance methods reduce sequence information into a single
number and the two sequences with the shortest distance are considered as closely
related taxa. They construct a tree in stepwise manner i.e the two most similar
sequences are grouped together, and then the next most similar sequence is added to it
and so on (Lindberg et al., 2011). Basically phenetic methods include two techniques.
They are Unweighted Pair Group Method with Arithmetic Mean (UPGMA) and
Neighbour Joining (NJ) (Felsenstein et al., 2004).
Unweighted Pair Group Method with Arithmetic Mean (UPGMA)
UPGMA is the simplest method to construct phylogenetic trees. It uses
clustering approach and uncorrected data to build a tree. This method is suitable for
large datasets consisting lineages with relatively constant rates of evolution.
Neighbor Joining (NJ)
This is a method often used to construct phylogenetic trees (Li, 1981; Faith,
1985). Neighbor joining is a special example of star decomposition method. In this
method, the phylogenetic tree is constructed from a star-like tree by grouping OTUs
with shortest distance of branch length together. This method is very suitable with
dataset consisting descendants with largely varying rates of evolution. This method
was discovered by N.Saitou and M.Nei (1987).
2.Cladistic methods:
The cladistic methods are character based methods (Farris et al., 1983). In
these methods, all possible topologies are evaluated and one that optimizes the
evolution is chosen as the correct tree. The principle behind cladistic method is
“Parsimony”. Cladistic methods group organisms that share derived characteristics in
a branching hierarchy tree are called a “Cladogram”. Cladogram is a branching, tree11
like diagram in which the endpoints of the branches represent specific species of
organisms (Weygoldt., 1998). In cladogram, the taxa sharing more derived characters
are kept more closely than those having fewer derived characters. This means
cladogram is built such that number of changes from one character state to the next is
the smallest. Cladistic methods emphasize more on the evolutionary origin of species
than the relationships. It assumes that a set of sequences descended from a common
ancestor by mutation and selective processes without hybridization or other by
horizontal gene transfers (Patterson et al., 1982, 1988).
These methods are best in comparing Phylogenetic trees for study with other
tree to determine different lines of evolution (Brinkman et al., 2011). There are two
cladistic methods to construct phylogenetic trees. They are Maximum parsimony and
Maximum likelihood (de Pinna., 1991).
Maximum parsimony
The sum of the minimum possible substitutions over all sites is known as the
tree length for a given topology. The topology with the minimum tree length is known
as maximum parsimony tree. This method was discovered by Fitch et al., (1971).
Maximum parsimony analysis with protein sequences is known as ‘Protein
parsimony’. Maximum parsimony is based upon the number of mutations in the
sequences. It writes each mutation in a score. The most parsimonious tree is that with
few mutations. The advantages of this method is fundamentally it reflects the
ancestral relationship. It uses all known evolutionary information (Jin Xiong, 2006).
Bootstrapping a phylogenetic tree:
Bootstrap values are calculated as a percentage of the number of times that the
particular node appears when we perform bootstrapping analysis on constructing
phylogeny (Rodrigo, 1993). For example: If 1000 iterations of bootstrapping are
performed and a node appears in 950 of the constructed trees, then it has a bootstrap
value of 95%. If a node generally appears in less than 95% of total number of
analysis, then it is regarded as being “less accurate”. Lower values are to be regarded
with even less confidence. One of the most commonly used tests of the reliability of
an inferred tree is bootstrap test, which is evaluated using bootstrap resampling
technique. As a general rule, if the bootstrap value for a given interior branch is 95%
or higher, then the topology at the branch is considered correct. It is used as a
Statistical method for obtaining an estimate of ‘error’. These characters are used to
evaluate the reliability of a tree. Generally one has to examine, how often a particular
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cluster in a tree appears when nucleotides or amino acids are resampled (Sanderson,
1995).
Phylogenetic tree evaluation:
The evolutionary relationship among the sequences mainly nucleic acid or
proteins are depicted by using a graph called a tree. Such evolutionary trees clearly
show the differences in species which are the result of many small changes that
accumulate over long periods (Back et al., 1993). The sequences are placed as ‘outer
branches’ of a tree, whereas the ‘inner part’ of the tree reflects the degree to which
different sequences are related. For instance, two sequences that are very much alike
will be located at neighboring ‘outside branches’ and will be joined to a common
branch beneath them. Less related sequences will be on branches that are more distant
from each other on the tree. The object of phylogenetic analysis is to discover the
branch arrangements and branch length in the trees that represent the relationship
among all the sequences (Felsenstein et al., 2004). Phylogenetic analysis of nucleic
acid and protein sequences is an important area of sequence analysis in the study of
the evolution and its relationship of a family of nucleic acids or protein sequences.
Thus, sequences that are the most closely related are identified as they occupy
neighboring branches on a Phylogenetic tree. Over a period of time, sequence
becomes more and more different through evolutionary change, and then their
comparison becomes much more difficult (Back, 1993). The evolutionary paths that
may have led to such differences is very high, a phylogenetic analysis of these vastly
different sequences becomes difficult for comparative understands evolutionary.
Changing perspectives in nematode phylogeny and classification:
A very great nematode diversity, and to generate a hypothesis on the
evolutionary origins of interesting properties and processes can be made along with
comparisons across taxa. Until recently, the data for most nematode phylogenies
consisted of relatively based on few morphological characters derived primarily from
light microscopy studies and often by individual effort of the lone taxonomist.
Molecular phylogenetics, bioinformatics and digital communication technologies
have substantially altered the dynamics of nematode systematic (Luong et al, 1999).
Blaxter et al. (1998) based on small subunit (SSU) rDNA sequences of 53 nematode
species constructed Phylogenetic tree.
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The first nematode classification was proposed by Schneider (1866) that was
based on somatic musculature. It was followed by Cobb (1919) who proposed a
classification based on stoma armature. Baylis and Daubney (1926) proposed another
classification system based on parasitism, which is zoo-parasitic nematode in one
group and all other nematodes in another group. Filipjev (1934) rejected the Baylis
and Daubney (1926) classification and he also proposed that marine nematodes are
the ancestors of all nematodes.
Micoletzky
(1922)
classified
nematodes
into
two
major
groups:
Odentopharyngidae (nematodes with teeth) and Tylenchidae (nematodes with stylets).
However, the most important nematode classification system was developed by the
Chitwoods (Chitwood and Chitwood, 1933; Chitwood, 1937) and it was based on the
presence of phasmids. He devide nematodes into two major groups: 1. Secrenentea
(nematodes with an excretory system) and 2. Adenophorea (nematodes with caudal
glands).
Meggenti (1963) suggested a classification system based on pharynx
structure and excretory system. It maintained the bipartite system of nematodes,
namely, 1. Secrenentea and 2. Adenophorea.
Meggenti’s system suggested that
plectids are not related to rhabditids because of structural differences in their basal
bulbs (Ref). De Coninck (1965) suggested that class Adenophorea be divided again
into two subclasses: a. Chromadoria and b. Enoplia. Andrassy (1974) rejected class
Adenophorea as a cohesive nematode group and suggested that phylum Nemata
should be divided based on the amphidial structure into three groups namely: a.
Secrenentea, b. Torquentia, and c. Penetrentia. Andrassy’s system was criticized and
did not receive collective acceptance by various researchers.
Based on the
morphological characters, Lorenzen (1981 and 1994) again divided phylum Nemata
into two groups: 1. Secrenentea and 2. Adenophorea and Adenophorea were divided
into two groups
a. Chromadoria and b. Enoplia.
The molecular data published to date confirm the presence of three early
nematode lineages, corresponding to the previously recognized subclasses
Chromadoria, Dorylaimia and Enoplia (Lorenzen, 1981; Inglis, 1983). The exact
order of appearance of these three lineages is not yet resolved. It seems likely that
Enoplia appeared first, and it is even possible that Dorylaimia and Chromadoria could
have originated within Enoplia. On the other hand, SSU data also allowed for the
possibility that Dorylaimia diverged first. It is an intriguing possibility because all
known Dorylaimia are absent from marine habitats. A “Dorylaimia first” topology
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would therefore imply that the ancestor of all nematodes was perhaps a freshwater
organisms, and not a marine animal as more commonly assumed by most of the
researchers (De Ley and Blaxter, 2004).
Aim of this study:
In this study we have evaluated the diagnostic utility of the ITS1 and ITS2
region for constructing phylogenetic trees and to see the relationship of host and plant
parasitic nematodes from selected crops.
To study molecular based taxonomy we compared with classical morphology
based classification of Chitwood (1958) and with modern phylogeny classification of
De Ley and Blaxter 2002 to determining taxonomic identity and taxonomic position
of nematodes.
Objectives of this study:
1. Isolation and identification of ITS gene of plant parasitic nematodes collected
from Rice, tomato and cotton crop fields.
2. To understand phytonematodes / phylogenetic relationship and host nematode
interactions.
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