Molecular Plant Breeding 2016, Vol.7, No.9, 1-16
http:// mpb.biopublisher.ca
4
A. niger
,
Aspergillua flavus
and
Aspergillus
parasiticus
were determined by RAPD analysis
(Swelim, 2005a) which revealed 37, 59, and 51 %
polymorphism, respectively. Furthermore, RAPD
analysis demonstrated that genetic similarity was
37 % in
A. niger
, 58 % in A. flavus, and 51.5% in A.
parasiticus (Aiat,
2006).
Random Amplified
Polymorphic DNA analysis was used in detecting
genetic diversity in many phytopathogenic fungi
(WÖstemeyer and Kraibich, 2002; Sharma et al., 2002;
Sharma, 2003). Due to high variability RAPD markers
can be used to detect differences within and among
species at genomic level (William et al., 1990; Parker
et al., 1998; Sunnucks, 2000) as well it is also helpful
to explore intra-specific variations in large number of
fungi on genetic bases (Fegan et al., 1993; Moore et
al., 2001).
2.1 Ribotyping
The 18S rRNA gene has been used to characterize
fungal strains at species level (Meyer et al., 2010).
Phylogenetic analyses of fungal taxa at different levels
can be done by using 18S rRNA gene that is
considered as phylogenetic marker. In all living
organisms ribosomal ribonucleic acid (rRNA) is
involved in protein synthesis and it comprises of 90 %
of total RNA (Forster and Toth, 2003). The ribosome
has two subunits smaller subunit (SSU) and large
subunit (LSU) (Higgs, 2000). The LSU acts as
ribozyme, which catalyzes the peptide bond formation.
All SSUs have one large ribosomal subunit molecule
termed as 16S in Archaea, Bacteria and 18S in
Eukaryotes (Moore, 2009). The 18S rRNA gene
consists of ~1900 nucleotides and responsible for the
translation of different proteins. The sequences of 18S
rRNA genes are widely used to find out evolutionary
relationship among different organisms (Smit et al.,
2007). The flanking region of the 18S rRNA gene is
highly conserved and has been used as a reliable
marker to determine environmental biodiversity in the
species of different organisms (Woese et al., 1990;
Hanif et al., 2012). To segregate fungi into diverse
strains within species amplification of rRNA gene for
ribotyping and SNPs analysis has become essential
molecular aspect (Balajee et al., 2008). Molecular
systematics is an important tool in recent taxonomy of
fungi (Bruns et al., 1991, Mitchell et al., 1995). DNA
sequence data of 18S, 26S, ITS (Internal Transcribed
Spacer) along with mitochondrial rDNA are
abundantly used in current phylogenetic studies in
case of eukaryotic cells (Wilmotte et al., 1993; Shan et
al., 2015; Zameer et al., 2015). Due to conserved
nature of 18S rDNAs they are applied in phylogenetic
analyses of higher taxonomic rank fungi (Swann and
Taylor, 1993). The advent of molecular phylogenetic
and the use of ribosomal RNA (rRNA) as a molecular
chronometer extended phylogenetic studies to
different organisms including the microbial world
where it was difficult to find distinguishable,
observable phenotypes and resulted in the
classification of life into a tripartite world (Woese et
al., 1990). A number of insertions and deletions have
been reported in variable domains of rRNA gene
including V2, V4, V6, 8, and V9 domains (Bruns et al.,
1991). Mitchell et al., (1995) have described that in
modern fungal technology molecular systematics has
been proven to be a valuable tool. 18S rRNA gene
sequences and internal transcribed spacer (ITS) region
has an essential role in characterization of eukaryotic
organisms. 18S rRNA gene is used in phylogenetic
analysis of fungi even at species level (Swann and
Taylor, 1993; Wilmotte et al., 1993; Javed et al.,
2015).
3 Biochemical and Molecular Studies of
Fungal Enzymes and Their Genes
Fungi are decomposers in most ecosystems make an
important contribution to the ecological balance and
also have great industrial application due to presence
of different enzyme genes (Yuan et al., 2006). Many
fungi form symbiotic relationships with other
organisms, mostly plants, while they also constitute
the majority of plant pathogens and some fungi also
cause diseases in animals and humans (Bernhard, et al.,
1995). Fungi thrive in diverse environments and can
exploit marginal living conditions in large part
because they produce different enzymes including
laccases, cellulases, catalases and superoxide
dismutases which are capable of performing difficult
chemical reactions (Wheeldon et al., 2008). According
to Wheeldon et al., (2008) many industrially important
enzymes including cellulases, catalases, laccases and
amylases are obtained from Aspergillus. Archer, (2000)
described that total sixteen (16) fungal enzymes are
used in the food industry and thirteen (13) of them
has been obtained from Aspergillus. Fungi have vital
