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10% of the total plant DNA. The most remarkable feature of rDNA is
the overall sequence homogeneity among members of the gene
family in a given species. The process by which this pattern of intra-
specific homogeneity and interspecific heterogeneity is maintained
has been called concerted evolution [13]. In plants, the rDNA cis-
tron encodes 18S, 26S and 5.8S rRNAs, which are separated by
the two internal transcribed spacers (ITS1 and ITS2). The cistron is
flanked by the 5’ and 3’ external transcribed spacers (5’-ETS and
3’-ETS). The nuclear ribosomal ITS region including the 5.8S gene
[Fig-2] has been the most widely used molecular marker at the in-
terspecific and intergeneric levels in plants. The region is relatively
short to sequence, with ITS1 200-300 bases long, ITS2 180-240
bases, and 5.8S and 5.8S ca. 160 bp in flowering plants. The ampli-
fication and sequencing primers are highly universal [14].
Fig. 1- Genus Limonium distribution in Saudi Arabia
The nuclear ribosomal transcription unit (NRTU) is comprised of
18S, 5.8S and 28S genes, two internal transcribed spacers (ITS-1
and ITS-2), and an intergenic spacer (IGS). After transcription, the
NRTU is processed to produce mature rRNAs that are key compo-
nents of cytoplasmic ribosomes. NRTU are found in hundreds to
thousands of tandem copies and usually several NRTU clusters are
present within plant genomes. The conserved regions (18S and
28S genes) of NRTU are used to infer phylogenetic relationships at
higher taxonomy levels, whereas the more rapidly evolving seg-
ments (ITS and IGS) are used for studies at the genic or population
levels [15,16]. For over a decade, sequences of internal transcribed
spacers (ITS) of NRTUs have been widely used to infer phylogenet-
ic relationships, genetic diversity and to unravel evolution in a wide
range of complexes in plants [15,16]. Although NRTUs are found in
thousands of copies within a genome, intra-genomic diversity is
generally low [17]. This homogeneity among NRTUs is attributed to
concerted evolution [18], a process that acts through gene conver-
sion and unequal crossing over. Despite the fact that homogeniza-
tion is a norm among NRTUs in a genome, extensive intra-
individual and intra-specific variation has been observed in various
plant species [19]. Evidence is accumulating that suggests that intra
-individual variation of nuclear ribosomal ITS regions should not be
considered as exceptional [20]. Because of the influence of concert-
ed evolution, the occurrence of ancestral polymorphisms is not the
most likely ultimate cause for intra-genomic variability in this mark-
er. Instead, a more frequent origin is the merging of different ITS
copies within the same genome as a consequence of gene flow.
Once the two copies meet, the fate of the polymorphism depends
on genetic, reproductive and population-level factors: specifically,
the number and location of ribosomal loci (on the same or different
chromosomes), the occurrence of polyploidy and/or apomixes [21],
and the relative abundance of different ITS copies in the breeding
populations [20].
Sequences of the nuclear rDNA internal transcribed spacers (ITS
region) have been widely applied to depict evolutionary relation-
ships at lower taxonomic levels, notably at the intrageneric ones
[18]. In addition, the ITS region has been a valuable tool for tracing
the hybrid origin of diploid [22] and polyploid [16,23] species in flow-
ering plants.
Since the first report of the utility of the cytochrome c oxidase subu-
nit 1 (CO1) as a DNA barcode to identify animals, DNA barcoding
has attracted worldwide attention [24.25]. Many loci such as ITS
[26], rbcL [27], psbA-trnH [ 28], and matK [28], combination of rbcL
and matK [29] etc. have earlier been proposed for plant DNA bar-
code. Nuclear genes can provide more information than barcoding
based on organellar DNA which is inherited from only one parent
[30]. It has been emphasized that an ideal barcode should possess
sufficient sequence variation to discriminate the taxon at species
level; however, it also need to have sufficiently conserved region so
that there is less variability within species than between species
[31]. The ITS2 shows significant sequence variability at the species
level or lower [32,33]. The availability of structural information of
ITS2 permits analysis even at higher taxonomic level too [32.34].
compared seven candidate DNA barcodes (psbA-trnH, matK, rbcL,
rpoC1, ycf5, ITS2, and ITS) and proposed that ITS2 has potential
for use as a standard DNA barcode to identify medicinal plants[35].
The ITS2 region has also been shown to be applicable in discrimi-
nating among a wide range of plants genera and families e.g. Aster-
aceae, Rutaceae, Rosaceae, Araliaceae [36-38]. Besides plants,
the ITS2 sequence also has potential for use in barcoding of ani-
mals. The secondary structure of ITS2 are conserved as well as
possesses sufficient variation in primary sequences and secondary
structure which also provides useful biological information for align-
ment; therefore, the ITS2 sequences is also used as molecular
morphological characteristics for species identification [39].
International Journal of Molecular Biology
ISSN: 0976-0482 & E-ISSN: 0976-0490, Volume 6, Issue 1, 2015
Al-Ghanem S.M.S.
Fig. 2- Internal
Transcribed Spacer Region