Biology Reference
In-Depth Information
2012
). Thus, in the view of
Taylor and Harris (2012)
, DNA barcoding has actu-
ally reinforced the need for qualified taxonomists by producing sequence data
that needs to be paired with a verified morphological type specimen.
Taylor and
Harris (2012)
suggested that Next-Generation sequencing will determine the
future of barcoding, because inexpensive sequencing machines may allow the
development of more data that can be used to identify species, and that “DNA
barcoding could soon become obsolete.”
Another concern about DNA barcodes is the discovery of
nuclear mitochon-
drial pseudogenes
(
numts
). Numts are nonfunctional copies of mtDNA in the
nucleus that can be found in a number of eukaryotes and can be coampli-
fied with mtDNA when using conserved universal PCR primers. Numts can be
highly divergent from the mtDNA sequences in the individual and sequencing
of numts, using the standard of 3% sequence divergence, can result in errone-
ous estimates of species diversity. More than 82 eukaryotes are known to have
numts, and it appears that numts may be more common than realized, provid-
ing a challenge to DNA barcoding as an accurate method for species identifica-
tion (
Song et al. 2008
). It was probably unrealistic to expect that a single gene
fragment could resolve all species-identification issues.
12.5.2 Ribosomal RNA
Ribosomes are a major component of cells that are involved in translating mes-
senger RNA (mRNA) into proteins. Ribosomes consist of ribosomal RNA (rRNA)
plus proteins. All ribosomes can be dissociated into two subunits, each contain-
ing rRNA and proteins. Ribosomal RNAs are used frequently to evaluate evolu-
tionary relationships among species because they are universally present and
abundant in cells. Ribosomal RNAs contain regions that are “conserved” and
regions that are more variable, so rRNAs can serve as both slow and fast clocks.
In eukaryotes, the genes encoding the 18S (small subunit) and 28S (large sub-
unit) rRNAs are clustered as tandem repeats in the nucleolus-organizing regions
of the nuclear chromosomes (
Figure 12.2
), but two ribosomal genes are found in
mitochondria (
Figure 12.1
). In most animals, there are 100-500 copies of rDNA in
the nuclear genome in tandemly repeated transcription units. Ribosomal gene
copy number ranges from as few as 45 in the fly
Sciara coprophila
to
>
3000 in
the grasshopper
Locusta migratoria
. In a survey of 30 species of mosquitoes,
copy numbers ranged from 39 to 1023 (
Kumar and Rai 1990
).
The repeated transcription unit of rRNAs is composed of a leader pro-
moter region known as the
External Transcribed Spacer
(
ETS
), an 18S rRNA
coding region, an
Internal noncoding Transcribed Spacer
region (
ITS
), a 28S
