Biology Reference
In-Depth Information
Class II: Hormogoneae (ex. Thuret 1875)
Order 1: Nostocales
:
Nostoc
, fi laments that multiply vegetatively by hormogonia usually with
heterocysts, unbranched.
Order 2: Stigonematales
:
Stigonema
, branched, heterocystous forms.
II. PHYLOGENY
Phylogenetic relationships tell us the manner in which the different groups of organisms have evolved
during the course of time. In case of eukaryotes (both animals and plants), macromorphological
features (organismal biology) form the main basis for drawing phylogenetic relationships. In case
of prokaryotes, the range of morphological features being very limited, a number other corollary
features have been taken into consideration. Along with morphological features, immunological,
physiological, biochemical, ecological as well as genetic features have been taken as the supporting
taxonomic features to identify bacteria and draw their phylogeny. This has given rise to a polyphasic
approach to taxonomy. In this connection, a single gene whose sequence is highly conserved and at
the same time shows variable sequences that could form the basis for identifi cation can be selected.
The fi rst choice fell on 16S rRNA gene. The projection of this gene as molecular marker for drawing
phylogenetic relationships has revolutionized thinking in biological world with the culmination of
the classifi cation of living organisms into bacterial, archaebacterial and eukaryotic domains (Woese
et al
., 1990). This triggered a large number of studies all world over and generated a wealth of
knowledge. These studies have clearly pointed out that the sequencing of 16S rRNA gene falls short
of differentiating bacteria up to or below the level of species. It turned out that the rRNA operon
that consists of internally transcribed sequences (ITS) between 16S and 23S rRNA could well serve
as a good parameter. This has no doubt helped in the identifi cation of bacteria up to strain level
and the resolving power of this ITS is found to be greater than simply sequencing of 16S rRNA.
Alternative searches for other ideal genes suited for this purpose resulted in the identifi cation of
some housekeeping genes such as RNA polymerase gene, cell division genes and genes involved
in DNA repair. Taking 16S rRNA phylogeny as the basis, comparisons have been made between
other gene markers selected and the resulting phylogenies. This gave rise to the concept of multi-
locus sequence typing (MLST). Another most promising, reliable but very expensive approach is
whole genome sequencing of bacteria and comparisons between the bacterial species in question.
The studies on genomics have converged with phylogeny resulting in an interesting area known as
Phylogenomics (Eisen, 1998; Eisen and Fraser, 2003). All these developments are detailed below.
1) 16S rRNA gene
The 16S rRNA gene has all the characteristics for a phylogenetic marker gene because of its universal
distribution in prokaryotes, functional consistency, the presence of variable and conserved regions and
high information content (Woese, 1987; Ludwig and Klenk, 2001; Figs. 9 and 10). Other attributes of
16S rRNA gene are (i) its suitable length of about 1500 bp, (ii) the presence of long highly conserved
regions useful for measuring distant phylogenetic relationships, (iii) the presence of suffi cient variable
regions to measure close relationships, (iv) not prone for rapid sequence change and (v) not liable for
getting transferred from one organism to another through lateral gene transfer (LGT). Woese (1987)
considered it an excellent molecular chronometer for fi nding out evolutionary relationships among
all living organisms. On the basis of 16S rRNA gene sequences, Woese
et al.
(1990) proposed a three
