Biology Reference
In-Depth Information
sp. PCC 7535,
Synechococcus
sp. strain JA-3-3A'b (also designated as Cyanobacteria bacterium Yellow
Stone A-Prime),
Synechococcus
sp. strain JA-2-3 B'a (2-13) (also known as Cyanobacteria bacterium
Yellow Stone B-Prime),
Trichodesmium erythraeum
IMS101,
Anabaena variabilis
ATCC 29413 and
Cyanobacterium
UCYN-A] are available on the website of DOE Joint Genome Institute (JGI; http://
www.jgi.doe.gov/) supported by US Department of Energy, Offi ce of Science, Walnut Creek,
California and the genomes of three other cyanobacteria (
Microcoleus chthonoplastes
PCC 7420,
L
.
aesturii
PCC 8106 and
Nodularia spumigena
CCY9414) are put on the website of JCVI. The particulars
of these 20 genomes will only be mentioned as given in the published literature for comparative
purposes only. Of the 59 strains of cyanobacteria,
P. marinus
(12 strains), 13 strains of
Synechococcus
(WH8102, CC9311, BL107, CC 9605, CC9902, RCC307, RS9916, RS9917, WH5701, WH7803, WH7805,
PCC 7002 and PCC 7335),
Cyanothece
sp. (CCY0110, ATCC 51142),
C
.
watsonii
WH8501,
T
.
erythraeum
IMS101,
Lyngbya majuscula
,
Lyngbya
sp. PCC 8106 and
No
.
spumigena
CCY9414 are marine in their
habitat where as the rest of the members are from other aquatic (freshwater or hot-spring) and
terrestrial (soil, rock, or symbiotic) habitats. Unicellular strains
C
.
watsonii
WH8501, seven strains
of
Cyanothece
sp. (CCY0110, ATCC 51142, PCC 7424, PCC 7425, PCC 7822, PCC 8801 and PCC 8802),
Oscillatoria
PCC 6506, three strains of
Synechococcus
[PCC 7335, JA-3-3A'b and JA-2-3B'a (2-13)],
T
.
erythraeum
IMS101 and the heterocystous fi lamentous forms listed above fi x nitrogen. However, in
these three unicellular genera there is a temporal separation of photosynthesis and nitrogen fi xation,
the former occurring in the day and the latter during the night time. A phylogenetic analysis of 38
sequenced cyanobacterial genomes, based on concatenated 23S and 16S rRNA sequences, revealed
well defi ned unicellular, fi lamentous non-heterocystous and heterocystous clusters. The smallest
genome is of 1.55 Mb (
Synechococcus
sp. strain RS9916) and the largest one (8.68 Mb) is represented by
M
.
chthonoplastes
PCC 7420 (Fig. 1; Frangeul
et al
., 2008). Fujisawa
et al
. (2010) divided the sequenced
genomes of cyanobacteria into six groups based on unicellular and fi lamentous habit with or without
the capacity to fi x nitrogen: (i) unicellular forms (ii) unicellular forms that fi x nitrogen, (iii) unicellular
or short fi lamentous, (iv) fi lamentous types, (v) fi lamentous, nitrogen-fi xing but non-heterocystous
forms and (vi) fi lamentous, nitrogen-fi xing and heterocystous members. The third group consists
of a single representative
Synechococcus
sp. strain PCC 7002 that exhibits a fi lamentous tendency
and marine in its habitat. The genome sequencing of
A
.
marina
CCMEE 5410,
Calothrix
sp. SCO1,
Gloeothece
sp. PCC 6909/1,
Prochlorococcus
sp. UH18301 and six
Synechococcus
strains (UW1, UW69,
UW90, UW92, CB0101 and CB0205) is in progress. One can access the complete microbial genomes
at http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi, the microbial genome sequencing projects
in progress at http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi and the eukaryotic genome
sequencing projects at http://www.ncbi.nlm.nih.gov/genomes/leuks.cgi.
I. METHODS
Sequencing refers to the recognition of the order in which nucleotides are arranged in a molecule of
DNA. A number of sequencing methods have been developed paving the way for automation as a
result of which the process is accomplished with ease and greater speed. Maxam-Gilbert sequencing
method (developed by A. Maxam and W. Gilbert during 1976-77) and chain termination method
discovered by Frederick Sanger and commonly known as Sanger method were the two earliest
sequencing methods. The latter method gained popularity due to the requirement of few toxic
chemicals and lower amounts of radioactivity. Sanger's method requires a single-stranded DNA
template, a DNA primer, a DNA polymerase, radioactively or fl uorescently-labelled nucleotides
and modifi ed nucleotides known as dideoxynucleotides. The addition of the each one of the four
